Alignments for a candidate for gcvP in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvP in Klebsiella michiganensis M5al

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate BWI76_RS23870 BWI76_RS23870 glycine dehydrogenase (aminomethyl-transferring)

Query= reanno::Koxy:BWI76_RS23870
         (957 letters)



>FitnessBrowser__Koxy:BWI76_RS23870
          Length = 957

 Score = 1909 bits (4946), Expect = 0.0
 Identities = 957/957 (100%), Positives = 957/957 (100%)

Query: 1   MTQTLGQLENRDAFIERHIGPDALQQQEMLKTVGADSLNALIGQIVPQDIQLATPPQVGE 60
           MTQTLGQLENRDAFIERHIGPDALQQQEMLKTVGADSLNALIGQIVPQDIQLATPPQVGE
Sbjct: 1   MTQTLGQLENRDAFIERHIGPDALQQQEMLKTVGADSLNALIGQIVPQDIQLATPPQVGE 60

Query: 61  ATTEFAALAELKAIAGRNKRFKSYIGMGYTAVQLPPVIQRNMLENPGWYTAYTPYQPEVS 120
           ATTEFAALAELKAIAGRNKRFKSYIGMGYTAVQLPPVIQRNMLENPGWYTAYTPYQPEVS
Sbjct: 61  ATTEFAALAELKAIAGRNKRFKSYIGMGYTAVQLPPVIQRNMLENPGWYTAYTPYQPEVS 120

Query: 121 QGRLESLLNFQQVTLDLTGLDIASASLLDEATAAAEAMAMAKRVSKLKNANRFFVAADVH 180
           QGRLESLLNFQQVTLDLTGLDIASASLLDEATAAAEAMAMAKRVSKLKNANRFFVAADVH
Sbjct: 121 QGRLESLLNFQQVTLDLTGLDIASASLLDEATAAAEAMAMAKRVSKLKNANRFFVAADVH 180

Query: 181 PQTLDVVRTRAETFGFDVIVDDAEKALDHQDVFGVLLQQVGTTGEVHDYSKLIADLKARK 240
           PQTLDVVRTRAETFGFDVIVDDAEKALDHQDVFGVLLQQVGTTGEVHDYSKLIADLKARK
Sbjct: 181 PQTLDVVRTRAETFGFDVIVDDAEKALDHQDVFGVLLQQVGTTGEVHDYSKLIADLKARK 240

Query: 241 VIVSVAADFMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEFKRSMPGR 300
           VIVSVAADFMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEFKRSMPGR
Sbjct: 241 VIVSVAADFMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEFKRSMPGR 300

Query: 301 IIGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVFHGPAGLKRI 360
           IIGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVFHGPAGLKRI
Sbjct: 301 IIGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVFHGPAGLKRI 360

Query: 361 ASRIHRLTDILADGLQKKGLKLRHAHYFDTLCVEVADKAAVLARAEALRINLRSDIHHAV 420
           ASRIHRLTDILADGLQKKGLKLRHAHYFDTLCVEVADKAAVLARAEALRINLRSDIHHAV
Sbjct: 361 ASRIHRLTDILADGLQKKGLKLRHAHYFDTLCVEVADKAAVLARAEALRINLRSDIHHAV 420

Query: 421 GITLDEATTREDVLNLFRAILGDDHGLDIDTLDKDVALDSRSIPASMLRDDAILTHPVFN 480
           GITLDEATTREDVLNLFRAILGDDHGLDIDTLDKDVALDSRSIPASMLRDDAILTHPVFN
Sbjct: 421 GITLDEATTREDVLNLFRAILGDDHGLDIDTLDKDVALDSRSIPASMLRDDAILTHPVFN 480

Query: 481 RYHSETEMMRYMHALERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPVD 540
           RYHSETEMMRYMHALERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPVD
Sbjct: 481 RYHSETEMMRYMHALERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPVD 540

Query: 541 QAEGYHQMIAQLSDWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLI 600
           QAEGYHQMIAQLSDWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLI
Sbjct: 541 QAEGYHQMIAQLSDWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLI 600

Query: 601 PSSAHGTNPASAQMAGMQVVVVACDKNGNIDLADLRAKAEQHAANLSCIMVTYPSTHGVY 660
           PSSAHGTNPASAQMAGMQVVVVACDKNGNIDLADLRAKAEQHAANLSCIMVTYPSTHGVY
Sbjct: 601 PSSAHGTNPASAQMAGMQVVVVACDKNGNIDLADLRAKAEQHAANLSCIMVTYPSTHGVY 660

