CS798 Final Project Log 20100810

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20100812.230514

The 84 DATE Tim Barrels ...
- http://www.mrc-lmb.cam.ac.uk/genomes/date/
- 82 structures were retrieved from PDB (two have been purged and their serial numbers retired)
- http://toolkit.tuebingen.mpg.de/hhrepid -- repeat finding
- http://www-lbit.iro.umontreal.ca/DILTAG/ -- repeat history construction
  - Okay-- here's the scoop: Anywhere on this page where I've indicated I've used HMMrep, I've actually used HMMrepID. HMMrep is somehow broken on the server side :( -- additionally, I can't seem to render the same alignments as those given in the paper. I must be missing some important algorithm parameters.
  - So far, it looks like there's insufficient signal strength.

Ideal Topology Template: BA BA BA BA BA BA BA BA

B = Beta Strand in template
A = Alpha Helix in template
b = beta strand outside of template
a = alpha helix outside of template
o = "random coil"
? = "missing density"
d = "domain"

0 = not feasible
1 = feasible
2 = expedite

firebrick = todo
blue = checkout
forestgreen = done

v:w:x:y:z => beta start, non-sse start, alpha start, non-sse start, end (exclusive).
BETANON-SSEALPHANON-SSE

1 : 1A4M.pdb (7 ; mono; 352) - BaaaA BA BA BA BA BA BaA BAaa
1 : 1A53.pdb (60; mono; 248) - aaBbbA BA BA BA BA BbbA BA BA
1 : 1A80.pdb (72; mono; 277) - bbBA BA BA BA BA BA BaA BAa
1 : 1ADS.pdb (68; mono; 315) - bbBA BA BA BA BA BA BAa BAao
1 : 1AFS.pdb (42; mono; 322) - bbBA BA BA BA BA BA BaA BAa

1AJ0.pdb

2 : 1AJ0.pdb (29; hodi; 282) - bbBA BA BA BA BA BA BA BA
- (1:16 ~~MKLFAQGTSLDLSHP~~)
1. 16:23:35:51:54 HVMGILNVTPDSFSDGGTHNSLIDAVKHANLMINAGAT
2. 54:59:71:89:92 IIDVGGESTRPGAAEVSVEEELQRVIPVVEAIAQRFEV
3. 92:97:100:109:113 WISVDTSKPEVIRESAKVGAH
4. 113:117:125:133:135 IINDIRSLSEPGALEAAAETGL
5. 135:140:157:175:179 PVCLMHMQGNPKTMQEAPKYDDVFAEVNRYFIEQIARCEQAGIA
6. 179:186:194:211:211 KEKLLLDPGFGFGKNLSHNYSLLARLAEFHHF
  - Chimera labels KEK as helix-like
  - 211:211 => no non-sse tail
7. 211:222:222:229:253 NLPLLVGMSRKSMIGQLLNVGPSERLSGSLACAVIAAMQGAH
  - Chimera labels 211:222 as non-sse-like -- is straight chain (X), occupies the space where one would expect a strand
  - 222:222 => no non-sse between X and helix
  - underline used to delineate between two otherwise consecutive bold regions :(
  - 232:250 are labelled as helix-like -- likely function as non-sse-like
8. 253:257:259:276:283 IIRVHDVKETVEAMRVVEATLSAKENKRYE

__prefix__ = MKLFAQGTSLDLSHP
HVMGILNVTPDSFSDGGTHNSLIDAVKHANLMINAGAT
IIDVGGESTRPGAAEVSVEEELQRVIPVVEAIAQRFEV
WISVDTSKPEVIRESAKVGAH
IINDIRSLSEPGALEAAAETGL
PVCLMHMQGNPKTMQEAPKYDDVFAEVNRYFIEQIARCEQAGIA
KEKLLLDPGFGFGKNLSHNYSLLARLAEFHHF
NLPLLVGMSRKSMIGQLLNVGPSERLSGSLACAVIAAMQGAH
IIRVHDVKETVEAMRVVEATLSAKENKRYE

The above images are broken apart by visual inspection into eight and four parts respectively;
- Trying HMMrep to do the cutting now since it's been known to do well with TIM Barrels.
HMMrep output below...

