Alignments for a candidate for gcvP in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvP in Bacteroides thetaiotaomicron VPI-5482

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate 350675 BT1147 glycine dehydrogenase [decarboxylating] (NCBI ptt file)

Query= reanno::WCS417:GFF4367
         (946 letters)



>FitnessBrowser__Btheta:350675
          Length = 949

 Score =  969 bits (2505), Expect = 0.0
 Identities = 501/936 (53%), Positives = 646/936 (69%), Gaps = 14/936 (1%)

Query: 13  ARHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLSEAEALAKIKAIA 72
           +RHIG  +ED   ML  +G DSL+ L    IP +I+    L L   L+E E    I  +A
Sbjct: 8   SRHIGINEEDTAVMLRKIGVDSLDELINKTIPANIRLKEPLALAKPLTEYEFGKHIADLA 67

Query: 73  GKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLIS 132
            KN+L+ TYIG G+YN  TP+ I RN+ ENP WYT+YTPYQ E+SQGRLEAL+NFQT + 
Sbjct: 68  SKNKLYTTYIGLGWYNTITPAVIQRNVFENPVWYTSYTPYQTEVSQGRLEALMNFQTAVC 127

Query: 133 DLTGLPIANASLLDEATAAAEAMTFC----KRLSKNKGSNAFFASIHSHPQTLDVLRTRA 188
           DLT +P+AN SLLDEATAAAEA+T       R  +  G+N  F   +  PQTL V+ TRA
Sbjct: 128 DLTAMPLANCSLLDEATAAAEAVTMMYALRSRTQQKAGANVVFVDENIFPQTLAVMTTRA 187

Query: 189 EPLGIDVVVGDERELTDVSPFFGALLQYPASNGDVFDYRELTERFHAAHGLVAVAADLLA 248
            P GI++ VG  +E       F  +LQYP S+G+V DY + T++ H A   VAVAAD+L+
Sbjct: 188 IPQGIELRVGKYKEFEPSPEIFACILQYPNSSGNVEDYADFTKKAHEADCKVAVAADILS 247

Query: 249 LTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGK 308
           L LLTPPGE+GAD+  G+ QR G P+ +GGP A YF+T+D +KR+MPGR++G S D++GK
Sbjct: 248 LALLTPPGEWGADIVFGTTQRLGTPMFYGGPSAGYFATRDEYKRNMPGRIIGWSKDKYGK 307

Query: 309 PALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARRVHQLTAIL 368
              R+A+QTREQHI+REKATSNICTAQ LLA +A  YAVYHG +G+  IA R+H +T  L
Sbjct: 308 LCYRMALQTREQHIKREKATSNICTAQALLATMAGFYAVYHGQEGIKTIASRIHSITVFL 367

Query: 369 AKGLTALGQNVEQAHFFDTLTLNTGANTAA--VHDKARAQRINLRVVDAERVGVSVDETT 426
            K L   G     A +FDTL      + +A  +   A ++ +NLR  +   VG S+DETT
Sbjct: 368 DKQLKKFGYTQVNAQYFDTLRFELPEHVSAQQIRTIALSKEVNLRYYENGDVGFSIDETT 427

Query: 427 TQADIETLWAIFA-----DGKALPDFAAQVESTLPAALLRQSPVLSHPVFNRYHSETELM 481
             A    L +IFA     D + + D   +  S +  AL R +P L+H VF+ YH+ETE+M
Sbjct: 428 DIAATNVLLSIFAIAAGKDYQKVEDVPEK--SNIDKALKRTTPFLTHEVFSNYHTETEMM 485

Query: 482 RYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYLELT 541
           RY+++L  KD++L ++MI LGSCTMKLNAA+EM+P++  EF ++HP  P +Q+ GY EL 
Sbjct: 486 RYIKRLDRKDISLAQSMISLGSCTMKLNAAAEMLPLSRPEFMSMHPLVPEDQAEGYRELI 545

Query: 542 SDLEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAHGTNP 601
           S+L   L   TG+  +SLQPN+G+ GEYAGL  IRAY +S G   R+  LIP+SAHGTNP
Sbjct: 546 SNLSEDLKVITGFAGVSLQPNSGAAGEYAGLRVIRAYLESIGQGHRNKILIPASAHGTNP 605

Query: 602 ATANMAGMRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIREICG 661
           A+A  AG   V  ACD +GNVD+ DLRAKA E+++ LAALMITYPSTHG+FE  I+EIC 
Sbjct: 606 ASAIQAGFETVTCACDEQGNVDMGDLRAKAEENKEALAALMITYPSTHGIFETEIKEICE 665