Query: 661 EETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPG 720
           EETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPG
Sbjct: 661 EETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPG 720

Query: 721 MGPIGVKSHLAQFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKQ 780
           MGPIGVKSHLAQFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKQ
Sbjct: 721 MGPIGVKSHLAQFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKQ 780

Query: 781 ASQMAILNANYIATRLKDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDF 840
           ASQMAILNANYIATRLKDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDF
Sbjct: 781 ASQMAILNANYIATRLKDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDF 840

Query: 841 GFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRGEIDRVKAGEWPLEDNPLVNA 900
           GFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRGEIDRVKAGEWPLEDNPLVNA
Sbjct: 841 GFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRGEIDRVKAGEWPLEDNPLVNA 900

Query: 901 PHTQGELVSAWNHPYARELAVFPAGLNNKYWPTVKRLDDVYGDRNLFCSCVPMSEYQ 957
           PHTQGELVSAWNHPYARELAVFPAGLNNKYWPTVKRLDDVYGDRNLFCSCVPMSEYQ
Sbjct: 901 PHTQGELVSAWNHPYARELAVFPAGLNNKYWPTVKRLDDVYGDRNLFCSCVPMSEYQ 957


Lambda     K      H
   0.320    0.135    0.399 

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: 2623
Number of extensions: 67
Number of successful extensions: 2
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: 957
Length of database: 957
Length adjustment: 44
Effective length of query: 913
Effective length of database: 913
Effective search space:   833569
Effective search space used:   833569
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 BWI76_RS23870 BWI76_RS23870 (glycine dehydrogenase (aminomethyl-transferring))
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.10357.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 1767.8   0.2          0 1767.7   0.2    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS23870  BWI76_RS23870 glycine dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS23870  BWI76_RS23870 glycine dehydrogenase (aminomethyl-transferring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1767.7   0.2         0         0       1     939 []      17     950 ..      17     950 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1767.7 bits;  conditional E-value: 0
                               TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGk 71 
                                             rh+Gpd+ +q++mlkt+G+d+lnali+q+vp+di+la+p++++ +++e++alaelk+ia +nk++ksyiG+
  lcl|FitnessBrowser__Koxy:BWI76_RS23870  17 RHIGPDALQQQEMLKTVGADSLNALIGQIVPQDIQLATPPQVGEATTEFAALAELKAIAGRNKRFKSYIGM 87 
                                             9********************************************************************** PP

                               TIGR00461  72 GyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeam 142
                                             Gy+a++lppviqrn+lenpgwytaytpyqpe+sqGrle+llnfq+v+ldltGl++a+asllde+taaaeam
  lcl|FitnessBrowser__Koxy:BWI76_RS23870  88 GYTAVQLPPVIQRNMLENPGWYTAYTPYQPEVSQGRLESLLNFQQVTLDLTGLDIASASLLDEATAAAEAM 158
                                             *********************************************************************** PP

                               TIGR00461 143 alsfrvskkk.ankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildy 212
                                             a+++rvsk k an+f+va dvhpqtl+vv+trae++g++vivdda+k  +++dv+Gvllq+++t+Ge++dy
  lcl|FitnessBrowser__Koxy:BWI76_RS23870 159 AMAKRVSKLKnANRFFVAADVHPQTLDVVRTRAETFGFDVIVDDAEKALDHQDVFGVLLQQVGTTGEVHDY 229
                                             **********99*********************************************************** PP

                               TIGR00461 213 kalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGr 283
                                              +li +lk rk++vsvaad +al+llt+pgk+Gadiv+GsaqrfGvp+GyGGphaaffa+kde+kr++pGr
  lcl|FitnessBrowser__Koxy:BWI76_RS23870 230 SKLIADLKARKVIVSVAADFMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEFKRSMPGR 300
                                             *********************************************************************** PP

                               TIGR00461 284 ivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsil 354
                                             i+Gvskda+Gntalr+a+qtreqhirr+ka+snict+qvllan+aslyav+hGp Glk+ia ri+rlt+il
  lcl|FitnessBrowser__Koxy:BWI76_RS23870 301 IIGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVFHGPAGLKRIASRIHRLTDIL 371
                                             *********************************************************************** PP

