Alignments for a candidate for gabT in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Desulfacinum infernum DSM 9756

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_073038495.1 BUB04_RS08145 4-aminobutyrate--2-oxoglutarate transaminase

Query= curated2:P94427
         (436 letters)



>NCBI__GCF_900129305.1:WP_073038495.1
          Length = 434

 Score =  424 bits (1090), Expect = e-123
 Identities = 213/427 (49%), Positives = 282/427 (66%)

Query: 10  TAQWQQKRDQFVSKGVSNGNRSLAVKGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVV 69
           T Q    R   V +G  +     A + EGA +YD+DGR FIDFAG I  +NVGHSHPKVV
Sbjct: 6   TDQLAALRASVVPQGPFHVTPFFAERAEGARIYDVDGREFIDFAGGIAVMNVGHSHPKVV 65

Query: 70  EAVKRQAEELIHPGFNVMMYPTYIELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIAR 129
            A+K QAE+  H  F+V+MY  Y+ LAEKLC + PG   K A+F NSGAE VENAVKIAR
Sbjct: 66  AAIKDQAEKFTHTCFHVVMYEPYLRLAEKLCRLTPGDFPKMALFANSGAEGVENAVKIAR 125

Query: 130 KYTKRQGVVSFTRGFHGRTNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSD 189
             T+R  ++ F  GFHGRT + M+MTSKVKPYKFGFGPFAPEVY+  +PY Y+ P G+S 
Sbjct: 126 YATRRPAIIVFEGGFHGRTLLAMTMTSKVKPYKFGFGPFAPEVYRMVYPYCYRCPLGLSY 185

Query: 190 ESYDDMVIQAFNDFFIASVAPETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVF 249
            + D        DFF+  VA E  A VV+EPV GEGGF++P   +   +A+ C+E+GI+F
Sbjct: 186 PACDVACADRLKDFFVEYVAAEQTAAVVVEPVLGEGGFVVPPPEYFGKLAAICRENGILF 245

Query: 250 VADEIQTGFARTGTYFAIEHFDVVPDLITVSKSLAAGLPLSGVIGRAEMLDAAAPGELGG 309
           V DE+QTG  RTG  FAIEH+  VPDL+  +KSLAAG+PLS V+GRAE+++A   G LGG
Sbjct: 246 VCDEVQTGIGRTGRMFAIEHWGEVPDLVISAKSLAAGMPLSAVVGRAEIMNAPHVGGLGG 305

Query: 310 TYAGSPLGCAAALAVLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRRLGAMAA 369
           TY G+P+ C AALAVL+I EEE L E++  +G        E  +E   +G++R LG M A
Sbjct: 306 TYGGNPVACRAALAVLEIFEEENLLEKARALGVKARGLLDEMAREVELVGEVRGLGPMLA 365

Query: 370 IEIVKDPDTREPDKTKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLSI 429
           +E+V D + + P   +A  +    ++ GL+++  G  GN++R L PLV +D  L  G+SI
Sbjct: 366 MELVTDRERKTPATDQAKQVVRTCHEKGLIVMNCGAYGNLLRLLMPLVTTDEELQRGMSI 425

Query: 430 LEAGLRA 436
           L   L++
Sbjct: 426 LRDALKS 432


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: 484
Number of extensions: 17
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: 436
Length of database: 434
Length adjustment: 32
Effective length of query: 404
Effective length of database: 402
Effective search space:   162408
Effective search space used:   162408
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_073038495.1 BUB04_RS08145 (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.2015401.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-173  563.4   0.1   1.4e-173  563.2   0.1    1.0  1  NCBI__GCF_900129305.1:WP_073038495.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900129305.1:WP_073038495.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  563.2   0.1  1.4e-173  1.4e-173       3     419 ..      13     431 ..      11     432 .. 0.98

  Alignments for each domain:
  == domain 1  score: 563.2 bits;  conditional E-value: 1.4e-173
                             TIGR00700   3 raaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpy 75 
                                           ra++v++G   +++++a +aega ++dvdG+++id+a+giav+nvGhshPkvv+a+k q+e++tht+f+vv+y
  NCBI__GCF_900129305.1:WP_073038495.1  13 RASVVPQGPFHVTPFFAERAEGARIYDVDGREFIDFAGGIAVMNVGHSHPKVVAAIKDQAEKFTHTCFHVVMY 85 
                                           8999********************************************************************* PP

                             TIGR00700  76 esyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPyk 148
                                           e y+ laekl++++Pg  +k a++ nsGae venavkiar  t+rp+++ f++gfhGrt l+m++t+kvkPyk
  NCBI__GCF_900129305.1:WP_073038495.1  86 EPYLRLAEKLCRLTPGDFPKMALFANSGAEGVENAVKIARYATRRPAIIVFEGGFHGRTLLAMTMTSKVKPYK 158
                                           ************************************************************************* PP

                             TIGR00700 149 iGfGPfapevyraPlpydyrdialdkqesldd.elaaiealfvadveaeqvaavvlePvqGeGGfivpakelv 220
                                           +GfGPfapevyr+ +py yr +++ +  + d    + ++++fv  v+aeq aavv+ePv GeGGf+vp+ e+ 
  NCBI__GCF_900129305.1:WP_073038495.1 159 FGFGPFAPEVYRMVYPYCYRCPLGLSYPACDVaCADRLKDFFVEYVAAEQTAAVVVEPVLGEGGFVVPPPEYF 231
                                           ******************************9745567899********************************* PP

                             TIGR00700 221 aavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglG 293
                                            ++a +c+e+gi+++ devqtG  rtG++faieh++++Pdl+  aksla+G+Pls+vvGraei++ap++GglG
  NCBI__GCF_900129305.1:WP_073038495.1 232 GKLAAICRENGILFVCDEVQTGIGRTGRMFAIEHWGEVPDLVISAKSLAAGMPLSAVVGRAEIMNAPHVGGLG 304
                                           ************************************************************************* PP

                             TIGR00700 294 GtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdtteP 365
                                           Gty+GnP+a+ aalavl+i eee l e+a+ +g   +  l e+ +ev+ +g+vrglG m+a+elv d + + P
  NCBI__GCF_900129305.1:WP_073038495.1 305 GTYGGNPVACRAALAVLEIFEEENLLEKARALGVKARGLLDEMAREVELVGEVRGLGPMLAMELVtDRERKTP 377
                                           *****************************************************************999999** PP

                             TIGR00700 366 daalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                            +  a+++  + +++Gl+++ +G++Gn++rll+Pl+ +de l+ g++il++al+
  NCBI__GCF_900129305.1:WP_073038495.1 378 ATDQAKQVVRTCHEKGLIVMNCGAYGNLLRLLMPLVTTDEELQRGMSILRDALK 431
                                           ***************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (434 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 15.20
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 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