Alignments for a candidate for gcvP in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvP in Escherichia coli BW25113

Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate 16983 b2903 glycine dehydrogenase (NCBI)

Query= CharProtDB::CH_003480
         (957 letters)



>FitnessBrowser__Keio:16983
          Length = 957

 Score = 1907 bits (4940), Expect = 0.0
 Identities = 957/957 (100%), Positives = 957/957 (100%)

Query: 1   MTQTLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGA 60
           MTQTLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGA
Sbjct: 1   MTQTLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGA 60

Query: 61  PATEYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVS 120
           PATEYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVS
Sbjct: 61  PATEYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVS 120

Query: 121 QGRLEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVH 180
           QGRLEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVH
Sbjct: 121 QGRLEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVH 180

Query: 181 PQTLDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRK 240
           PQTLDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRK
Sbjct: 181 PQTLDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRK 240

Query: 241 IVVSVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGR 300
           IVVSVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGR
Sbjct: 241 IVVSVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGR 300

Query: 301 IIGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRI 360
           IIGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRI
Sbjct: 301 IIGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRI 360

Query: 361 ANRIHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVADKAGVLTRAEAAEINLRSDILNAV 420
           ANRIHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVADKAGVLTRAEAAEINLRSDILNAV
Sbjct: 361 ANRIHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVADKAGVLTRAEAAEINLRSDILNAV 420

Query: 421 GITLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDVAHDSRSIQPAMLRDDEILTHPVFN 480
           GITLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDVAHDSRSIQPAMLRDDEILTHPVFN
Sbjct: 421 GITLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDVAHDSRSIQPAMLRDDEILTHPVFN 480

Query: 481 RYHSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPE 540
           RYHSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPE
Sbjct: 481 RYHSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPE 540

Query: 541 QAEGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLI 600
           QAEGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLI
Sbjct: 541 QAEGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLI 600

Query: 601 PASAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVY 660
           PASAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVY
Sbjct: 601 PASAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVY 660

Query: 661 EETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPG 720
           EETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPG
Sbjct: 661 EETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPG 720

Query: 721 MGPIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKK 780
           MGPIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKK
Sbjct: 721 MGPIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKK 780

Query: 781 ASQVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDY 840
           ASQVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDY
Sbjct: 781 ASQVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDY 840

Query: 841 GFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNA 900
           GFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNA
Sbjct: 841 GFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNA 900

Query: 901 PHIQSELVAEWAHPYSREVAVFPAGVADKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957
           PHIQSELVAEWAHPYSREVAVFPAGVADKYWPTVKRLDDVYGDRNLFCSCVPISEYQ
Sbjct: 901 PHIQSELVAEWAHPYSREVAVFPAGVADKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957


Lambda     K      H
   0.319    0.134    0.395 

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: 2699
Number of extensions: 74
Number of successful extensions: 1
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 16983 b2903 (glycine dehydrogenase (NCBI))
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.915.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 1843.9   0.6          0 1843.7   0.6    1.0  1  lcl|FitnessBrowser__Keio:16983  b2903 glycine dehydrogenase (NCB


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16983  b2903 glycine dehydrogenase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1843.7   0.6         0         0       1     939 []      17     950 ..      17     950 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1843.7 bits;  conditional E-value: 0
                       TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyatilp 79 
                                     rh+Gpd+a+q++ml+++G+++lnal++q+vpkdi+la+p++++apa+ey+alaelk+ias+nk+++syiG+Gy+a++lp
  lcl|FitnessBrowser__Keio:16983  17 RHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAPATEYAALAELKAIASRNKRFTSYIGMGYTAVQLP 95 
                                     9****************************************************************************** PP

                       TIGR00461  80 pviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkk.ankfv 157
                                     pvi+rn+lenpgwytaytpyqpe+sqGrleallnfq+v+ldltGl++a+asllde+taaaeama+++rvsk k an+f+
  lcl|FitnessBrowser__Keio:16983  96 PVILRNMLENPGWYTAYTPYQPEVSQGRLEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKnANRFF 174
                                     *************************************************************************99**** PP