Repeats        3
P-value  0.00028
Length        60
Offset        66

ID Probab  P-value RepScore RepScoreNorm Cols Query HMM Template HMM
A1  78.50  2.4e-05    16.14         0.42   38   27-65      86-124  
A2  89.00  5.2e-08    34.90         0.58   60   66-125     66-125  
A3  81.42  1.7e-04    17.74         0.57   32  141-175     75-106

A1  Mon_Aug_16_14:   27-65    +0 --------------------KHANLMINAGA...T-IIDVGGEStRPGAAEVSVEEELQRVIP-...............
A2  Mon_Aug_16_14:   66-125  +15 VVEAIAQRFEVWISVDTSKPEVIRESAKVGA...HIINDIRSLS.EPGALEAAAETGLPVCLMHmqgnpktmqeapkyd
A3  Mon_Aug_16_14:  141-175   +0 ---------DVFAEVNRYFIEQIARCEQAGIakeKLLLDPGFGF.-------------------...............

Alignment:

Trace:

DILTAG with new alignment:

1 : 1AK5.pdb (27; tetr; 503) - obbBA BA BA BA BA BA BA BbbAa
1 : 1AQ0.pdb (4 ; mono; 312) - BA BA BaA BA BA BA BA BA
0 : 1AQM.pdb (70; mono; 669) - BA BbbA BbbbbbbA BA Bo Ba BA BbbAd

1AW5.pdb

2 : 1AW5.pdb (36; octo; 342) - oBboA BA BA BA BA BA BA BA
- (1:43 ~~MHTAEFLETEPTEISSVLAGGYNHPLLRQWQSERQLTKNMLI~~)
1. 43:49:71:81:85 FPLFISDNPDDFTEIDSAPNINRIGVNRLKDYLKPLVAKGLR
  - underlined segments are a pair of matching anti-parallel strands
2. 85:92:111:123:127 SVILFGVPLIPGTKDPVGTAADDPAGPVIQGIRFIREKFPEL
  - underlined segment is a spurious short helix region
3. 127:133:154:172:175 YIICDVCLCEYTSHGHCGVLYDDGTINRERSVSRLAAVAVNYAKAGAH
4. CVAPSDMIDGRIRDIKRGLINANLAHK
5. TFVLSYAAKFSGNLYGPARDAACSAPSNGDRKCYQLPPAGRGLARRALERDMSEGAD
  - not a beta-strand, but is straight and fits into template: TFVLSYAAKFSG
  - tertiary structure for this segment is unsolved: RDAACSAPSNGDRK
6. GIIVKPSTFYLDIVRDASEICKDL
7. PICAYHVSGEYAMLHAAAEKGVVDLKTIAFESHQGFLRAGAR
  - skewed helix: SGEYAMLHAAAE
  - template fitting helix: LKTIAFESHQGFLRA
8. LIITYLAPEFLDWLDE

__prefix__ = MHTAEFLETEPTEISSVLAGGYNHPLLRQWQSERQLTKNMLI
FPLFISDNPDDFTEIDSAPNINRIGVNRLKDYLKPLVAKGLR
SVILFGVPLIPGTKDPVGTAADDPAGPVIQGIRFIREKFPEL
YIICDVCLCEYTSHGHCGVLYDDGTINRERSVSRLAAVAVNYAKAGAH
CVAPSDMIDGRIRDIKRGLINANLAHK
TFVLSYAAKFSGNLYGPARDAACSAPSNGDRKCYQLPPAGRGLARRALERDMSEGAD
GIIVKPSTFYLDIVRDASEICKDL
PICAYHVSGEYAMLHAAAEKGVVDLKTIAFESHQGFLRAGAR
LIITYLAPEFLDWLDE

Repeats        3
P-value   0.0091
Length        77
Offset       128

ID Probab  P-value RepScore RepScoreNorm Cols Query HMM Template HMM
A1  89.51  9.6e-10    43.19         0.56   77  128-204    128-204  
A2  81.72  2.0e-03    23.65         0.33   65  205-284    135-204  
A3  86.25  1.7e-05    24.55         0.61   43  285-327    135-177

