Alignments for a candidate for gabT in Nocardioides dokdonensis FR1436

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Nocardioides dokdonensis FR1436

Align 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_068110315.1 I601_RS12790 4-aminobutyrate--2-oxoglutarate transaminase

Query= curated2:P63505
         (449 letters)



>NCBI__GCF_001653335.1:WP_068110315.1
          Length = 448

 Score =  552 bits (1422), Expect = e-162
 Identities = 281/445 (63%), Positives = 329/445 (73%), Gaps = 10/445 (2%)

Query: 3   SLQQSRRLVTEIPGPASQALTHRRAAAVSSGVGVTLPVFVARAGGGIVEDVDGNRLIDLG 62
           SL Q RRLVT+IPGP S     R+ + V+ GVG  LPVFV  AGGG++ DVDGN LIDLG
Sbjct: 11  SLPQVRRLVTDIPGPLSVKHLERKKSFVADGVGTALPVFVTAAGGGVIVDVDGNSLIDLG 70

Query: 63  SGIAVTTIGNSSPRVVDAVRTQVAEFTHTCFMVTPYEGYVAVAEQLNRITPGSGPKRSVL 122
           SGIAVT++GN++P VV  V  QV  FTHTCFMVTPYEGYV V E L R+TPG   K+S L
Sbjct: 71  SGIAVTSVGNAAPAVVRNVHAQVDAFTHTCFMVTPYEGYVDVCEALARLTPGEHAKKSAL 130

Query: 123 FNSGAEAVENAVKIARSYTGKPAVVAFDHAYHGRTNLTMALTAKSMPYKSGFGPFAPEIY 182
           FNSGAEAVENAVKIAR  TGK AV  FDHAYHGRTNLTMA+T+K+MPYK GFGPFA E+Y
Sbjct: 131 FNSGAEAVENAVKIARVATGKDAVAVFDHAYHGRTNLTMAMTSKNMPYKHGFGPFAGEVY 190

Query: 183 RAPLSYPYRDGLLDKQLATNGELAAARAIGVIDKQVGANNLAALVIEPIQGEGGFIVPAE 242
           RAP+SYP RDGL       +G  AAARAI V+DKQVGA NLA +VIEP+ GEGGF+VPA 
Sbjct: 191 RAPMSYPLRDGL-------SGPEAAARAIDVLDKQVGATNLACVVIEPVLGEGGFVVPAS 243

Query: 243 GFLPALLDWCRKNHVVFIADEVQTGFARTGAMFACEHEGPDGLEPDLICTAKGIADGLPL 302
           GFLPAL +WC  N V+ +ADE+QTGF RTGA FAC+ E   G+ PDL+ +AKG+A GLPL
Sbjct: 244 GFLPALREWCTANDVLLVADEIQTGFCRTGAWFACDDE---GVVPDLVTSAKGMAGGLPL 300

Query: 303 SAVTGRAEIMNAPHVGGLGGTFGGNPVACAAALATIATIESDGLIERARQIERLVTDRLT 362
           +AVTGRAE+M+A H GGLGGT+GGNP+ACAAAL  I  +E + L  RAR+IE LV  RL 
Sbjct: 301 AAVTGRAELMDAVHAGGLGGTYGGNPIACAAALGAIEEMEGNDLAARAREIEALVRRRLE 360

Query: 363 TLQAVDDRIGDVRGRGAMIAVELVKSGTTEPDAGLTERLATAAHAAGVIILTCGMFGNII 422
            L A    + +VRGRGAM+A+EL   GTT PD       +   HA GV+ LTCG +GN+ 
Sbjct: 361 ALAAEHPVVAEVRGRGAMMAMELCAPGTTTPDPARAAAASAYCHAHGVVTLTCGTWGNVF 420

Query: 423 RLLPPLTIGDELLSEGLDIVCAILA 447
           R LPPLTI DELL E  D+V    A
Sbjct: 421 RFLPPLTISDELLEEAFDVVAEAFA 445


Lambda     K      H
   0.319    0.137    0.397 

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: 682
Number of extensions: 31
Number of successful extensions: 3
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: 449
Length of database: 448
Length adjustment: 33
Effective length of query: 416
Effective length of database: 415
Effective search space:   172640
Effective search space used:   172640
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_068110315.1 I601_RS12790 (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.1160270.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.6e-175  567.4   6.1   8.8e-175  567.2   6.1    1.0  1  NCBI__GCF_001653335.1:WP_068110315.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001653335.1:WP_068110315.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  567.2   6.1  8.8e-175  8.8e-175       2     419 ..      33     445 ..      32     446 .. 0.97

  Alignments for each domain:
  == domain 1  score: 567.2 bits;  conditional E-value: 8.8e-175
                             TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 
                                           r++++v+ Gvg++l+v+++ a+g+++ dvdGn lidl++giav++vG+  P vv  v+ qv+ +tht+f+v+p
  NCBI__GCF_001653335.1:WP_068110315.1  33 RKKSFVADGVGTALPVFVTAAGGGVIVDVDGNSLIDLGSGIAVTSVGNAAPAVVRNVHAQVDAFTHTCFMVTP 105
                                           889********************************************************************** PP

                             TIGR00700  75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147
                                           ye+yv++ e l++++Pg + kk++l+nsGaeavenavkiar  tg+++v  f++++hGrtnltma+t+k +Py
  NCBI__GCF_001653335.1:WP_068110315.1 106 YEGYVDVCEALARLTPGEHAKKSALFNSGAEAVENAVKIARVATGKDAVAVFDHAYHGRTNLTMAMTSKNMPY 178
                                           ************************************************************************* PP

                             TIGR00700 148 kiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvad..veaeqvaavvlePvqGeGGfivpake 218
                                           k GfGPfa+evyraP++y++rd+++  +       aa++a+ v d  v+a ++a+vv+ePv GeGGf+vpa +
  NCBI__GCF_001653335.1:WP_068110315.1 179 KHGFGPFAGEVYRAPMSYPLRDGLSGPE-------AAARAIDVLDkqVGATNLACVVIEPVLGEGGFVVPASG 244
                                           ***********************99443.......344444444444************************** PP

                             TIGR00700 219 lvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGg 291
                                           +++a++++c  ++++l+ade+qtGf rtG+ fa++ e+++Pdl+t ak++a+GlPl++v+Grae++da ++Gg
  NCBI__GCF_001653335.1:WP_068110315.1 245 FLPALREWCTANDVLLVADEIQTGFCRTGAWFACDDEGVVPDLVTSAKGMAGGLPLAAVTGRAELMDAVHAGG 317
                                           ************************************************************************* PP

                             TIGR00700 292 lGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdtte 364
                                           lGGty+GnP+a+aaal  ++ +e + l+ ra++i+ lv+ +l  l +e p++++vrg+Gam+a+el  p+tt 
  NCBI__GCF_001653335.1:WP_068110315.1 318 LGGTYGGNPIACAAALGAIEEMEGNDLAARAREIEALVRRRLEALAAEHPVVAEVRGRGAMMAMELCAPGTTT 390
                                           ************************************************************************* PP

                             TIGR00700 365 PdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                           Pd a a++ +a+ +a+G++ lt+G +Gn+ r+l+Pltisdell+e+++++ +a+a
  NCBI__GCF_001653335.1:WP_068110315.1 391 PDPARAAAASAYCHAHGVVTLTCGTWGNVFRFLPPLTISDELLEEAFDVVAEAFA 445
                                           **************************************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (448 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 22.04
//
[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