                       TIGR00461 158 vakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalvsvaadllalt 236
                                     va+dvhpqtl+vv+trae++g+evivdda+kv +++dv+Gvllq+++t+Gei+dy+ali+elksrk++vsvaad++al+
  lcl|FitnessBrowser__Keio:16983 175 VASDVHPQTLDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKIVVSVAADIMALV 253
                                     ******************************************************************************* PP

                       TIGR00461 237 lltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkats 315
                                     llt+pgk+Gadiv+GsaqrfGvp+GyGGphaaffa+kdeykr++pGri+Gvskda+Gntalr+a+qtreqhirr+ka+s
  lcl|FitnessBrowser__Keio:16983 254 LLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRIIGVSKDAAGNTALRMAMQTREQHIRREKANS 332
                                     ******************************************************************************* PP

                       TIGR00461 316 nictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeae 394
                                     nict+qvllan+aslyavyhGp+Glk+ia+ri+rlt+ilaagl++k+++lr+++yfdtl+vev++ka+  vl++ae+ae
  lcl|FitnessBrowser__Keio:16983 333 NICTSQVLLANIASLYAVYHGPVGLKRIANRIHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVADKAG--VLTRAEAAE 409
                                     ********************************************************************..********* PP

                       TIGR00461 395 inlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvan...sfpaellrddeilrdevfnryhsete 470
                                     inlr+++l++vgi+ldettt+e+v++l++vl+g dn+gl++++l++dva+   s+++++lrddeil+++vfnryhsete
  lcl|FitnessBrowser__Keio:16983 410 INLRSDILNAVGITLDETTTRENVMQLFNVLLG-DNHGLDIDTLDKDVAHdsrSIQPAMLRDDEILTHPVFNRYHSETE 487
                                     *********************************.89************99999************************** PP

                       TIGR00461 471 llrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdais 549
                                     ++ry+h+le+kdlalnq+miplGsctmklna+aem+pitwpefae+hpf+p+eq+eGy+++iaql++wlv++tG+da++
  lcl|FitnessBrowser__Keio:16983 488 MMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPEQAEGYQQMIAQLADWLVKLTGYDAVC 566
                                     ******************************************************************************* PP

                       TIGR00461 550 lqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagde 628
                                     +qpnsGaqGeyaGl +ir+yhesr+e+hr+iclipasahGtnpasa+maG++vv+v+cdk+Gnidl+dl+akae+agd+
  lcl|FitnessBrowser__Keio:16983 567 MQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIPASAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDN 645
                                     ******************************************************************************* PP

                       TIGR00461 629 laavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpi 707
                                     l+++mvtypst+Gv+eetirev+++vh+fGGqvyldGanmnaqvG+tspg++Gadv+hlnlhktf+iphGGGGpgmgpi
  lcl|FitnessBrowser__Keio:16983 646 LSCIMVTYPSTHGVYEETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGMGPI 724
                                     ******************************************************************************* PP

                       TIGR00461 708 gvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanylakrlkday 786
                                     gvk+hlapf+p+   +svv++eg+ +++gavsaap+Gsasilpis+myi+mmGaeGlkkas+vailnany+a+rl+da+
  lcl|FitnessBrowser__Keio:16983 725 GVKAHLAPFVPG---HSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKKASQVAILNANYIASRLQDAF 800
                                     ************...899************************************************************* PP

                       TIGR00461 787 kilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmveptesesleeldrfidamiaik 865
                                     ++l++grd+rvahecild+r+lke++gi++ld+akrl+dyGfhapt+sfpvaGtlmvepteses++eldrfidam+ai+
  lcl|FitnessBrowser__Keio:16983 801 PVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDYGFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIR 879
                                     ******************************************************************************* PP

                       TIGR00461 866 eeidavkaGeiklednilknaphslqslivaewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
                                     +eid+vkaG+++ledn+l+naph +qs++vaewa+pysre+a++pa+v++  k+wptv+rldd+yGdrnl+csc
  lcl|FitnessBrowser__Keio:16983 880 AEIDQVKAGVWPLEDNPLVNAPH-IQSELVAEWAHPYSREVAVFPAGVAD--KYWPTVKRLDDVYGDRNLFCSC 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: 0.04u 0.03s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 13.31
//
[ok]

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

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Protein sequences (fasta format)
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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