A1  Mon_Aug_16_21:  128-204   +0 IICDVCLCEYTS...HGHCGVLY............DDGTINRERSVSRLAAVAVNYAKAGAHCVAPSDMIDGRIRDIKRG
A2  Mon_Aug_16_21:  205-284   +0 -------LSYAAkfsGNLYGPARdaacsapsngdrKCYQLPPAGRGLARRA-LERDMSEGADGIIVKPSTF-YLDIVRDA
A3  Mon_Aug_16_21:  285-327   +0 -------CAYHV...SGEYAMLH............AAAEKGVVDLKTIAFESHQGFLRAGARLII---------------

A1  Mon_Aug_16_21:  128-204   +0 LINANLAHKTFV
A2  Mon_Aug_16_21:  205-284   +0 SE-I-C-KDLPI
A3  Mon_Aug_16_21:  285-327   +0 ------------

1B54.pdb

2 : 1B54.pdb (2 ; mono; 257) - BA BA BA BA BA BA BA BA

__prefix__ = MSTGITYDEDRKTQLIAQYESVREVVNAEAKNVHVNENASKI
LLLVVSKLKPASDIQILYDHGVR
EFGENYVQELIEKAKLLPDDI
KWHFIGGLQTNKCKDLAKVPN
LYSVETIDSLKKAKKLNESRAKFQPDCNP
ILCNVQINTSHEDQKSGLNNEAEIFEVIDFFLSEECKY
IKLNGLMTIGSWNVSHEDSKENRDFATLVEWKKKIDAKFGTSL
KLSMGMSADFREAIRQGTA
EVRIGTDIFGARPPKNEARII

1B5T.pdb

2 : 1B5T.pdb (39; hote; 296) - BA BA BA BA BA BA BaoaoA BA
in the seventh strand: IIPGILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVK
- non-template helix: NFKQAKKFADM
- non-template helix: PAWMAQMFD
- correct helix: DAETRKLVGANIAMDMVKILSRE

__prefix__ = GQI
NVSFEFFPPRTSEMEQTLWNSIDRLSSLKPK
FVSVTYGANSGERDRTHSIIKGIKDRTGLE
AAPHLTCIDATPDELRTIARDYWNNGIR
HIVALRGDLPPGSGKPEMYASDLVTLLKEVADF
DISVAAYPEVHPEAKSAQADLLNLKRKVDAGAN
RAITQFFFDVESYLRFRDRCVSAGIDVE
IIPGILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVK
DFHFYTLNRAEMSYAICHTLGVRPA

1BD0.pdb

2 : 1BD0.pdb (34; dime; 388) - aBA BA BA BA BA BA BA BAd

__prefix__ = MNDFHRDTWAEVDLDAIYDNVENLRRLLPDDT
HIMAVVKANAYGHGDVQVARTALEAGAS
RLAVAFLDEALALREKGIEA
PILVLGASRPADAALAAQQR
IALTVFRSDWLEEASALYSGPFP
IHFHLKMDTGMGRLGVKDEEETKRIVALIERHPH
FVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPP
LVHCANSAASLRFPDRTFN
MVRFGIAMYGLAPSPGIKPLLPYPLKEA
__suffix__ = FSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLP
__suffix__ = VGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAIGAGESSA

1 : 1BF2.pdb (26; mono; 776) - dBA BA BA BA Bo BaoA BA BAd
1 : 1BG4.pdb (53; mono; 302) - BA BA BA BA BA BboA BboA BboA
1 : 1BGG.pdb (8 ; octa; 448) - bBaoA BA BA BaoA BAaao BbbA BA BbbA

1BQC.pdb

2 : 1BQC.pdb (17; mono; 279) - bbBA BA BA BA BA BA BA BA

: 1BQG.pdb () - BA BA BA BA BA BA BA BA
1 : 1BYA.pdb (83; mono; 495) - BA BA BoaoA BoaoA BoaoA BA BA BAo
: 1C7S.pdb () - BA BA BA BA BA BA BA BA
: 1C9W.pdb () - BA BA BA BA BA BA BA BA
1 : 1CB7.pdb (50; hete) - aaaBA BoaoA BA BA BA BA BA BAd
1 : 1CIU.pdb (10; mono; 710) - BA BA BA BA BA BaA BA BAd