                               TIGR00461 355 aaglkrknyelrnktyfdtltvevgekaasevlkaaeeaeinlravvltevgialdetttkedvldllkvl 425
                                             a gl++k+++lr+++yfdtl+vev++kaa  vl +ae+  inlr+++  +vgi+lde+tt+edvl+l++ +
  lcl|FitnessBrowser__Koxy:BWI76_RS23870 372 ADGLQKKGLKLRHAHYFDTLCVEVADKAA--VLARAEALRINLRSDIHHAVGITLDEATTREDVLNLFRAI 440
                                             ****************************9..**************************************** PP

                               TIGR00461 426 agkdnlglsseelsedvan...sfpaellrddeilrdevfnryhsetellrylhrleskdlalnqsmiplG 493
                                             +g d++gl++++l++dva    s+pa +lrdd il+++vfnryhsete++ry+h le+kdlalnq+miplG
  lcl|FitnessBrowser__Koxy:BWI76_RS23870 441 LG-DDHGLDIDTLDKDVALdsrSIPASMLRDDAILTHPVFNRYHSETEMMRYMHALERKDLALNQAMIPLG 510
                                             **.55************86667************************************************* PP

                               TIGR00461 494 sctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlr 564
                                             sctmklna+aem+pitwpefae+hpf+p +q+eGy+++iaql +wlv++tG+da+++qpnsGaqGeyaGl 
  lcl|FitnessBrowser__Koxy:BWI76_RS23870 511 SCTMKLNAAAEMIPITWPEFAELHPFCPVDQAEGYHQMIAQLSDWLVKLTGYDAVCMQPNSGAQGEYAGLL 581
                                             *********************************************************************** PP

                               TIGR00461 565 virsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvt 635
                                             +ir+yhesr+e+hr+iclip sahGtnpasa+maG++vv+v+cdk+Gnidl dl+akae+++ +l+++mvt
  lcl|FitnessBrowser__Koxy:BWI76_RS23870 582 AIRHYHESRNEGHRDICLIPSSAHGTNPASAQMAGMQVVVVACDKNGNIDLADLRAKAEQHAANLSCIMVT 652
                                             *********************************************************************** PP

                               TIGR00461 636 ypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgp 706
                                             ypst+Gv+eetirev+++vh+fGGqvyldGanmnaqvG+tspg++Gadv+hlnlhktf+iphGGGGpgmgp
  lcl|FitnessBrowser__Koxy:BWI76_RS23870 653 YPSTHGVYEETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGMGP 723
                                             *********************************************************************** PP

                               TIGR00461 707 igvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnany 777
                                             igvkshla f+p+   +svv++eg+ +++gavsaap+Gsasilpis+myi+mmGaeGlk+as++ailnany
  lcl|FitnessBrowser__Koxy:BWI76_RS23870 724 IGVKSHLAQFVPG---HSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKQASQMAILNANY 791
                                             *************...899**************************************************** PP

                               TIGR00461 778 lakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmveptes 848
                                             +a+rlkda+++l++grd+rvahecild+r+lke++gi++ld+akrl+d+Gfhapt+sfpvaGtlmveptes
  lcl|FitnessBrowser__Koxy:BWI76_RS23870 792 IATRLKDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDFGFHAPTMSFPVAGTLMVEPTES 862
                                             *********************************************************************** PP

                               TIGR00461 849 esleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaaypapvlkyfkf 919
                                             es++eldrfidam+ai+ eid vkaGe++ledn+l+naph  q ++v+ w++py+re a++pa++ +  k+
  lcl|FitnessBrowser__Koxy:BWI76_RS23870 863 ESKVELDRFIDAMLAIRGEIDRVKAGEWPLEDNPLVNAPH-TQGELVSAWNHPYARELAVFPAGLNN--KY 930
                                             ****************************************.8999*******************987..** PP

                               TIGR00461 920 wptvarlddtyGdrnlvcsc 939
                                             wptv+rldd+yGdrnl+csc
  lcl|FitnessBrowser__Koxy:BWI76_RS23870 931 WPTVKRLDDVYGDRNLFCSC 950
                                             ******************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (939 nodes)
Target sequences:                          1  (957 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 12.68
//
[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