Alignments for a candidate for gabT in Pseudomonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Pseudomonas stutzeri A1501

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate WP_020307792.1 PST_RS03780 4-aminobutyrate--2-oxoglutarate transaminase

Query= metacyc::MONOMER-11537
         (425 letters)



>NCBI__GCF_000013785.1:WP_020307792.1
          Length = 426

 Score =  726 bits (1873), Expect = 0.0
 Identities = 362/425 (85%), Positives = 393/425 (92%)

Query: 1   MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60
           MSKTN SLM+RR AAVPRGVGQIHPIFAD AKN++V DVEGREFIDFAGGIAVLNTGH+H
Sbjct: 1   MSKTNESLMQRRVAAVPRGVGQIHPIFADHAKNSSVVDVEGREFIDFAGGIAVLNTGHLH 60

Query: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120
           PKI+ AV +QL+KLTHTCFQVLAYEPYVELCEKINA+VPGDFAKKTLLVTTGSEAVENAV
Sbjct: 61  PKIVKAVEDQLHKLTHTCFQVLAYEPYVELCEKINARVPGDFAKKTLLVTTGSEAVENAV 120

Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180
           KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKV PYSAGMGLMPGGIFRA YP  +HGVS
Sbjct: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVAPYSAGMGLMPGGIFRAQYPCAIHGVS 180

Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240
           +DDSIASIERIFKNDAEPRDIAAII+EPVQGEGGF VAPK+FM RLRALCD+HGILLIAD
Sbjct: 181 VDDSIASIERIFKNDAEPRDIAAIIVEPVQGEGGFNVAPKDFMARLRALCDEHGILLIAD 240

Query: 241 EVQTGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300
           EVQTGAGRTGTFFAMEQMGV ADLTTFAKS+ GGFP+AGVCGKAE MDAIAPGGLGGTYA
Sbjct: 241 EVQTGAGRTGTFFAMEQMGVVADLTTFAKSVGGGFPIAGVCGKAEIMDAIAPGGLGGTYA 300

Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360
           G+P++CAAALAVME+FEEEHLLDRCKAV E+L TGLKAIQAK+  IGEVR LGAMIA+EL
Sbjct: 301 GNPLSCAAALAVMEIFEEEHLLDRCKAVAEKLTTGLKAIQAKHKEIGEVRGLGAMIAIEL 360

Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420
           FE+GD  +P AA  +Q+VA+AR+KGLILLSCGTY NVLRVLVPLT  D  L++GLAI+ E
Sbjct: 361 FEDGDLARPAAALTSQIVARAREKGLILLSCGTYYNVLRVLVPLTVEDELLERGLAILGE 420

Query: 421 CFAEL 425
           CF EL
Sbjct: 421 CFDEL 425


Lambda     K      H
   0.320    0.137    0.394 

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: 748
Number of extensions: 18
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: 425
Length of database: 426
Length adjustment: 32
Effective length of query: 393
Effective length of database: 394
Effective search space:   154842
Effective search space used:   154842
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_020307792.1 PST_RS03780 (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.12142.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-165  535.0   5.7   5.9e-165  534.8   5.7    1.0  1  lcl|NCBI__GCF_000013785.1:WP_020307792.1  PST_RS03780 4-aminobutyrate--2-o


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013785.1:WP_020307792.1  PST_RS03780 4-aminobutyrate--2-oxoglutarate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.8   5.7  5.9e-165  5.9e-165       1     416 [.      10     420 ..      10     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 534.8 bits;  conditional E-value: 5.9e-165
                                 TIGR00700   1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthta 69 
                                               qrr aav++Gvg   +++a +a+++ + dv+G+++id+a+giavln+Gh hPk+v+av+ q+++ltht+
  lcl|NCBI__GCF_000013785.1:WP_020307792.1  10 QRRVAAVPRGVGQIHPIFADHAKNSSVVDVEGREFIDFAGGIAVLNTGHLHPKIVKAVEDQLHKLTHTC 78 
                                               89******************************************************************* PP

                                 TIGR00700  70 fqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltm 138
                                               fqv+ ye yvel ek+na  Pg   kk++l+++G+eavenavkiar+ tgr gv+af++++hGrt +t+
  lcl|NCBI__GCF_000013785.1:WP_020307792.1  79 FQVLAYEPYVELCEKINARVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTL 147
                                               ********************************************************************* PP

                                 TIGR00700 139 altakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvq 207
                                                lt+kv+Py  G+G +++ ++ra +p  +++ ++      dd +a+ie++f+ d e++++aa+++ePvq
  lcl|NCBI__GCF_000013785.1:WP_020307792.1 148 GLTGKVAPYSAGMGLMPGGIFRAQYPCAIHGVSV------DDSIASIERIFKNDAEPRDIAAIIVEPVQ 210
                                               ****************************999877......88899************************ PP

                                 TIGR00700 208 GeGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsg 276
                                               GeGGf+v++k+++a ++ lc+ehgi+liadevqtG  rtG++fa+e ++++ dl t aks+ +G+P++g
  lcl|NCBI__GCF_000013785.1:WP_020307792.1 211 GEGGFNVAPKDFMARLRALCDEHGILLIADEVQTGAGRTGTFFAMEQMGVVADLTTFAKSVGGGFPIAG 279
                                               ********************************************************************* PP

                                 TIGR00700 277 vvGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigd 345
                                               v G+aei+da apGglGGtyaGnPl++aaalav++i eee l +r++ + + ++  l  ++++ + ig+
  lcl|NCBI__GCF_000013785.1:WP_020307792.1 280 VCGKAEIMDAIAPGGLGGTYAGNPLSCAAALAVMEIFEEEHLLDRCKAVAEKLTTGLKAIQAKHKEIGE 348
                                               ********************************************************************* PP

                                 TIGR00700 346 vrglGamiavelv.dpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglki 413
                                               vrglGamia+el  d d + P aal+ +i a+a+++Gl+ll++G + n++r+l Plt+ dell+ gl i
  lcl|NCBI__GCF_000013785.1:WP_020307792.1 349 VRGLGAMIAIELFeDGDLARPAAALTSQIVARAREKGLILLSCGTYYNVLRVLVPLTVEDELLERGLAI 417
                                               ***********99899***************************************************** PP

                                 TIGR00700 414 lea 416
                                               l +
  lcl|NCBI__GCF_000013785.1:WP_020307792.1 418 LGE 420
                                               976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (426 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: 10.76
//
[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