Alignments for a candidate for gabT in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Pseudomonas fluorescens FW300-N2C3

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate AO356_10715 AO356_10715 4-aminobutyrate aminotransferase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_10715
          Length = 425

 Score =  816 bits (2107), Expect = 0.0
 Identities = 414/425 (97%), Positives = 418/425 (98%)

Query: 1   MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60
           MSKTNA LM RR AAVPRGVGQIHPIFA+SAKNATVTDVEGREFIDFAGGIAVLNTGHVH
Sbjct: 1   MSKTNADLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60

Query: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120
           PKIIAAVT QLNKLTHTCFQVLAYEPYVE+CEKINAKVPGDFAKKTLLVTTGSEAVENAV
Sbjct: 61  PKIIAAVTAQLNKLTHTCFQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120

Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180
           KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS
Sbjct: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180

Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240
           IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD
Sbjct: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240

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

Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360
           GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQ KYPVIGEVRALGAMIAVEL
Sbjct: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQKKYPVIGEVRALGAMIAVEL 360

Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420
           FENGD+HKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPD QLDKGLAIIEE
Sbjct: 361 FENGDTHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEE 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: 814
Number of extensions: 24
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 AO356_10715 AO356_10715 (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.4023.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   7.5e-167  541.1   8.1   8.5e-167  540.9   8.1    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10715  AO356_10715 4-aminobutyrate amin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10715  AO356_10715 4-aminobutyrate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.9   8.1  8.5e-167  8.5e-167       2     418 ..      11     422 ..      10     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 540.9 bits;  conditional E-value: 8.5e-167
                                       TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqvee 64 
                                                     rr+aav++Gvg   +++a +a++a++ dv+G+++id+a+giavln+Gh hPk+++av  q+++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10715  11 RRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTAQLNK 73 
                                                     89************************************************************* PP

                                       TIGR00700  65 lthtafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafs 127
                                                     ltht+fqv+ ye yve+ ek+na  Pg   kk++l+++G+eavenavkiar+ tgr gv+af+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10715  74 LTHTCFQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFT 136
                                                     *************************************************************** PP

                                       TIGR00700 128 rgfhGrtnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfv 190
                                                     +++hGrt +t+ lt+kv Py  G+G +++ ++ra +p ++++ +       dd +a+ie++f+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10715 137 GAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSI------DDSIASIERIFK 193
                                                     *****************************************9877......88899******* PP

                                       TIGR00700 191 adveaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaie 253
                                                      d e++++aa+++ePvqGeGGf v++ke+++ ++ lc++hgi+liadevqtG  rtG++fa+e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10715 194 NDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAME 256
                                                     *************************************************************** PP

                                       TIGR00700 254 heddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieee 316
                                                      +++  dl t aks+a+G+Pl+gv G+ae +da apGglGGtyaG+P+a+aaalav+++ eee
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10715 257 QMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEE 319
                                                     *************************************************************** PP

                                       TIGR00700 317 glieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaal 378
                                                      l +r++ +g+++   l  ++++ p+ig+vr lGamiavel  + dt++P+aa  +++ a+a+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10715 320 HLLDRCKAVGERLVTGLKAIQKKYPVIGEVRALGAMIAVELFeNGDTHKPNAAAVAQVVAKAR 382
                                                     ****************************************997899***************** PP

                                       TIGR00700 379 aaGlllltaGifGniirlltPltisdelldeglkileaal 418
                                                      +Gl+ll++G +Gn++r+l Plt +de+ld+gl i+e+ +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10715 383 DKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEECF 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: 00:00:00.01
# Mc/sec: 9.71
//
[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