GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Desulfoscipio geothermicus DSM 3669

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_207545101.1 BM299_RS02525 4-aminobutyrate--2-oxoglutarate transaminase

Query= curated2:P94427
         (436 letters)



>NCBI__GCF_900115975.1:WP_207545101.1
          Length = 434

 Score =  443 bits (1139), Expect = e-129
 Identities = 209/423 (49%), Positives = 298/423 (70%)

Query: 9   TTAQWQQKRDQFVSKGVSNGNRSLAVKGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKV 68
           T A+   ++ Q +++G+SN       K +GA + D++G+ +IDF G IGTLN GH    V
Sbjct: 4   TNAELVARKHQLIARGISNSTEVFVEKAQGATIVDVEGKEYIDFYGGIGTLNAGHCPAPV 63

Query: 69  VEAVKRQAEELIHPGFNVMMYPTYIELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIA 128
           VEA+K QAE+L+H  F V MY  Y++LAEKL  + PG+ +K+ +F+NSGAE VENAVKIA
Sbjct: 64  VEAIKNQAEKLLHTCFMVTMYEPYLDLAEKLIELTPGNFDKRVMFVNSGAECVENAVKIA 123

Query: 129 RKYTKRQGVVSFTRGFHGRTNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMS 188
           R Y KR G++SF   FHGRT MTMS+TSKVKPYKFGFGPFAPEVY+ P  Y Y+     +
Sbjct: 124 RSYAKRTGIISFECAFHGRTLMTMSLTSKVKPYKFGFGPFAPEVYKIPSAYCYRCTYRST 183

Query: 189 DESYDDMVIQAFNDFFIASVAPETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIV 248
                   ++ F+  F A V PE +A +++EPVQGEGGFI+P   F+  +   C +HGI+
Sbjct: 184 YPECGLHCLEQFDRMFAAEVPPENIAAMIIEPVQGEGGFIVPPPEFLPGLRKICDKHGII 243

Query: 249 FVADEIQTGFARTGTYFAIEHFDVVPDLITVSKSLAAGLPLSGVIGRAEMLDAAAPGELG 308
            +ADE+QTGF RTG  FA EHF + PDL+T++KS+AAG+PLS V+G+A++++A  PGE+G
Sbjct: 244 LIADEVQTGFGRTGKMFACEHFGLEPDLMTMAKSIAAGMPLSAVVGKADIMNAPNPGEIG 303

Query: 309 GTYAGSPLGCAAALAVLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRRLGAMA 368
           GTY+G+P+ CAA LA +D ++++ L ER+  IG   + +    ++++P IGD+R LGAM 
Sbjct: 304 GTYSGNPVSCAAGLATIDFMQQQNLVERANVIGDKTKQRMLAMQEKYPIIGDVRGLGAMN 363

Query: 369 AIEIVKDPDTREPDKTKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLS 428
           A+E+VKD +T+EP K + AA+  +   NG++++ AGI  N++R L PLVI+D  L +GL 
Sbjct: 364 AMELVKDRNTKEPAKEETAAVIKHCVDNGVIVIGAGIFSNVVRTLIPLVITDEQLEKGLD 423

Query: 429 ILE 431
           +LE
Sbjct: 424 VLE 426


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: 471
Number of extensions: 9
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: 434
Length adjustment: 32
Effective length of query: 404
Effective length of database: 402
Effective search space:   162408
Effective search space used:   162408
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_207545101.1 BM299_RS02525 (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.1821650.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-179  581.1   0.7   6.3e-179  580.9   0.7    1.0  1  NCBI__GCF_900115975.1:WP_207545101.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900115975.1:WP_207545101.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  580.9   0.7  6.3e-179  6.3e-179       2     419 ..      11     430 ..      10     431 .. 0.97

  Alignments for each domain:
  == domain 1  score: 580.9 bits;  conditional E-value: 6.3e-179
                             TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 
                                           r+++ +++G++++++v++ ka+ga++ dv+G+++id+ +gi++ln Gh    vvea+k+q+e+l ht+f+v++
  NCBI__GCF_900115975.1:WP_207545101.1  11 RKHQLIARGISNSTEVFVEKAQGATIVDVEGKEYIDFYGGIGTLNAGHCPAPVVEAIKNQAEKLLHTCFMVTM 83 
                                           78899******************************************************************** PP

                             TIGR00700  75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147
                                           ye y++laekl +++Pg  +k+ +++nsGae venavkiar+y++r g+++f+ +fhGrt +tm+lt+kvkPy
  NCBI__GCF_900115975.1:WP_207545101.1  84 YEPYLDLAEKLIELTPGNFDKRVMFVNSGAECVENAVKIARSYAKRTGIISFECAFHGRTLMTMSLTSKVKPY 156
                                           ************************************************************************* PP

                             TIGR00700 148 kiGfGPfapevyraPlpydyrdialdk.qeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakel 219
                                           k+GfGPfapevy++P +y yr +   +  e+    l+ ++++f a+v +e++aa+++ePvqGeGGfivp+ e+
  NCBI__GCF_900115975.1:WP_207545101.1 157 KFGFGPFAPEVYKIPSAYCYRCTYRSTyPECGLHCLEQFDRMFAAEVPPENIAAMIIEPVQGEGGFIVPPPEF 229
                                           *******************99876544133334499************************************* PP

                             TIGR00700 220 vaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGgl 292
                                           ++ ++++c++hgi+liadevqtGf rtGk+fa+eh++ +Pdl+t+aks+a+G+Pls+vvG+a+i++ap+pG++
  NCBI__GCF_900115975.1:WP_207545101.1 230 LPGLRKICDKHGIILIADEVQTGFGRTGKMFACEHFGLEPDLMTMAKSIAAGMPLSAVVGKADIMNAPNPGEI 302
                                           ************************************************************************* PP

                             TIGR00700 293 GGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdtte 364
                                           GGty+GnP+++aa la++d ++++ l+era+ ig   k++++ ++e+ p igdvrglGam a+elv d +t+e
  NCBI__GCF_900115975.1:WP_207545101.1 303 GGTYSGNPVSCAAGLATIDFMQQQNLVERANVIGDKTKQRMLAMQEKYPIIGDVRGLGAMNAMELVkDRNTKE 375
                                           ******************************************************************999**** PP

                             TIGR00700 365 PdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                           P +  ++++ ++   +G++++ aGif n++r l Pl+i+de+l++gl++le+a+a
  NCBI__GCF_900115975.1:WP_207545101.1 376 PAKEETAAVIKHCVDNGVIVIGAGIFSNVVRTLIPLVITDEQLEKGLDVLEQAVA 430
                                           **************************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (434 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: 17.72
//
[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:

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