Alignments for a candidate for gabT in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Desulfobacter vibrioformis DSM 8776

Align Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized)
to candidate WP_035239836.1 Q366_RS13500 4-aminobutyrate--2-oxoglutarate transaminase

Query= curated2:P94427
         (436 letters)



>NCBI__GCF_000745975.1:WP_035239836.1
          Length = 415

 Score =  436 bits (1120), Expect = e-127
 Identities = 222/421 (52%), Positives = 287/421 (68%), Gaps = 19/421 (4%)

Query: 14  QQKRDQFVSKGVSNGNRSLAVKGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVK 73
           Q  R+Q +  G ++G        +GA + D+ G+++IDFAG I  +NVGHSHPKVV A+K
Sbjct: 8   QTLRNQVIPNGHASGTTCYVDSAKGAIITDVQGKQYIDFAGGIAVMNVGHSHPKVVAAIK 67

Query: 74  RQAEELIHPGFNVMMYPTYIELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKYTK 133
            QAE+  H  F V  Y   + LA++LC I PG+ +KKA+F+NSGAEAVENAVKIAR YT+
Sbjct: 68  AQAEKFTHTCFMVNPYDVAVRLADRLCKITPGTFDKKALFVNSGAEAVENAVKIARYYTQ 127

Query: 134 RQGVVSFTRGFHGRTNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYD 193
           RQGVV+F   +HGRT +TM+MT+KVKPYK GFGP APEVY+APF  +             
Sbjct: 128 RQGVVTFDGSYHGRTYLTMAMTTKVKPYKCGFGPLAPEVYRAPFGNF------------- 174

Query: 194 DMVIQAFNDFFIASVAPETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADE 253
               +AF DFFI  + PE  A VV+EP+QGEGGFI P   F+  VA FCK++GIVF+ADE
Sbjct: 175 ----KAFTDFFITGINPENTAAVVIEPIQGEGGFIAPPADFLPQVAQFCKDNGIVFIADE 230

Query: 254 IQTGFARTGTYFAIEHFDVVPDLITVSKSLAAGLPLSGVIGRAEMLDAAAPGELGGTYAG 313
           IQ+G  R+G  FAIE+F V PDL+TV+KS+AAG+PLS V+GR E++D+  PG LGGTY  
Sbjct: 231 IQSGMGRSGKMFAIENFGVEPDLMTVAKSIAAGMPLSAVVGRKEIMDSVHPGGLGGTYGA 290

Query: 314 SPLGCAAALAVLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRRLGAMAAIEIV 373
           +P+ CAAA AVLDI EEE L E+++ IG+ +      W Q+F  +G++R +GAM    IV
Sbjct: 291 NPVACAAAHAVLDIFEEENLLEKAQAIGEKLGATFGAWTQKFDHVGEVRGIGAMRGYTIV 350

Query: 374 KDPDTREPDKTKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLSILEAG 433
               T  PDK K   ++AY   NGL+ L  GI GN+IR L PLVI D  L +GL I+EAG
Sbjct: 351 NADGTPAPDKAK--TLSAYCFDNGLITLVCGIEGNVIRVLMPLVIEDDQLQKGLDIMEAG 408

Query: 434 L 434
           L
Sbjct: 409 L 409


Lambda     K      H
   0.319    0.136    0.393 

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: 489
Number of extensions: 13
Number of successful extensions: 3
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: 436
Length of database: 415
Length adjustment: 32
Effective length of query: 404
Effective length of database: 383
Effective search space:   154732
Effective search space used:   154732
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_035239836.1 Q366_RS13500 (4-aminobutyrate--2-oxoglutarate transaminase)
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

# 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/TIGR00700.hmm
# target sequence database:        /tmp/gapView.1068760.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00700  [M=420]
Accession:   TIGR00700
Description: GABAtrnsam: 4-aminobutyrate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-169  549.7  11.3     3e-168  545.7  11.3    1.9  1  NCBI__GCF_000745975.1:WP_035239836.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745975.1:WP_035239836.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  545.7  11.3    3e-168    3e-168       3     419 ..      11     410 ..       9     411 .. 0.97

  Alignments for each domain:
  == domain 1  score: 545.7 bits;  conditional E-value: 3e-168
                             TIGR00700   3 raaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpy 75 
                                           r++++++G + +++ ++ +a+ga++ dv+G+++id+a+giav+nvGhshPkvv+a+k q+e++tht+f+v py
  NCBI__GCF_000745975.1:WP_035239836.1  11 RNQVIPNGHASGTTCYVDSAKGAIITDVQGKQYIDFAGGIAVMNVGHSHPKVVAAIKAQAEKFTHTCFMVNPY 83 
                                           8999********************************************************************* PP

                             TIGR00700  76 esyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPyk 148
                                           +  v la++l++i+Pg+ +kka+++nsGaeavenavkiar yt+r+gvv+f++++hGrt+ltma+t+kvkPyk
  NCBI__GCF_000745975.1:WP_035239836.1  84 DVAVRLADRLCKITPGTFDKKALFVNSGAEAVENAVKIARYYTQRQGVVTFDGSYHGRTYLTMAMTTKVKPYK 156
                                           ************************************************************************* PP

                             TIGR00700 149 iGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelva 221
                                            GfGP+apevyraP+                 +++a+ ++f++ +++e+ aavv+eP+qGeGGfi p+ ++++
  NCBI__GCF_000745975.1:WP_035239836.1 157 CGFGPLAPEVYRAPFG----------------NFKAFTDFFITGINPENTAAVVIEPIQGEGGFIAPPADFLP 213
                                           **************95................356999*********************************** PP

                             TIGR00700 222 avaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGG 294
                                           +va++ck++giv+iade+q+G+ r+Gk+faie ++++Pdl+tvaks+a+G+Pls+vvGr ei+d+ +pGglGG
  NCBI__GCF_000745975.1:WP_035239836.1 214 QVAQFCKDNGIVFIADEIQSGMGRSGKMFAIENFGVEPDLMTVAKSIAAGMPLSAVVGRKEIMDSVHPGGLGG 286
                                           ************************************************************************* PP

                             TIGR00700 295 tyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpd.ttePd 366
                                           ty+ nP+a+aaa+avldi eee l e+a+ ig+ +  +   + ++++ +g+vrg Gam    +v++d t  Pd
  NCBI__GCF_000745975.1:WP_035239836.1 287 TYGANPVACAAAHAVLDIFEEENLLEKAQAIGEKLGATFGAWTQKFDHVGEVRGIGAMRGYTIVNADgTPAPD 359
                                           ***************************************************************9765166677 PP

                             TIGR00700 367 aalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                           +  a+ ++a+   +Gl+ l +Gi Gn+ir+l+Pl+i d++l++gl+i+ea+la
  NCBI__GCF_000745975.1:WP_035239836.1 360 K--AKTLSAYCFDNGLITLVCGIEGNVIRVLMPLVIEDDQLQKGLDIMEAGLA 410
                                           6..56799******************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (415 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.91
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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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 2024 update 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