Alignments for a candidate for gabT in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Pseudomonas putida KT2440

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate PP_0214 PP_0214 4-aminobutyrate aminotransferase

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



>FitnessBrowser__Putida:PP_0214
          Length = 425

 Score =  738 bits (1905), Expect = 0.0
 Identities = 370/425 (87%), Positives = 396/425 (93%), Gaps = 1/425 (0%)

Query: 1   MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60
           MSKTN SLM+RR AAVPRGVGQIHPIF D+AKN+TV DVEGRE IDFAGGIAVLNTGH+H
Sbjct: 1   MSKTNESLMQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLH 60

Query: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120
           PK++AAV EQL K++HTCFQVLAYEPYVELCEKIN  VPGDF KKTLLVTTGSEAVENAV
Sbjct: 61  PKVVAAVQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAV 120

Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180
           KIARAATGRAGVIAFTG YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRAL+P+ELHG+S
Sbjct: 121 KIARAATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGIS 180

Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240
           +DD+IAS+ERIFKNDAEPRDIAAII+EPVQGEGGF  APKE MKRLRALCDQHGILLIAD
Sbjct: 181 VDDAIASVERIFKNDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIAD 240

Query: 241 EVQTGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300
           EVQTGAGRTGTFFAMEQMGV  DLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA
Sbjct: 241 EVQTGAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300

Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360
           GSPIACAAALAV+EVFEEE LLDR KAVGERL  GL+ IQ KYP+IG+VR LG+MIAVE+
Sbjct: 301 GSPIACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEV 360

Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420
           FE G +H PNAAAV QVVAKAR+KGLILLSCGTYGNVLR+LVPLT+ DA LDKGLAIIEE
Sbjct: 361 FEKG-THTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEE 419

Query: 421 CFAEL 425
           CFAE+
Sbjct: 420 CFAEI 424


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: 776
Number of extensions: 19
Number of successful extensions: 2
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 PP_0214 PP_0214 (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.23939.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.7e-169  548.3   4.9   5.3e-169  548.2   4.9    1.0  1  lcl|FitnessBrowser__Putida:PP_0214  PP_0214 4-aminobutyrate aminotra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0214  PP_0214 4-aminobutyrate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.2   4.9  5.3e-169  5.3e-169       1     418 [.      10     421 ..      10     423 .. 0.99

  Alignments for each domain:
  == domain 1  score: 548.2 bits;  conditional E-value: 5.3e-169
                           TIGR00700   1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpy 75 
                                         qrr aav++Gvg   ++++  a+++++ dv+G++lid+a+giavln+Gh hPkvv+av++q+ ++ ht+fqv+ y
  lcl|FitnessBrowser__Putida:PP_0214  10 QRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAY 84 
                                         89************************************************************************* PP

                           TIGR00700  76 esyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiG 150
                                         e yvel ek+n++ Pg  +kk++l+++G+eavenavkiar+ tgr gv+af++g+hGrt +t+ lt+kv Py  G
  lcl|FitnessBrowser__Putida:PP_0214  85 EPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAG 159
                                         *************************************************************************** PP

                           TIGR00700 151 fGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavas 225
                                         +G +++ ++ra +p+++++i++      dd +a++e++f+ d e++++aa++lePvqGeGGf  ++kel++ ++ 
  lcl|FitnessBrowser__Putida:PP_0214 160 MGLMPGGIFRALFPSELHGISV------DDAIASVERIFKNDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRA 228
                                         *******************988......88999****************************************** PP

                           TIGR00700 226 lckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnP 300
                                         lc++hgi+liadevqtG  rtG++fa+e +++ Pdl t aks+a+G+Pl+gv G+ae +da apGglGGtyaG+P
  lcl|FitnessBrowser__Putida:PP_0214 229 LCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSP 303
                                         *************************************************************************** PP

                           TIGR00700 301 lavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdttePdaalaekiaa 375
                                         +a+aaalav+++ eee l +r++ +g++++  l e++++ p igdvrglG+miave+ + +t+ P+aa   ++ a
  lcl|FitnessBrowser__Putida:PP_0214 304 IACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEVFEKGTHTPNAAAVGQVVA 378
                                         *************************************************************************** PP

                           TIGR00700 376 aalaaGlllltaGifGniirlltPltisdelldeglkileaal 418
                                         +a+++Gl+ll++G +Gn++r+l Plt  d+lld+gl i+e+ +
  lcl|FitnessBrowser__Putida:PP_0214 379 KAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECF 421
                                         ***************************************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: 8.14
//
[ok]

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

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Protein sequences (fasta format)
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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