GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Desulfovibrio vulgaris Hildenborough

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate 207835 DVU2347 acetylornithine aminotransferase

Query= uniprot:A1S8Y2
         (425 letters)



>MicrobesOnline__882:207835
          Length = 399

 Score =  191 bits (486), Expect = 3e-53
 Identities = 140/432 (32%), Positives = 213/432 (49%), Gaps = 41/432 (9%)

Query: 1   MSLTNDSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLH 60
           M+ + ++L  R  + +    G+ +P+  +RAE + +WD EGREYID   GIAV + GH H
Sbjct: 1   MTTSFEALKNREESLLCRTYGR-YPISVQRAEGSRMWDHEGREYIDLLSGIAVTSLGHCH 59

Query: 61  PKVKAAVAEQLEKFSHTCFMVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAI 120
           P++   +A Q  K  H   +    E  + + EKL   +      K+    SG+EA E AI
Sbjct: 60  PELAEVMARQARKLVHVSNLFY-QEEQLDLAEKLLSTL---HCTKAFFCNSGAEANEAAI 115

Query: 121 KVARAYTKRAG------VIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPC 174
           K+AR Y +R        V+  T  +HGRT+A +A TG+   +  G   M A   +AE+  
Sbjct: 116 KLARRYMQRVRGVDAHEVVTLTGAFHGRTLATVAATGQER-FQDGFAPMPAGFRQAEW-- 172

Query: 175 ALHGVSEDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREG 234
                 + DA+ +        A     A +++E VQGEGG    T  + + + +LC  +G
Sbjct: 173 -----GDIDALRA--------AITPATAGVLVEMVQGEGGVRPMTQDYARAVADLCREKG 219

Query: 235 IMLIADEVQTGAGRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGG 294
           ++L+ DE+QTG  RTG F+A +  GV  DI T AK++A G P+  +    EV      G 
Sbjct: 220 VLLMVDEIQTGLCRTGRFWAHQHYGVEPDIVTSAKALANGLPMGAMMTTDEVAQGFVAGS 279

Query: 295 LGGTYGGSPLACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYP-QIAEVRGLG 353
              T+G   L  + A A +++ + ++L ER+ A+G         + ++ P  I EVRG G
Sbjct: 280 HATTFGAGALVSSVAAATLDIMKRDRLDERATAVGGRAMERFRAIGAKLPGTIEEVRGYG 339

Query: 354 SMIAIELMENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLE 413
            MI I L  +GK       +V  E   RG +  +  T   VLR LVP    DE     L 
Sbjct: 340 LMIGIVLTFSGK-------EVWKELVARGFVCNN--TQEKVLR-LVPALTIDE---ADLT 386

Query: 414 IMAECFEAVLGK 425
             A+  E +L +
Sbjct: 387 AFADTLEDILAR 398


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: 363
Number of extensions: 22
Number of successful extensions: 5
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: 399
Length adjustment: 31
Effective length of query: 394
Effective length of database: 368
Effective search space:   144992
Effective search space used:   144992
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: 50 (23.9 bits)

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