1CNV.pdb

2 : 1CNV.pdb (47; mono; 324) - BA BA BA BA BA BA BA BA

0 : 1CTN.pdb (59; mono; 563) - dBo BaoA BaA BA BA BA BdA BA
: 1D8C.pdb () - BA BA BA BA BA BA BA BA

1D9E.pdb

2 : 1D9E.pdb (75; hotr; 284) - bbBA BA BA BA BA BA BA BA

1DBT.pdb

2 : 1DBT.pdb (5 ; hodi; 239) - BA BA BA BA BA BA BA BA

1 : 1DE5.pdb (77; hote; 419) - aaBA BA BA BA BA BA BA BAoaaaa
: 1DHP.pdb () - BA BA BA BA BA BA BA BA
: 1DJX.pdb () - BA BA BA BA BA BA BA BA
: 1DXE.pdb () - BA BA BA BA BA BA BA BA
: 1ECE.pdb () - BA BA BA BA BA BA BA BA
1 : 1EGM.pdb (80; cplx; 224) - dBA BA BA BAa BA BA BA BAd
1 : 1EZW.pdb (78; ? ; 348) - BA BA BA BA BA BA BAd BA
: 1F2J.pdb () - BA BA BA BA BA BA BA BA
: 1F61.pdb () - BA BA BA BA BA BA BA BA
: 1F6Y.pdb () - BA BA BA BA BA BA BA BA
: 1FCB.pdb () - BA BA BA BA BA BA BA BA
0 : 1FIY.pdb (12; hote; 883) - dBaaA BAaaaa BoaaA BA BA BA BaoA BAd
1 : 1FRB.pdb ( 5; mono; 315) - bbBA BA BA BA BA BA BaA BAao
: 1FWJ.pdb () - BA BA BA BA BA BA BA BA
: 1GHS.pdb () - BA BA BA BA BA BA BA BA
: 1GOX.pdb () - BA BA BA BA BA BA BA BA
: 1LUC.pdb () - BA BA BA BA BA BA BA BA
: 1MNS.pdb () - BA BA BA BA BA BA BA BA
: 1MUC.pdb () - BA BA BA BA BA BA BA BA
: 1NAL.pdb () - BA BA BA BA BA BA BA BA
: 1NAR.pdb () - BA BA BA BA BA BA BA BA
: 1ONR.pdb () - BA BA BA BA BA BA BA BA
: 1OYA.pdb () - BA BA BA BA BA BA BA BA
: 1PII.pdb () - BA BA BA BA BA BA BA BA
: 1PKL.pdb () - BA BA BA BA BA BA BA BA
: 1PSC.pdb () - BA BA BA BA BA BA BA BA
: 1PUD.pdb () - BA BA BA BA BA BA BA BA
: 1PYM.pdb () - BA BA BA BA BA BA BA BA

1QFE.pdb

2 : 1QFE.pdb (48; hodi; 252) - bbBA BA BA BA BA BA Bo BA

1QO2.pdb

2 : 1QO2.pdb (79; hote; 241) - ? ? ? ? ? ? ? ?

__prefix__ = ML
VVPAIDLFRGKVARMIKGRKENTIFYEKDPVELVEKLIEEGFTL
IHVVDLSNAIENSGENLPVLEKLSEFAEH
IQIGGGIRSLDYAEKLRKLGYR
RQIVSSKVLEDPSFLKSLREIDV
EPVFSLDTRGGRVAFKGWLAEEEIDPVSLLKRLKEYGLE
EIVHTEIEKDGTLQEHDFSLTKKIAIEAEV
KVLAAGGISSENSLKTAQKVHTETNGL
LKGVIVGRAFLEGILTVEVMKRYAR

