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.20218.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: 7.40
//
[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