Alignments for a candidate for gabT in Halomonas xinjiangensis TRM 0175

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Halomonas xinjiangensis TRM 0175

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate WP_043527315.1 JH15_RS04225 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000759345.1:WP_043527315.1
          Length = 432

 Score =  419 bits (1076), Expect = e-121
 Identities = 206/421 (48%), Positives = 278/421 (66%)

Query: 3   SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62
           +N +L + + + +  G       FADRAEN  +WD +G   +DFAGGI VLN GH HPKV
Sbjct: 2   NNAQLNELKQRYVANGAASPATQFADRAENALIWDADGNRLIDFAGGIGVLNIGHRHPKV 61

Query: 63  VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122
           V AV+AQL K+ HTC  V+ YE Y+++ E ++Q  P     K +L  +G+EA+ENAVK+A
Sbjct: 62  VEAVKAQLDKVMHTCQTVMPYEGYVKVAEKLSQITPVRGHAKVMLANSGAEALENAVKVA 121

Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182
           RAAT ++  I F G YHGRT  T+A+ GKV PY+   G MPG+V+RA YP P HG+SED+
Sbjct: 122 RAATGKNNVICFDGGYHGRTFMTMAMNGKVAPYATDFGSMPGNVFRAPYPVPYHGVSEDE 181

Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242
           A+  +    K DA P+D AAIV+EPV GEGGFYA+  +F++ +R +CDEHGI+LI DEVQ
Sbjct: 182 ALRGLKMALKTDANPKDTAAIVLEPVLGEGGFYAAPASFLKAIRDICDEHGILLIIDEVQ 241

Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302
           SG GRTG +FA+E  GV PD+   AKS+A G P++ V G  +VMDA     LGGTY G+P
Sbjct: 242 SGFGRTGKMFAIEHSGVEPDIICMAKSMADGMPISAVVGTDKVMDASGGNSLGGTYTGSP 301

Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFED 362
           ++C A L VL+VFE+E +L+K+  LG KL        +    + + R LGAM A +L  D
Sbjct: 302 VSCAATLAVLEVFEEEKILEKSQALGDKLAKRFSQWEQDFDCVDNGRNLGAMAAFDLVSD 361

Query: 363 GDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422
              + PDA L   +  RAR+KGL+LLSCG Y N +R L+P+TIED  + +GL ++     
Sbjct: 362 KAQHTPDADLAGALCKRAREKGLVLLSCGLYGNTIRFLMPVTIEDDILEEGLGVVESALK 421

Query: 423 E 423
           E
Sbjct: 422 E 422


Lambda     K      H
   0.320    0.137    0.401 

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: 525
Number of extensions: 18
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: 426
Length of database: 432
Length adjustment: 32
Effective length of query: 394
Effective length of database: 400
Effective search space:   157600
Effective search space used:   157600
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: 51 (24.3 bits)

Align candidate WP_043527315.1 JH15_RS04225 (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.1703314.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.2e-161  521.8   1.0     6e-161  521.6   1.0    1.0  1  NCBI__GCF_000759345.1:WP_043527315.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000759345.1:WP_043527315.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.6   1.0    6e-161    6e-161       4     419 ..      11     421 ..       8     422 .. 0.98

  Alignments for each domain:
  == domain 1  score: 521.6 bits;  conditional E-value: 6e-161
                             TIGR00700   4 aaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpye 76 
                                           + +v++G +  ++ +a +ae+a + d dGnrlid+a+gi+vln+Gh+hPkvveavk q+++++ht+ +v+pye
  NCBI__GCF_000759345.1:WP_043527315.1  11 QRYVANGAASPATQFADRAENALIWDADGNRLIDFAGGIGVLNIGHRHPKVVEAVKAQLDKVMHTCQTVMPYE 83 
                                           56799999999************************************************************** PP

                             TIGR00700  77 syvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPyki 149
                                           +yv++aekl++i+P+ g++k +l nsGaea+enavk+ar+ tg++ v++f++g+hGrt++tma+ +kv+Py +
  NCBI__GCF_000759345.1:WP_043527315.1  84 GYVKVAEKLSQITPVRGHAKVMLANSGAEALENAVKVARAATGKNNVICFDGGYHGRTFMTMAMNGKVAPYAT 156
                                           ************************************************************************* PP

                             TIGR00700 150 GfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaa 222
                                            fG ++++v+raP+p +y++ +   +e+    l+ ++   ++d ++++ aa+vlePv GeGGf  ++  +++a
  NCBI__GCF_000759345.1:WP_043527315.1 157 DFGSMPGNVFRAPYPVPYHGVSE--DEA----LRGLKMALKTDANPKDTAAIVLEPVLGEGGFYAAPASFLKA 223
                                           ********************988..555....5578888899******************************* PP

                             TIGR00700 223 vaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGt 295
                                           ++++c+ehgi+li devq+Gf rtGk+faieh +++Pd+i++aks+adG+P+s+vvG  +++da+    lGGt
  NCBI__GCF_000759345.1:WP_043527315.1 224 IRDICDEHGILLIIDEVQSGFGRTGKMFAIEHSGVEPDIICMAKSMADGMPISAVVGTDKVMDASGGNSLGGT 296
                                           ************************************************************************* PP

                             TIGR00700 296 yaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePda 367
                                           y+G+P+++aa+lavl++ eee + e+++ +g  + ++  ++++ ++ + + r+lGam+a +lv d   + Pda
  NCBI__GCF_000759345.1:WP_043527315.1 297 YTGSPVSCAATLAVLEVFEEEKILEKSQALGDKLAKRFSQWEQDFDCVDNGRNLGAMAAFDLVsDKAQHTPDA 369
                                           ***************************************************************8888899*** PP

                             TIGR00700 368 alaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                            la ++ ++a+++Gl+ll++G++Gn ir+l+P+ti d++l+egl ++e+al+
  NCBI__GCF_000759345.1:WP_043527315.1 370 DLAGALCKRAREKGLVLLSCGLYGNTIRFLMPVTIEDDILEEGLGVVESALK 421
                                           ************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (432 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: 00:00:00.00
# Mc/sec: 19.93
//
[ok]

This GapMind analysis is from Sep 24 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 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