GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Williamsia sterculiae CPCC 203464

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_076476008.1 BW971_RS02060 4-aminobutyrate--2-oxoglutarate transaminase

Query= curated2:P63505
         (449 letters)



>NCBI__GCF_900156495.1:WP_076476008.1
          Length = 452

 Score =  547 bits (1410), Expect = e-160
 Identities = 283/439 (64%), Positives = 330/439 (75%), Gaps = 8/439 (1%)

Query: 4   LQQSRRLVTEIPGPASQALTHRRAAAVSSGVGVTLPVFVARAGGGIVEDVDGNRLIDLGS 63
           L Q R LVT +PGP S AL  RRAAAV++GVG  +P++ A A GGI+ DVDGN LIDLGS
Sbjct: 9   LPQKRHLVTPLPGPESSALAKRRAAAVAAGVGSVVPIYAADADGGIIVDVDGNSLIDLGS 68

Query: 64  GIAVTTIGNSSPRVVDAVRTQVAEFTHTCFMVTPYEGYVAVAEQLNRITPGSGPKRSVLF 123
           GIAVT +G S+P V DAV  Q   FTHTCFMVTPYEGYVAVAE+LN +TPG   KRSVLF
Sbjct: 69  GIAVTGVGASNPAVADAVAAQAHHFTHTCFMVTPYEGYVAVAEKLNELTPGDHEKRSVLF 128

Query: 124 NSGAEAVENAVKIARSYTGKPAVVAFDHAYHGRTNLTMALTAKSMPYKSGFGPFAPEIYR 183
           NSGAEAVENAVK+AR  TG+ A+VAFDHAYHGRTNLTMALTAK+ PYK  FGPFAPEIYR
Sbjct: 129 NSGAEAVENAVKVARLATGRDAIVAFDHAYHGRTNLTMALTAKTQPYKYNFGPFAPEIYR 188

Query: 184 APLSYPYRDGLLDKQLATNGELAAARAIGVIDKQVGANNLAALVIEPIQGEGGFIVPAEG 243
            P+SYPYRD      L T+G  AA RAI  I+ Q+G   +A L+IEPIQGEGGFIVPA G
Sbjct: 189 MPMSYPYRD-----DLGTDGVSAAKRAIRQIETQIGGEAVAGLLIEPIQGEGGFIVPAPG 243

Query: 244 FLPALLDWCRKNHVVFIADEVQTGFARTGAMFACEHEGPDGLEPDLICTAKGIADGLPLS 303
           FL  L +W R N VVFIADEVQ GF RTG  FA E E   G+ PD++ TAKGIA G+PLS
Sbjct: 244 FLTTLAEWARDNGVVFIADEVQAGFCRTGTWFASEAE---GIVPDIVTTAKGIAGGMPLS 300

Query: 304 AVTGRAEIMNAPHVGGLGGTFGGNPVACAAALATIATIESDGLIERARQIERLVTDRLTT 363
           A+TGRA++++  H GGLGGT+GGNPVACAAALATIA +E   L  RA  IE +   RL T
Sbjct: 301 AITGRADLLDKVHPGGLGGTYGGNPVACAAALATIAEMEELDLNARAHHIEEIALPRLRT 360

Query: 364 LQAVDDRIGDVRGRGAMIAVELVKSGTTEPDAGLTERLATAAHAAGVIILTCGMFGNIIR 423
           L    D IGDVRGRGAM+A+E+V+ GT  P   L +++A AA  AGV+IL  G FGN+IR
Sbjct: 361 LADDLDVIGDVRGRGAMLAIEIVEPGTDTPAPALAKKVAAAALEAGVVILVTGTFGNVIR 420

Query: 424 LLPPLTIGDELLSEGLDIV 442
           LLPPL I DE L +G+D++
Sbjct: 421 LLPPLVIDDETLVDGIDVL 439


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: 680
Number of extensions: 28
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: 452
Length adjustment: 33
Effective length of query: 416
Effective length of database: 419
Effective search space:   174304
Effective search space used:   174304
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_076476008.1 BW971_RS02060 (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.3514298.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-176  572.2   6.3   3.1e-176  572.0   6.3    1.0  1  NCBI__GCF_900156495.1:WP_076476008.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900156495.1:WP_076476008.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.0   6.3  3.1e-176  3.1e-176       1     419 [.      29     444 ..      29     445 .. 0.97

  Alignments for each domain:
  == domain 1  score: 572.0 bits;  conditional E-value: 3.1e-176
                             TIGR00700   1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvv 73 
                                           +rraaav+ Gvg +++++aa a+g+++ dvdGn lidl++giav+ vG s+P v +av  q++++tht+f+v+
  NCBI__GCF_900156495.1:WP_076476008.1  29 KRRAAAVAAGVGSVVPIYAADADGGIIVDVDGNSLIDLGSGIAVTGVGASNPAVADAVAAQAHHFTHTCFMVT 101
                                           69*********************************************************************** PP

                             TIGR00700  74 pyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkP 146
                                           pye+yv++aekln+++Pg +ek++vl+nsGaeavenavk+ar  tgr+++vaf++++hGrtnltmaltak++P
  NCBI__GCF_900156495.1:WP_076476008.1 102 PYEGYVAVAEKLNELTPGDHEKRSVLFNSGAEAVENAVKVARLATGRDAIVAFDHAYHGRTNLTMALTAKTQP 174
                                           ************************************************************************* PP

                             TIGR00700 147 ykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvad..veaeqvaavvlePvqGeGGfivpak 217
                                           yk+ fGPfape+yr+P++y+yrd ++     +d++ aa +a+  ++  ++ e va +++eP+qGeGGfivpa 
  NCBI__GCF_900156495.1:WP_076476008.1 175 YKYNFGPFAPEIYRMPMSYPYRDDLG-----TDGVSAAKRAIRQIEtqIGGEAVAGLLIEPIQGEGGFIVPAP 242
                                           ***********************999.....55555555555555444************************* PP

                             TIGR00700 218 elvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapG 290
                                           ++++++a++ +++g+v+iadevq+Gf rtG+ fa e e+ +Pd++t+ak++a+G+Pls+++Gra++ld  +pG
  NCBI__GCF_900156495.1:WP_076476008.1 243 GFLTTLAEWARDNGVVFIADEVQAGFCRTGTWFASEAEGIVPDIVTTAKGIAGGMPLSAITGRADLLDKVHPG 315
                                           ************************************************************************* PP

                             TIGR00700 291 glGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdtt 363
                                           glGGty+GnP+a+aaala+++ +ee  l+ ra++i+++   +l +l +  ++igdvrg+Gam+a+e+v+p+t 
  NCBI__GCF_900156495.1:WP_076476008.1 316 GLGGTYGGNPVACAAALATIAEMEELDLNARAHHIEEIALPRLRTLADDLDVIGDVRGRGAMLAIEIVEPGTD 388
                                           ************************************************************************* PP

                             TIGR00700 364 ePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                            P  ala+k+aaaal+aG+++l +G fGn+irll+Pl+i de l +g+++le++l 
  NCBI__GCF_900156495.1:WP_076476008.1 389 TPAPALAKKVAAAALEAGVVILVTGTFGNVIRLLPPLVIDDETLVDGIDVLEQSLH 444
                                           ****************************************************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (452 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: 29.23
//
[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:

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:

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:

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:

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