: 1QPO.pdb () - BA BA BA BA BA BA BA BA
: 1QR7.pdb () - BA BA BA BA BA BA BA BA
: 1QRQ.pdb () - BA BA BA BA BA BA BA BA
: 1QTW.pdb () - BA BA BA BA BA BA BA BA
2 : 1RPX.pdb (9 ; hexa; 280) - BA BA BA BA BA BA BA BA

1THF.pdb

2 : 1THF.pdb (82; mono; 253) - BA BA BA BA BA BA BA BA

__prefix__ = MLAK
RIIACLDVKDGRVVKGSNFENLRDSGDPVELGKFYSEIGID
ELVFLDITASVEKRKTMLELVEKVAEQIDI
PFTVGGGIHDFETASELILRGAD
KVSINTAAVENPSLITQIAQTFGSQA
VVVAIDAKRVDGEFMVFTYSGKKNTGILLRDWVVEVEKRGAG
EILLTSIDRDGTKSGYDTEMIRFVRPLTTL
PIIASGGAGKMEHFLEAFLAGAD
AALAASVFHFREIDVRELKEYLKKHGVNVRLEGL

: 1TPF.pdb () - BA BA BA BA BA BA BA BA
: 1UOK.pdb () - BA BA BA BA BA BA BA BA
: 1URO.pdb () - BA BA BA BA BA BA BA BA
1 : 1XYA.pdb (67; dime; 386) - BA BA BA BA BA BA BA BAa

2ALR.pdb

? : 2ALR.pdb (20; ? ; ? ) - ? ? ? ? ? ? ? ?

__prefix__ = AASCVLLHTGQKMPL
IGLGTWKSEPGQVKAAVKYALSVGYR
HIDCAAIYGNEPEIGEALKEDVGPGKAVPREEL
FVTSKLWNTKHHPEDVEPALRKTLADLQLEYLD
LYLMHWPYAFERGDNPFPKNADGTICYDSTHYKETWKALEALVAKGLVQ
ALGLSNFNSRQIDDILSVASVRPA
VLQVECHPYLAQNELIAHCQARGL
EVTAYSPLGSSDRAWRDPDEPVLLEEPVVLALAEKYGRSPAQILLRWQVQRKV
ICIPKSITPSRILQNIKVFDFTFSPEEMKQLNALNKNWRYIVP
__suffix__ = MLTVDGKRVPRDAGHPLYPFNDPY

0 : 2AMG.pdb (3 ; mono; 551) - BA BbbA BA BA BA BA BA BAbbbbb
0 : 2CHR.pdb (38; octa; 370) - dBA BA BA BA BA BA BA BAb
1 : 2DIK.pdb (41; hodi; 873) - BA BaoA BoaA BA BA BaoA BA BA
0 : 2DOR.pdb (63; hodi; 311) - bbBA BbbA BA BA BA BbbbbA BA BA
0 : 2EBN.pdb (15; mono; 339) - Bb BboA BA BA Bo Bo BA BA
2 : 2EXO.pdb (25; mono; 312) - aBA BA BA BA BA BA BA BAa
2 : 2HVM.pdb (35; mono; 273) - BA BboA BA BA BA BA BA BA
0 : 2TMD.pdb (61; hodi; 729) - bbBA BA BbbboA BA BA BA BA BAm
2 : 2TPS.pdb (18; mono; 222) - aBA BA BA BA BA BA BA BA
0 : 2WSY.pdb (54; tetr; 268) - aBA BaoA BA BA BA BA BA BaA
0 : 4REQ.pdb (65; hedi; 637) - aaBA BA BaoA BaoAao BA BA BA BAd
0 : 7ENL.pdb (32; dime; 436) - bB aA BbbA BA BA BA BA BAb
0 : 7ODC.pdb (14; hodi; 461) - bBAb BAbo BA BA BA BA BA BAd*

1FQ0.pdb -- added from HHMrep paper

>1FQ0:A|PDBID|CHAIN|SEQUENCE
MKNWKTSAESILTTGPVVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVPEAIVGAGTVLNPQQL
AEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLKEFKFFPAEANGGVKALQAIAGPFSQVRFCP
TGGISPANYRDYLALKSVLCIGGSWLVPADALEAGDYDRITKLAREAVEGAKL