Query: 662 IIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSH 721
           IIH  G QVY+DGANMNA VGL  PG  G DV HLNLHKTF  PHGGGGPGVGPI V  H
Sbjct: 666 IIHACGAQVYMDGANMNAQVGLTNPGFIGADVCHLNLHKTFASPHGGGGPGVGPICVAEH 725

Query: 722 LTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYISMMGGAGLKRASQLAILNANYISR 781
           L PFLPGH+     +  V AAPFGSA ILPIT+ YI MMG  GL +A+++AILNANY++ 
Sbjct: 726 LVPFLPGHSIFGSTQNQVSAAPFGSAGILPITYGYIRMMGTEGLTQATKIAILNANYLAA 785

Query: 782 RLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAGT 841
            L++ Y ++Y G+ G V HE IL+ R + + +GIS +D+AKRL+D+G+HAPT+SFPV GT
Sbjct: 786 CLKDTYGIVYRGATGFVGHEMILECRKVHEETGISENDIAKRLMDYGYHAPTLSFPVHGT 845

Query: 842 LMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPHTAAELVSE-WTH 900
           LMIEPTESES  ELD F + M+ I +EI+ V+N   DK+DN L NAPH   E+V++ W H
Sbjct: 846 LMIEPTESESLAELDNFVDVMLNIWKEIQEVKNEEADKNDNVLINAPHPEYEIVNDNWEH 905

Query: 901 PYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLV 936
            YTRE+A YP+ S+ E K+W  V RVDN  GDR L+
Sbjct: 906 SYTREKAAYPIESVRENKFWVNVARVDNTLGDRKLL 941


Lambda     K      H
   0.319    0.135    0.398 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1951
Number of extensions: 68
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 946
Length of database: 949
Length adjustment: 44
Effective length of query: 902
Effective length of database: 905
Effective search space:   816310
Effective search space used:   816310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)

Align candidate 350675 BT1147 (glycine dehydrogenase [decarboxylating] (NCBI ptt file))
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00461.hmm
# target sequence database:        /tmp/gapView.29367.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00461  [M=939]
Accession:   TIGR00461
Description: gcvP: glycine dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
          0 1296.4   0.1          0 1296.2   0.1    1.0  1  lcl|FitnessBrowser__Btheta:350675  BT1147 glycine dehydrogenase [de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350675  BT1147 glycine dehydrogenase [decarboxylating] (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1296.2   0.1         0         0       1     936 [.       9     941 ..       9     944 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1296.2 bits;  conditional E-value: 0
                          TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyat 76 
                                        rh+G +e +   ml+ +G+d+l++li++ +p +irl+ pl l  p +eye  +++  +asknk +++yiG G+y+t
  lcl|FitnessBrowser__Btheta:350675   9 RHIGINEEDTAVMLRKIGVDSLDELINKTIPANIRLKEPLALAKPLTEYEFGKHIADLASKNKLYTTYIGLGWYNT 84 
                                        9*************************************************************************** PP

                          TIGR00461  77 ilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrv...s 149
                                        i+p viqrn++enp wyt+ytpyq+e+sqGrleal+nfqt v dlt +++an sllde+taaaea+ + + +   +
  lcl|FitnessBrowser__Btheta:350675  85 ITPAVIQRNVFENPVWYTSYTPYQTEVSQGRLEALMNFQTAVCDLTAMPLANCSLLDEATAAAEAVTMMYALrsrT 160
                                        *****************************************************************99999874222 PP

                          TIGR00461 150 kkk..ankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrk 223
                                        ++k  an  +v++++ pqtl v+ tra p gie+ v+  ++++ + +++ ++lqyp ++G++ dy ++++++++  
  lcl|FitnessBrowser__Btheta:350675 161 QQKagANVVFVDENIFPQTLAVMTTRAIPQGIELRVGKYKEFEPSPEIFACILQYPNSSGNVEDYADFTKKAHEAD 236
                                        344468999******************************************************************* PP

                          TIGR00461 224 alvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrl 299
                                          v+vaad+l+l+lltppg+ Gadiv+G++qr+G p+ yGGp a +fa++deykr++pGri+G skd+ G+   r+
  lcl|FitnessBrowser__Btheta:350675 237 CKVAVAADILSLALLTPPGEWGADIVFGTTQRLGTPMFYGGPSAGYFATRDEYKRNMPGRIIGWSKDKYGKLCYRM 312
                                        **************************************************************************** PP

