GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|MicrobesOnline__882:207835 DVU2347 acetylornithine
           aminotransferase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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