Alignments for a candidate for gabT in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Pseudomonas simiae WCS417

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate GFF179 PS417_00900 4-aminobutyrate aminotransferase

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



>FitnessBrowser__WCS417:GFF179
          Length = 425

 Score =  810 bits (2091), Expect = 0.0
 Identities = 409/425 (96%), Positives = 419/425 (98%)

Query: 1   MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60
           MSKTNASLMKRREAAVPRGVGQIHPIFA+SAKNATVTDVEGREFIDFAGGIAVLNTGHVH
Sbjct: 1   MSKTNASLMKRREAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60

Query: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120
           PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV
Sbjct: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120

Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180
           KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGG+FRAL+PNELHGVS
Sbjct: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGVFRALFPNELHGVS 180

Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240
            DD+IASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPK FMKRLR LCD+HGILLIAD
Sbjct: 181 DDDAIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKSFMKRLRELCDKHGILLIAD 240

Query: 241 EVQTGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300
           EVQTGAGRTGTFFAMEQMGV ADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA
Sbjct: 241 EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300

Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360
           GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL
Sbjct: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360

Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420
           F++GD+HKPNAAAVA VVAKAR+KGLILLSCGTYGNVLRVLVPLTSPD QLDKGLAIIEE
Sbjct: 361 FDDGDTHKPNAAAVASVVAKAREKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEE 420

Query: 421 CFAEL 425
           CF+EL
Sbjct: 421 CFSEL 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: 820
Number of extensions: 19
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: 425
Length adjustment: 32
Effective length of query: 393
Effective length of database: 393
Effective search space:   154449
Effective search space used:   154449
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 GFF179 PS417_00900 (4-aminobutyrate aminotransferase)
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.30806.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   8.2e-168  544.2   6.6   9.3e-168  544.1   6.6    1.0  1  lcl|FitnessBrowser__WCS417:GFF179  PS417_00900 4-aminobutyrate amin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF179  PS417_00900 4-aminobutyrate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  544.1   6.6  9.3e-168  9.3e-168       1     418 [.      10     422 ..      10     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 544.1 bits;  conditional E-value: 9.3e-168
                          TIGR00700   1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpye 76 
                                        +rr+aav++Gvg   +++a +a++a++ dv+G+++id+a+giavln+Gh hPk+++av +q+++ltht+fqv+ ye
  lcl|FitnessBrowser__WCS417:GFF179  10 KRREAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAYE 85 
                                        69************************************************************************** PP

                          TIGR00700  77 syvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiGfG 152
                                         yvel ek+na  Pg   kk++l+++G+eavenavkiar+ tgr gv+af++++hGrt +t+ lt+kv Py  G+G
  lcl|FitnessBrowser__WCS417:GFF179  86 PYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMG 161
                                        **************************************************************************** PP

                          TIGR00700 153 PfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavaslck 228
                                         +++ v+ra +p ++++ +       dd +a+ie++f+ d e++++aa+++ePvqGeGGf v++k +++ +++lc+
  lcl|FitnessBrowser__WCS417:GFF179 162 LMPGGVFRALFPNELHGVSD------DDAIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKSFMKRLRELCD 231
                                        ****************9887......78899********************************************* PP

                          TIGR00700 229 ehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlava 304
                                        +hgi+liadevqtG  rtG++fa+e +++  dl t aks+a+G+Pl+gv G+ae +da apGglGGtyaG+P+a+a
  lcl|FitnessBrowser__WCS417:GFF179 232 KHGILLIADEVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACA 307
                                        **************************************************************************** PP

                          TIGR00700 305 aalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaala 379
                                        aalav+++ eee l +r++ +g+++   l  ++++ p+ig+vr lGamiavel  d dt++P+aa  + + a+a++
  lcl|FitnessBrowser__WCS417:GFF179 308 AALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFdDGDTHKPNAAAVASVVAKARE 383
                                        ****************************************************99789******************* PP

                          TIGR00700 380 aGlllltaGifGniirlltPltisdelldeglkileaal 418
                                        +Gl+ll++G +Gn++r+l Plt +de+ld+gl i+e+ +
  lcl|FitnessBrowser__WCS417:GFF179 384 KGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEECF 422
                                        ***********************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (425 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.38
//
[ok]

This GapMind analysis is from Sep 17 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