Alignments for a candidate for gabT in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate WP_068174237.1 HTA01S_RS18580 4-aminobutyrate--2-oxoglutarate transaminase

Query= metacyc::MONOMER-11537
         (425 letters)



>NCBI__GCF_001592305.1:WP_068174237.1
          Length = 432

 Score =  572 bits (1473), Expect = e-167
 Identities = 283/415 (68%), Positives = 335/415 (80%)

Query: 4   TNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKI 63
           TNA LM RR+AA+PRGVGQ H IF    +NA V DVEGR +IDFAGGIAVLNTGH +P +
Sbjct: 8   TNAMLMARRQAAIPRGVGQSHAIFIAKGENAEVWDVEGRRYIDFAGGIAVLNTGHRNPAV 67

Query: 64  IAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIA 123
           I AV  QL++ THTCFQVLAYEPYVEL E++NAK PGDFAKKTL +TTG+EAVENA+KIA
Sbjct: 68  IEAVKAQLDQYTHTCFQVLAYEPYVELAERLNAKAPGDFAKKTLFLTTGAEAVENAIKIA 127

Query: 124 RAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDD 183
           RA TGRAGVIAFTG YHGRT+MTLGLTGKV PY  G G  PG IF A +PN LHGVS+ D
Sbjct: 128 RAHTGRAGVIAFTGGYHGRTLMTLGLTGKVAPYKTGFGPFPGEIFHARFPNALHGVSVQD 187

Query: 184 SIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQ 243
           +I S+E+IFKND E R +AAIIIEPVQGEGGF VAP E M+RLRALCDQHGILL+ DEVQ
Sbjct: 188 AIDSVEQIFKNDIEARRVAAIIIEPVQGEGGFNVAPPELMQRLRALCDQHGILLVCDEVQ 247

Query: 244 TGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSP 303
           TGAGRTGT+FA EQ GV  DL T AKS+AGGFP++ V G+AE MDA A GGLGGTYAGSP
Sbjct: 248 TGAGRTGTWFACEQTGVAPDLITLAKSMAGGFPISAVVGRAEVMDAPAAGGLGGTYAGSP 307

Query: 304 IACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFEN 363
           +ACAAALAV++ FE+  LL R + VG+R+   L+A+  K+  I +VR LGAM+A+EL +N
Sbjct: 308 LACAAALAVLDEFEKHDLLQRSRDVGQRITASLQALAKKHKCIADVRGLGAMVAMELCKN 367

Query: 364 GDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAII 418
           GD H+P+A     + A+A  +GL++L+CGTYGNV+R+LVPLT  DA LD+GLAII
Sbjct: 368 GDPHQPDADLTKALAAEATKRGLVILTCGTYGNVVRILVPLTVSDAVLDEGLAII 422


Lambda     K      H
   0.320    0.137    0.394 

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: 656
Number of extensions: 14
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: 425
Length of database: 432
Length adjustment: 32
Effective length of query: 393
Effective length of database: 400
Effective search space:   157200
Effective search space used:   157200
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_068174237.1 HTA01S_RS18580 (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.3342953.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-182  592.0   4.0   3.1e-182  591.8   4.0    1.0  1  NCBI__GCF_001592305.1:WP_068174237.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001592305.1:WP_068174237.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  591.8   4.0  3.1e-182  3.1e-182       2     419 ..      15     427 ..      14     428 .. 0.99

  Alignments for each domain:
  == domain 1  score: 591.8 bits;  conditional E-value: 3.1e-182
                             TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 
                                           rr+aa+++Gvg +  +++ak+e+ae+ dv+G+r+id+a+giavln+Gh++P v+eavk q++++tht+fqv+ 
  NCBI__GCF_001592305.1:WP_068174237.1  15 RRQAAIPRGVGQSHAIFIAKGENAEVWDVEGRRYIDFAGGIAVLNTGHRNPAVIEAVKAQLDQYTHTCFQVLA 87 
                                           8************************************************************************ PP

                             TIGR00700  75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147
                                           ye yvelae+lna aPg   kk+++l++Gaeavena+kiar++tgr gv+af++g+hGrt +t+ lt+kv+Py
  NCBI__GCF_001592305.1:WP_068174237.1  88 YEPYVELAERLNAKAPGDFAKKTLFLTTGAEAVENAIKIARAHTGRAGVIAFTGGYHGRTLMTLGLTGKVAPY 160
                                           ************************************************************************* PP

                             TIGR00700 148 kiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelv 220
                                           k+GfGPf++e+++a +p  +++ ++  q+++d    ++e++f+ d+ea++vaa+++ePvqGeGGf+v++ el+
  NCBI__GCF_001592305.1:WP_068174237.1 161 KTGFGPFPGEIFHARFPNALHGVSV--QDAID----SVEQIFKNDIEARRVAAIIIEPVQGEGGFNVAPPELM 227
                                           **********************999..88888....99*********************************** PP

                             TIGR00700 221 aavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglG 293
                                           + ++ lc++hgi+l+ devqtG  rtG+ fa+e  ++ Pdlit+aks+a+G+P+s+vvGrae++dapa+GglG
  NCBI__GCF_001592305.1:WP_068174237.1 228 QRLRALCDQHGILLVCDEVQTGAGRTGTWFACEQTGVAPDLITLAKSMAGGFPISAVVGRAEVMDAPAAGGLG 300
                                           ************************************************************************* PP

                             TIGR00700 294 GtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdtteP 365
                                           GtyaG+Pla+aaalavld  e++ l +r++++g++++  l  l ++ + i+dvrglGam+a+el  + d ++P
  NCBI__GCF_001592305.1:WP_068174237.1 301 GTYAGSPLACAAALAVLDEFEKHDLLQRSRDVGQRITASLQALAKKHKCIADVRGLGAMVAMELCkNGDPHQP 373
                                           ****************************************************************9677899** PP

                             TIGR00700 366 daalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                           da l++++aa+a+++Gl++lt+G +Gn++r+l Plt+sd+ ldegl i+ a+l+
  NCBI__GCF_001592305.1:WP_068174237.1 374 DADLTKALAAEATKRGLVILTCGTYGNVVRILVPLTVSDAVLDEGLAIIGASLE 427
                                           *************************************************99986 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: 00:00:00.01
# Mc/sec: 15.82
//
[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