Alignments for a candidate for gabT in Thauera aminoaromatica S2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Thauera aminoaromatica S2

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_004314496.1 C665_RS13470 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000310185.1:WP_004314496.1
          Length = 433

 Score =  516 bits (1330), Expect = e-151
 Identities = 249/421 (59%), Positives = 314/421 (74%)

Query: 4   NKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVV 63
           N + M RR+ A+PRGVGQ HP+FA +A N  VWDVEGR ++DF  GIAV+NTGH HP+VV
Sbjct: 12  NADFMARRAAALPRGVGQAHPLFATKALNAEVWDVEGRRFIDFVAGIAVVNTGHCHPRVV 71

Query: 64  AAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR 123
           AA +AQL   SHTCFQV+AY+ YL L E +N   PGD AKKT+LV+TG+EAVENAVKIAR
Sbjct: 72  AAAQAQLTHFSHTCFQVVAYDGYLRLAERLNALAPGDAAKKTMLVSTGAEAVENAVKIAR 131

Query: 124 AATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDA 183
           A T R G IAF+GA+HGRT   L LTGKV+PY  G+G  PG +Y A YPC LHGIS +DA
Sbjct: 132 AFTGRPGVIAFNGAFHGRTLLALGLTGKVDPYKLGVGPFPGEIYHAPYPCALHGISVEDA 191

Query: 184 IASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQS 243
           I  I  +FKND     +AA ++EPVQGEGG+Y +   F+QRLRAL D+HGI+LIADE+QS
Sbjct: 192 IHGIELLFKNDIEARRVAAFIVEPVQGEGGYYPAPAEFLQRLRALADKHGILLIADEIQS 251

Query: 244 GAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPI 303
           G GR G +FA+E  GV PD+ T AK + GGFP+A V GRAEVMDA+APGGLG TYAG P+
Sbjct: 252 GIGRCGKMFAVEHSGVMPDIITLAKGLGGGFPVAAVVGRAEVMDALAPGGLGSTYAGAPM 311

Query: 304 ACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDG 363
           AC AAL VL V E+E L ++A  +G+ ++  L  +A +H  IGDVRGLGAM+A+E F DG
Sbjct: 312 ACAAALAVLDVMEEEKLCERALAIGEHMQRRLRDLAVRHKCIGDVRGLGAMVAVEFFHDG 371

Query: 364 DHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFDE 423
           DH +P  ++   ++A A  +GL+LLSCG Y NVLR++VPLTIE A + +GL++++   D 
Sbjct: 372 DHARPAPEIAKAVIAAALQRGLLLLSCGSYGNVLRLMVPLTIEQAVLDEGLDLLAAAMDA 431

Query: 424 A 424
           A
Sbjct: 432 A 432


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: 617
Number of extensions: 22
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: 426
Length of database: 433
Length adjustment: 32
Effective length of query: 394
Effective length of database: 401
Effective search space:   157994
Effective search space used:   157994
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_004314496.1 C665_RS13470 (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.26044.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-170  553.2   3.9   1.8e-170  553.0   3.9    1.0  1  lcl|NCBI__GCF_000310185.1:WP_004314496.1  C665_RS13470 4-aminobutyrate--2-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000310185.1:WP_004314496.1  C665_RS13470 4-aminobutyrate--2-oxoglutarate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.0   3.9  1.8e-170  1.8e-170       2     418 ..      18     429 ..      17     431 .. 0.99

  Alignments for each domain:
  == domain 1  score: 553.0 bits;  conditional E-value: 1.8e-170
                                 TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtaf 70 
                                               rraaa ++Gvg + + +a+ka +ae+ dv+G+r+id+ agiav+n+Gh hP+vv+a + q+ ++ ht+f
  lcl|NCBI__GCF_000310185.1:WP_004314496.1  18 RRAAALPRGVGQAHPLFATKALNAEVWDVEGRRFIDFVAGIAVVNTGHCHPRVVAAAQAQLTHFSHTCF 86 
                                               8******************************************************************** PP

                                 TIGR00700  71 qvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltma 139
                                               qvv y++y+ lae+lna+aPg   kk++l+++Gaeavenavkiar++tgrpgv+af+++fhGrt l++ 
  lcl|NCBI__GCF_000310185.1:WP_004314496.1  87 QVVAYDGYLRLAERLNALAPGDAAKKTMLVSTGAEAVENAVKIARAFTGRPGVIAFNGAFHGRTLLALG 155
                                               ********************************************************************* PP

                                 TIGR00700 140 ltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqG 208
                                               lt+kv Pyk+G GPf++e+y+aP+p  +++i++      +d ++ ie lf+ d+ea++vaa ++ePvqG
  lcl|NCBI__GCF_000310185.1:WP_004314496.1 156 LTGKVDPYKLGVGPFPGEIYHAPYPCALHGISV------EDAIHGIELLFKNDIEARRVAAFIVEPVQG 218
                                               ******************************998......567779************************ PP

                                 TIGR00700 209 eGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgv 277
                                               eGG+  ++ e+++ ++ l ++hgi+liade+q+G  r Gk+fa+eh ++ Pd+it+ak+l +G+P+++v
  lcl|NCBI__GCF_000310185.1:WP_004314496.1 219 EGGYYPAPAEFLQRLRALADKHGILLIADEIQSGIGRCGKMFAVEHSGVMPDIITLAKGLGGGFPVAAV 287
                                               ********************************************************************* PP

                                 TIGR00700 278 vGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdv 346
                                               vGrae++da apGglG tyaG+P+a+aaalavld++eee l+era  ig+ ++ +l +l    + igdv
  lcl|NCBI__GCF_000310185.1:WP_004314496.1 288 VGRAEVMDALAPGGLGSTYAGAPMACAAALAVLDVMEEEKLCERALAIGEHMQRRLRDLAVRHKCIGDV 356
                                               ********************************************************************* PP

                                 TIGR00700 347 rglGamiavelv.dpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkil 414
                                               rglGam+ave+  d d + P   +a+++ aaal++Gllll++G +Gn++rl+ Plti  + ldegl++l
  lcl|NCBI__GCF_000310185.1:WP_004314496.1 357 RGLGAMVAVEFFhDGDHARPAPEIAKAVIAAALQRGLLLLSCGSYGNVLRLMVPLTIEQAVLDEGLDLL 425
                                               **********98899****************************************************** PP

                                 TIGR00700 415 eaal 418
                                                aa+
  lcl|NCBI__GCF_000310185.1:WP_004314496.1 426 AAAM 429
                                               9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (433 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.85
//
[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 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