Repeats        7
P-value   0.0096
Length        23
Offset        72

ID Probab  P-value RepScore RepScoreNorm Cols Query HMM Template HMM
A1  37.08  1.1e-02     3.88         0.30   13   35-47      82-94   
A2  18.31  2.7e-01     1.47         0.11   13   50-62      73-85   
A3  75.98  3.9e-05    13.03         0.57   23   72-94      72-94   
A4  63.90  7.1e-04     8.98         0.43   21   95-115     74-94   
A5  58.26  2.4e-03     7.01         0.47   15  116-130     75-89   
A6  32.21  2.0e-01     3.35         0.16   21  137-160     72-92   
A7  62.00  1.5e-02     8.85         0.40   22  161-182     72-93

A1  Mon_Aug_16_16:   35-47    +2 ----------ALVAGG...VRVLEVTlr.......
A2  Mon_Aug_16_16:   50-62    +9 -TECAVDAIRAIAK--...-------evpeaivga
A3  Mon_Aug_16_16:   72-94    +0 GTVLNPQQLAEVTEAG...AQFAISP.........
A4  Mon_Aug_16_16:   95-115   +0 --GLTEPLLKAATEGT...IPLIPGI.........
A5  Mon_Aug_16_16:  116-130   +6 ---STVSELMLGMDYG...LK-----efkffp...
A6  Mon_Aug_16_16:  137-160   +0 AEANGGVKALQAIAGPfsqVRFCP--.........
A7  Mon_Aug_16_16:  161-182   +0 TGGISPANYRDYLALK...SVLCIG-.........

__prefix__ = MKNWKTSAESILTTGP
VVPVIVVKKLEHAVPMAKALVAGGVR
VLEVTLRTECAVDAIRAIAKEVPEA
IVGAGTVLNPQQLAEVTEAGAQF
AISPGLTEPLLKAATEGTIP
LIPGISTVSELMLGMDYGLK
EFKFFPAEANGGVKALQAIAGPFSQV
RFCPTGGISPANYRDYLALKSVLC
IGGSWLVPADALEAGDYDRITKLAREAVEGAKL

20100812.020205

The TIM Barrel DATE data set is small, consisting only of ~80 proteins
Of these, there aren't too many that are even compatible with the hypothesis -- that is, they're too divergent structurally
Do one of two things:
- Remove the ones that are too different, and use a limited set
- Change datasets
I'm going to try the first option -- there should be a number of structures that are just symmetrical enough.

20100810.095955

CS 798 Dan Brown Phylogeny Final Project

The project that I proposed to Dan Brown sees the analysis of a large number of TIM Barrels
For this, I will analyze my own archives and figure out what I have available first
- I will extend the database given selected data -- this is OK as it is more of a proof of concept rather than a full blown analysis
In ZincSVN, there is a copy of DATE, relevant parts of SCOP and CATH
I should look through those to see if there's anything I can use.
There is one week to do this project from here -- here's a breakdown of my intermediate objectives
1. Hypothesis: "TIM Barrels consist of clusters of proteins which have unique duplication histories"
2. Analyze, Select, Collect, Organize data from the archive
3. Cluster similar nodes together -- give Robert Edgar's clustering software a try
4. Create the duplication histories for representative sequences using Mathieu Lajoie's software.
  - Requires: Breaking apart the TIM Barrels into their putative eighths (OK, Mathieu Lajoie will verify or reject the hypotheses)
5. Describe the resulting clusters in the project paper
6. Reject or Support hypothesis
Each point above can take 4 to 8 hours depending on how quickly I work.

CS798 Final Project Log 20100810

From SnOwy - Ed's Wiki Notebook

20100812.230514

1AJ0.pdb

1AW5.pdb

1B54.pdb

1B5T.pdb

1BD0.pdb

1BQC.pdb

1CNV.pdb

1D9E.pdb

1DBT.pdb

1QFE.pdb

1QO2.pdb

1THF.pdb

2ALR.pdb

1FQ0.pdb -- added from HHMrep paper

20100812.020205

20100810.095955

CS 798 Dan Brown Phylogeny Final Project

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