                          TIGR00461 300 alqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtlt 375
                                        alqtreqhi+r+katsnictaq+lla++a  yavyhG  G+k ia ri+++t+ l + lk+ +y   n++yfdtl+
  lcl|FitnessBrowser__Btheta:350675 313 ALQTREQHIKREKATSNICTAQALLATMAGFYAVYHGQEGIKTIASRIHSITVFLDKQLKKFGYTQVNAQYFDTLR 388
                                        **************************************************************************** PP

                          TIGR00461 376 vevgekaase.vlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedv.ansfpae 449
                                         e+ e+++++ + + a ++e+nlr    ++vg+++dett  +    ll ++a+    g + +++++   ++ ++++
  lcl|FitnessBrowser__Btheta:350675 389 FELPEHVSAQqIRTIALSKEVNLRYYENGDVGFSIDETTDIAATNVLLSIFAIAA--GKDYQKVEDVPeKSNIDKA 462
                                        *****9988779999**************************************66..6666666543314479*** PP

                          TIGR00461 450 llrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqv 525
                                        l+r+  +l++evf +yh+ete++ry++rl++kd++l+qsmi lGsctmklna+aemlp++ pef  +hp+ p +q+
  lcl|FitnessBrowser__Btheta:350675 463 LKRTTPFLTHEVFSNYHTETEMMRYIKRLDRKDISLAQSMISLGSCTMKLNAAAEMLPLSRPEFMSMHPLVPEDQA 538
                                        **************************************************************************** PP

                          TIGR00461 526 eGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlk 601
                                        eGy+eli++l ++l  itGf ++slqpnsGa GeyaGlrvir y+es g++hrn  lipasahGtnpasa  aG++
  lcl|FitnessBrowser__Btheta:350675 539 EGYRELISNLSEDLKVITGFAGVSLQPNSGAAGEYAGLRVIRAYLESIGQGHRNKILIPASAHGTNPASAIQAGFE 614
                                        **************************************************************************** PP

                          TIGR00461 602 vvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltsp 677
                                         v+ +cd++Gn+d+ dl+akae++ + laa+m+typst+G+fe+ i+e+++i+h  G qvy+dGanmnaqvGlt+p
  lcl|FitnessBrowser__Btheta:350675 615 TVTCACDEQGNVDMGDLRAKAEENKEALAALMITYPSTHGIFETEIKEICEIIHACGAQVYMDGANMNAQVGLTNP 690
                                        **************************************************************************** PP

                          TIGR00461 678 gdlGadvchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisy 753
                                        g++Gadvchlnlhktf+ phGGGGpg+gpi+v  hl+pflp++++           ++++vsaap+Gsa ilpi+y
  lcl|FitnessBrowser__Btheta:350675 691 GFIGADVCHLNLHKTFASPHGGGGPGVGPICVAEHLVPFLPGHSIFG--------STQNQVSAAPFGSAGILPITY 758
                                        ******************************************76643........34678**************** PP

                          TIGR00461 754 myikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfh 829
                                         yi+mmG+eGl++a+++ailnanyla+ lkd+y i+++g  + v he+il+ r++ e++gi++ d+akrl+dyG+h
  lcl|FitnessBrowser__Btheta:350675 759 GYIRMMGTEGLTQATKIAILNANYLAACLKDTYGIVYRGATGFVGHEMILECRKVHEETGISENDIAKRLMDYGYH 834
                                        **************************************************************************** PP

                          TIGR00461 830 aptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysre 905
                                        aptlsfpv Gtlm+eptesesl eld f+d m+ i +ei++vk+ e +++dn+l naph   + +  +w ++y+re
  lcl|FitnessBrowser__Btheta:350675 835 APTLSFPVHGTLMIEPTESESLAELDNFVDVMLNIWKEIQEVKNEEADKNDNVLINAPHPEYEIVNDNWEHSYTRE 910
                                        ***********************************************************8888888889999**** PP

                          TIGR00461 906 eaaypapvlkyfkfwptvarlddtyGdrnlv 936
                                        +aayp+  ++++kfw  var+d+t Gdr+l+
  lcl|FitnessBrowser__Btheta:350675 911 KAAYPIESVRENKFWVNVARVDNTLGDRKLL 941
                                        *****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (939 nodes)
Target sequences:                          1  (949 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.10
# Mc/sec: 8.67
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources