Alignments for a candidate for gabT in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Shewanella oneidensis MR-1

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate 200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)

Query= uniprot:A1S8Y2
         (425 letters)



>FitnessBrowser__MR1:200454
          Length = 425

 Score =  735 bits (1898), Expect = 0.0
 Identities = 367/423 (86%), Positives = 393/423 (92%)

Query: 1   MSLTNDSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLH 60
           MS TNDSLM RR+AAVAGGVGQIHP+FT RAENA+VWDVEGRE+IDFAGGIAVLNTGHLH
Sbjct: 1   MSTTNDSLMARRQAAVAGGVGQIHPIFTARAENASVWDVEGREFIDFAGGIAVLNTGHLH 60

Query: 61  PKVKAAVAEQLEKFSHTCFMVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAI 120
           PKVKAAVA QLE FSHTCFMVLGYESY+ VCEKLNQLVPGDFAKK+ALFTSGSEAVENA+
Sbjct: 61  PKVKAAVAAQLEDFSHTCFMVLGYESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAV 120

Query: 121 KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVS 180
           KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLM ANVFRAEFPCALHGVS
Sbjct: 121 KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGVS 180

Query: 181 EDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIAD 240
           +DDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYA +P FM+RLR LCDREGIMLIAD
Sbjct: 181 DDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAVSPAFMQRLRALCDREGIMLIAD 240

Query: 241 EVQTGAGRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYG 300
           EVQTGAGRTGTFFAMEQMGV+ADITTFAKSIAGGFPLSGITGRA+VMDAIGPGGLGGTYG
Sbjct: 241 EVQTGAGRTGTFFAMEQMGVSADITTFAKSIAGGFPLSGITGRAQVMDAIGPGGLGGTYG 300

Query: 301 GSPLACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIEL 360
           G+PLACAAALAV+EVFEEEKLLER+NAIG  IKSA+  +   +PQIA+VRGLG+M AIEL
Sbjct: 301 GNPLACAAALAVLEVFEEEKLLERANAIGDRIKSALNTMQVEHPQIADVRGLGAMNAIEL 360

Query: 361 MENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFE 420
           ME+GKPAP+YC Q+L EARNRGLILLSCGTYGNVLRILVP+T  D Q+  GL I+   F 
Sbjct: 361 MEDGKPAPQYCAQILAEARNRGLILLSCGTYGNVLRILVPLTVSDTQLDAGLGILKTSFN 420

Query: 421 AVL 423
           AVL
Sbjct: 421 AVL 423


Lambda     K      H
   0.319    0.136    0.391 

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: 647
Number of extensions: 6
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 200454 SO1276 (4-aminobutyrate aminotransferase (NCBI ptt file))
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.21042.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-163  530.5   5.3   1.4e-163  530.3   5.3    1.0  1  lcl|FitnessBrowser__MR1:200454  SO1276 4-aminobutyrate aminotran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200454  SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.3   5.3  1.4e-163  1.4e-163       2     417 ..      11     418 ..      10     421 .. 0.98

  Alignments for each domain:
  == domain 1  score: 530.3 bits;  conditional E-value: 1.4e-163
                       TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpyesyve 80 
                                     rr+aav+ Gvg   ++++a+ae+a + dv+G+++id+a+giavln+Gh hPkv +av  q+e++ ht+f+v+ yesy++
  lcl|FitnessBrowser__MR1:200454  11 RRQAAVAGGVGQIHPIFTARAENASVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFSHTCFMVLGYESYIQ 89 
                                     89***************************************************************************** PP

                       TIGR00700  81 laeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiGfGPfapevy 159
                                     + ekln++ Pg   kk++l++sG+eavenavk+ar+yt+r gv+af+ g+hGrt  ++alt+kv+Py  G+G ++++v+
  lcl|FitnessBrowser__MR1:200454  90 VCEKLNQLVPGDFAKKTALFTSGSEAVENAVKVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMSANVF 168
                                     ******************************************************************************* PP

                       TIGR00700 160 raPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliade 238
                                     ra +p  +++ +       dd +a+ie++f+ d e+ ++aa++lePvqGeGGf   +  +++ ++ lc+++gi+liade
  lcl|FitnessBrowser__MR1:200454 169 RAEFPCALHGVSD------DDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAVSPAFMQRLRALCDREGIMLIADE 241
                                     *********9987......67788******************************************************* PP

                       TIGR00700 239 vqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeg 317
                                     vqtG  rtG++fa+e +++  d+ t aks+a+G+Plsg++Gra+++da  pGglGGty+GnPla+aaalavl++ eee 
  lcl|FitnessBrowser__MR1:200454 242 VQTGAGRTGTFFAMEQMGVSADITTFAKSIAGGFPLSGITGRAQVMDAIGPGGLGGTYGGNPLACAAALAVLEVFEEEK 320
                                     ******************************************************************************* PP

                       TIGR00700 318 lieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdttePdaalaekiaaaalaaGlllltaGifGniirl 396
                                     l era+ ig ++k  l +++ e p+i+dvrglGam a+el++ +  +P    +++i a+a+++Gl+ll++G +Gn++r+
  lcl|FitnessBrowser__MR1:200454 321 LLERANAIGDRIKSALNTMQVEHPQIADVRGLGAMNAIELMEDG--KPAPQYCAQILAEARNRGLILLSCGTYGNVLRI 397
                                     ****************************************9876..56666789999********************** PP

                       TIGR00700 397 ltPltisdelldeglkileaa 417
                                     l Plt+sd++ld+gl il+ +
  lcl|FitnessBrowser__MR1:200454 398 LVPLTVSDTQLDAGLGILKTS 418
                                     ******************976 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: 7.62
//
[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