GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Desulfovibrio vulgaris Miyazaki F

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 8502443 DvMF_3149 acetylornithine aminotransferase (RefSeq)

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Miya:8502443
          Length = 402

 Score =  201 bits (510), Expect = 5e-56
 Identities = 127/387 (32%), Positives = 199/387 (51%), Gaps = 24/387 (6%)

Query: 71  GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130
           G  + L D  G+E++D L G  + ++GH +  +      Q  K    S       +  LA
Sbjct: 30  GQGSRLWDVDGREYVDLLSGIAVTSLGHCHEELAEVAAAQARKLVHVSNLFYQEEQLDLA 89

Query: 131 KTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSP---RGKFTFIATSGAFHGKSLGA 187
           + L  L+      +FFCNSG E+ EAA+KLA+ Y      R  +  I  +GAFHG++L  
Sbjct: 90  ERL--LSTSHCTKAFFCNSGAEANEAAIKLARRYMQRVQGREAYEIITLTGAFHGRTLAT 147

Query: 188 LSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVI 247
           ++AT ++ F+  F P+  GFR VP G+IEA+R A+      G   A V++E +QGEGGV 
Sbjct: 148 VAATGQAKFQDGFYPMPEGFRQVPSGDIEALRAAI------GPQTAGVLVEVVQGEGGVC 201

Query: 248 LPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVM 307
              P Y  AV+ LC E G L + DE+Q GM RTG+ ++ ++  ++PDI+  AKAL  G +
Sbjct: 202 PLDPDYARAVQALCREKGVLFMTDEIQAGMCRTGRFWSFQNYGLEPDIVSCAKALANG-L 260

Query: 308 PIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLL 367
           P+GA + T+EV          H TTFG   L  A A  T+ ++L  +L  +A  +G  ++
Sbjct: 261 PMGAMMTTDEVARGFVAGS--HATTFGAGALVSAVASRTVEIMLRDDLAGRAATEGARIM 318

Query: 368 DGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAK---T 424
           D FR + ++ P  +   RG G+++ +          F  +   Q ++  G + N      
Sbjct: 319 DRFRAMGQKLPGTIDHVRGLGLMIGVVLA-------FPGKEVWQALIDRGFICNLTQDCV 371

Query: 425 IRIEPPLTLTIEQCELVIKAARKALAA 451
           +R+ P LT+     +    A    L+A
Sbjct: 372 LRLLPALTIPRADLDAFADALEDILSA 398


Lambda     K      H
   0.320    0.135    0.393 

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: 387
Number of extensions: 20
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: 459
Length of database: 402
Length adjustment: 32
Effective length of query: 427
Effective length of database: 370
Effective search space:   157990
Effective search space used:   157990
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)

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