GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Shewanella sp. ANA-3

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate 7025943 Shewana3_3091 4-aminobutyrate aminotransferase (RefSeq)

Query= uniprot:A1S8Y2
         (425 letters)



>FitnessBrowser__ANA3:7025943
          Length = 425

 Score =  749 bits (1934), Expect = 0.0
 Identities = 373/423 (88%), Positives = 399/423 (94%)

Query: 1   MSLTNDSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLH 60
           MS TNDSLM RR+AAVAGGVGQIHPVFT RAENATVWDVEGRE+IDFAGGIAVLNTGHLH
Sbjct: 1   MSTTNDSLMARRQAAVAGGVGQIHPVFTARAENATVWDVEGREFIDFAGGIAVLNTGHLH 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
           +DDAMASIERIFKNDAEPS+IAAIILEPVQGEGGFYAA+P FM+RLR LCDREGIMLIAD
Sbjct: 181 DDDAMASIERIFKNDAEPSNIAAIILEPVQGEGGFYAASPEFMQRLRALCDREGIMLIAD 240

Query: 241 EVQTGAGRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYG 300
           EVQTGAGRTGTFFAMEQMGV+ADITTFAKSIAGGFPLSGITG+AEVMDAIGPGGLGGTYG
Sbjct: 241 EVQTGAGRTGTFFAMEQMGVSADITTFAKSIAGGFPLSGITGKAEVMDAIGPGGLGGTYG 300

Query: 301 GSPLACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIEL 360
           G+PLACAAALAV+EVFEEEKLLER+NAIG+ IKSA+  +   +PQIA+VRGLG+MIAIEL
Sbjct: 301 GNPLACAAALAVLEVFEEEKLLERANAIGERIKSALNTMQVEHPQIADVRGLGAMIAIEL 360

Query: 361 MENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFE 420
           ME GKPAP+YC Q+L EARNRGLILLSCGTYGNVLRILVP+T PDEQ+  GL I+  CF+
Sbjct: 361 MEEGKPAPQYCAQILAEARNRGLILLSCGTYGNVLRILVPLTVPDEQLAAGLGILKSCFD 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: 663
Number of extensions: 10
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 7025943 Shewana3_3091 (4-aminobutyrate aminotransferase (RefSeq))
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.2666.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.1e-166  539.0   5.4   3.6e-166  538.8   5.4    1.0  1  lcl|FitnessBrowser__ANA3:7025943  Shewana3_3091 4-aminobutyrate am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7025943  Shewana3_3091 4-aminobutyrate aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  538.8   5.4  3.6e-166  3.6e-166       2     417 ..      11     418 ..      10     421 .. 0.98

  Alignments for each domain:
  == domain 1  score: 538.8 bits;  conditional E-value: 3.6e-166
                         TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpyesy 78 
                                       rr+aav+ Gvg   +v++a+ae+a++ dv+G+++id+a+giavln+Gh hPkv +av  q+e++ ht+f+v+ yesy
  lcl|FitnessBrowser__ANA3:7025943  11 RRQAAVAGGVGQIHPVFTARAENATVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFSHTCFMVLGYESY 87 
                                       89*************************************************************************** PP

                         TIGR00700  79 velaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiGfGPfa 155
                                       +++ ekln++ Pg   kk++l++sG+eavenavk+ar+yt+r gv+af+ g+hGrt  ++alt+kv+Py  G+G ++
  lcl|FitnessBrowser__ANA3:7025943  88 IQVCEKLNQLVPGDFAKKTALFTSGSEAVENAVKVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMS 164
                                       ***************************************************************************** PP

                         TIGR00700 156 pevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavaslckehgi 232
                                       ++v+ra +p  +++ +       dd +a+ie++f+ d e+ ++aa++lePvqGeGGf  ++ e+++ ++ lc+++gi
  lcl|FitnessBrowser__ANA3:7025943 165 ANVFRAEFPCALHGVSD------DDAMASIERIFKNDAEPSNIAAIILEPVQGEGGFYAASPEFMQRLRALCDREGI 235
                                       *************9987......67788************************************************* PP

                         TIGR00700 233 vliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalav 309
                                       +liadevqtG  rtG++fa+e +++  d+ t aks+a+G+Plsg++G+ae++da  pGglGGty+GnPla+aaalav
  lcl|FitnessBrowser__ANA3:7025943 236 MLIADEVQTGAGRTGTFFAMEQMGVSADITTFAKSIAGGFPLSGITGKAEVMDAIGPGGLGGTYGGNPLACAAALAV 312
                                       ***************************************************************************** PP

                         TIGR00700 310 ldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdttePdaalaekiaaaalaaGllllt 386
                                       l++ eee l era+ ig+++k  l +++ e p+i+dvrglGamia+el++ +   P    +++i a+a+++Gl+ll+
  lcl|FitnessBrowser__ANA3:7025943 313 LEVFEEEKLLERANAIGERIKSALNTMQVEHPQIADVRGLGAMIAIELMEEGK--PAPQYCAQILAEARNRGLILLS 387
                                       ************************************************98765..6666789999************ PP

                         TIGR00700 387 aGifGniirlltPltisdelldeglkileaa 417
                                       +G +Gn++r+l Plt++de+l +gl il++ 
  lcl|FitnessBrowser__ANA3:7025943 388 CGTYGNVLRILVPLTVPDEQLAAGLGILKSC 418
                                       ***************************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: 7.28
//
[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