Alignments for a candidate for gabT in Bacillus altitudinis 41KF2b

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Bacillus altitudinis 41KF2b

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_035703857.1 BA79_RS15810 4-aminobutyrate--2-oxoglutarate transaminase

Query= curated2:P94427
         (436 letters)



>NCBI__GCF_000691145.1:WP_035703857.1
          Length = 438

 Score =  723 bits (1866), Expect = 0.0
 Identities = 356/437 (81%), Positives = 393/437 (89%), Gaps = 1/437 (0%)

Query: 1   MSQTTAS-ITTAQWQQKRDQFVSKGVSNGNRSLAVKGEGAELYDLDGRRFIDFAGAIGTL 59
           MSQTT +  +T +WQ KRDQ+V++GVSNGNR LA KG+GAEL+D+DG RFIDFAGAIGTL
Sbjct: 1   MSQTTTNRFSTEEWQGKRDQYVARGVSNGNRHLATKGKGAELFDIDGNRFIDFAGAIGTL 60

Query: 60  NVGHSHPKVVEAVKRQAEELIHPGFNVMMYPTYIELAEKLCGIAPGSHEKKAIFLNSGAE 119
           NVGHSHPKVVEAVK QA+ LIHPGFNVMMY +YIELAEKLC + PG H+KKAIFLNSGAE
Sbjct: 61  NVGHSHPKVVEAVKAQADSLIHPGFNVMMYESYIELAEKLCHLTPGDHDKKAIFLNSGAE 120

Query: 120 AVENAVKIARKYTKRQGVVSFTRGFHGRTNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPY 179
           AVENAVKIARKYTKRQ VVSFTRGFHGRTNMTMSMTSKVKPYKFGFGPFA EVYQAP+PY
Sbjct: 121 AVENAVKIARKYTKRQAVVSFTRGFHGRTNMTMSMTSKVKPYKFGFGPFASEVYQAPYPY 180

Query: 180 YYQKPAGMSDESYDDMVIQAFNDFFIASVAPETVACVVMEPVQGEGGFIIPSKRFVQHVA 239
           YYQKP G+SD +YD+ +I  FN FF+A+VAPETVACVVMEPVQGEGGFI+PSKRFVQHVA
Sbjct: 181 YYQKPEGLSDAAYDEYIIDQFNQFFVATVAPETVACVVMEPVQGEGGFIVPSKRFVQHVA 240

Query: 240 SFCKEHGIVFVADEIQTGFARTGTYFAIEHFDVVPDLITVSKSLAAGLPLSGVIGRAEML 299
           SFC++HGIVFVADEIQTGFARTG YFAIEHFDVVPDLITVSKSLAAGLPLSGV+GR E+L
Sbjct: 241 SFCQQHGIVFVADEIQTGFARTGKYFAIEHFDVVPDLITVSKSLAAGLPLSGVVGRKELL 300

Query: 300 DAAAPGELGGTYAGSPLGCAAALAVLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIG 359
           DAA PGELGGTYAGSPLGC AALAVLDIIE E LNERSE IG++IEDKA EW+ ++ FIG
Sbjct: 301 DAADPGELGGTYAGSPLGCVAALAVLDIIETEQLNERSEHIGQVIEDKANEWRSQYSFIG 360

Query: 360 DIRRLGAMAAIEIVKDPDTREPDKTKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVIS 419
           ++RRLGAMAAIEIV+D  TR PDK  AAAIAAYAN++GLLLLTAGINGNIIRFLTPLVI+
Sbjct: 361 EVRRLGAMAAIEIVEDQKTRTPDKKTAAAIAAYANKHGLLLLTAGINGNIIRFLTPLVIT 420

Query: 420 DSLLNEGLSILEAGLRA 436
           D LL EGL I+E    A
Sbjct: 421 DELLQEGLGIIEDAFTA 437


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: 657
Number of extensions: 14
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: 436
Length of database: 438
Length adjustment: 32
Effective length of query: 404
Effective length of database: 406
Effective search space:   164024
Effective search space used:   164024
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_035703857.1 BA79_RS15810 (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.4114610.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.3e-219  712.4   1.2   8.5e-219  712.2   1.2    1.0  1  NCBI__GCF_000691145.1:WP_035703857.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691145.1:WP_035703857.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  712.2   1.2  8.5e-219  8.5e-219       2     418 ..      17     435 ..      16     437 .. 0.99

  Alignments for each domain:
  == domain 1  score: 712.2 bits;  conditional E-value: 8.5e-219
                             TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 
                                           +r+++v++Gv++++r la+k++gael d+dGnr+id+a++i++lnvGhshPkvveavk q++ l+h++f+v++
  NCBI__GCF_000691145.1:WP_035703857.1  17 KRDQYVARGVSNGNRHLATKGKGAELFDIDGNRFIDFAGAIGTLNVGHSHPKVVEAVKAQADSLIHPGFNVMM 89 
                                           8************************************************************************ PP

                             TIGR00700  75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147
                                           yesy+elaekl+ ++Pg ++kka++lnsGaeavenavkiarkyt+r++vv+f+rgfhGrtn+tm++t+kvkPy
  NCBI__GCF_000691145.1:WP_035703857.1  90 YESYIELAEKLCHLTPGDHDKKAIFLNSGAEAVENAVKIARKYTKRQAVVSFTRGFHGRTNMTMSMTSKVKPY 162
                                           ************************************************************************* PP

                             TIGR00700 148 kiGfGPfapevyraPlpydyrdialdkqesldd.elaaiealfvadveaeqvaavvlePvqGeGGfivpakel 219
                                           k+GfGPfa+evy+aP+py+y+++ + ++ ++d+ +++ ++++fva v++e+va+vv+ePvqGeGGfivp+k++
  NCBI__GCF_000691145.1:WP_035703857.1 163 KFGFGPFASEVYQAPYPYYYQKPEGLSDAAYDEyIIDQFNQFFVATVAPETVACVVMEPVQGEGGFIVPSKRF 235
                                           *********************************899************************************* PP

                             TIGR00700 220 vaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGgl 292
                                           v++vas+c++hgiv++ade+qtGfartGk+faieh+d++Pdlitv+ksla+GlPlsgvvGr e+lda+ pG+l
  NCBI__GCF_000691145.1:WP_035703857.1 236 VQHVASFCQQHGIVFVADEIQTGFARTGKYFAIEHFDVVPDLITVSKSLAAGLPLSGVVGRKELLDAADPGEL 308
                                           ************************************************************************* PP

                             TIGR00700 293 GGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdtte 364
                                           GGtyaG+Pl++ aalavldiie e l+er+e+ig++++dk+ e++ +  +ig+vr+lGam+a+e+v d +t+ 
  NCBI__GCF_000691145.1:WP_035703857.1 309 GGTYAGSPLGCVAALAVLDIIETEQLNERSEHIGQVIEDKANEWRSQYSFIGEVRRLGAMAAIEIVeDQKTRT 381
                                           ******************************************************************9999*** PP

                             TIGR00700 365 PdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaal 418
                                           Pd+  a++iaa+a+++GlllltaGi+Gniir+ltPl+i+dell+egl i+e+a+
  NCBI__GCF_000691145.1:WP_035703857.1 382 PDKKTAAAIAAYANKHGLLLLTAGINGNIIRFLTPLVITDELLQEGLGIIEDAF 435
                                           ***************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (438 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 23.24
//
[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