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.5072.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.45
//
[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:

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