Aligments for a candidate for gabT in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Aligments for a candidate for gabT in Pseudomonas fluorescens FW300-N2E3

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate AO353_11510 AO353_11510 4-aminobutyrate aminotransferase

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



>FitnessBrowser__pseudo3_N2E3:AO353_11510
          Length = 425

 Score =  820 bits (2118), Expect = 0.0
 Identities = 413/425 (97%), Positives = 422/425 (99%)

Query: 1   MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60
           MSKTNASLMKRREAAVPRGVGQIHPIFAD AKN+TVTDVEGREFIDFAGGIAVLNTGH+H
Sbjct: 1   MSKTNASLMKRREAAVPRGVGQIHPIFADHAKNSTVTDVEGREFIDFAGGIAVLNTGHLH 60

Query: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120
           PK+IAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVEN++
Sbjct: 61  PKVIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENSI 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
           GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL
Sbjct: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360

Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420
           FENGDSHKPNAAAVA+VVAKARDKGLILLSCGTYGNVLRVLVPLT+PD QLDKGLAI+EE
Sbjct: 361 FENGDSHKPNAAAVAKVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAIMEE 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: 825
Number of extensions: 22
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 AO353_11510 AO353_11510 (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.1052.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   9.2e-166  537.5   6.0     1e-165  537.3   6.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11510  AO353_11510 4-aminobutyrate amin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_11510  AO353_11510 4-aminobutyrate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  537.3   6.0    1e-165    1e-165       1     418 [.      10     422 ..      10     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 537.3 bits;  conditional E-value: 1e-165
                                     TIGR00700   1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveel 65 
                                                   +rr+aav++Gvg   +++a +a+++++ dv+G+++id+a+giavln+Gh hPkv++av +q+++l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11510  10 KRREAAVPRGVGQIHPIFADHAKNSTVTDVEGREFIDFAGGIAVLNTGHLHPKVIAAVTEQLNKL 74 
                                                   69*************************************************************** PP

                                     TIGR00700  66 thtafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgf 130
                                                   tht+fqv+ ye yvel ek+na  Pg   kk++l+++G+eaven++kiar+ tgr gv+af++++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11510  75 THTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARAATGRAGVIAFTGAY 139
                                                   ***************************************************************** PP

                                     TIGR00700 131 hGrtnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadvea 195
                                                   hGrt +t+ lt+kv Py  G+G +++ ++ra +p ++++ +       dd +a+ie++f+ d e+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11510 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSI------DDSIASIERIFKNDAEP 198
                                                   **************************************9877......88899************ PP

                                     TIGR00700 196 eqvaavvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPd 260
                                                   +++aa+++ePvqGeGGf v++ke+++ ++ lc++hgi+liadevqtG  rtG++fa+e +++  d
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11510 199 RDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAAD 263
                                                   ***************************************************************** PP

                                     TIGR00700 261 litvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqi 325
                                                   l t aks+a+G+Pl+gv G+ae +da apGglGGtyaG+P+a+aaalav+++ eee l +r++ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11510 264 LTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAV 328
                                                   ***************************************************************** PP

                                     TIGR00700 326 gklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaalaaGlllltaGi 389
                                                   g+++   l  ++++ p+ig+vr lGamiavel  + d+++P+aa  +k+ a+a+ +Gl+ll++G 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11510 329 GERLVTGLKAIQAKYPVIGEVRALGAMIAVELFeNGDSHKPNAAAVAKVVAKARDKGLILLSCGT 393
                                                   *******************************9968899*************************** PP

                                     TIGR00700 390 fGniirlltPltisdelldeglkileaal 418
                                                   +Gn++r+l Plt +de+ld+gl i+e+ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11510 394 YGNVLRVLVPLTAPDEQLDKGLAIMEECF 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: 7.05
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, or view the source code.

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