GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Shewanella loihica PV-4

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 5208501 Shew_1012 glutamate-1-semialdehyde-2,1-aminomutase (RefSeq)

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__PV4:5208501
          Length = 428

 Score =  169 bits (427), Expect = 2e-46
 Identities = 119/363 (32%), Positives = 181/363 (49%), Gaps = 24/363 (6%)

Query: 5   NESLLKRRQAAVPRGVGQI---------HPVVAERAENSTVWDVEGREYIDFAGGIAVLN 55
           +E+L ++ +  +P GV             P   E+A+ + ++D +G+ YID+ G    + 
Sbjct: 4   SETLFEQAKKTIPGGVNSPVRAFNGVGGSPRFIEKADGAYIYDADGKAYIDYVGSWGPMI 63

Query: 56  TGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEA 115
            GH HPK+  AV   L  + +        E  + +AE++ + VP    ++  +V+SG+EA
Sbjct: 64  LGHNHPKIRQAV---LDAVENGLSFGAPTELEVRMAEKVIEMVPS--MEQVRMVSSGTEA 118

Query: 116 VENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCE 175
             +A+++AR  T R  ++ F G YHG     L   G     + G    PG I    A   
Sbjct: 119 TMSAIRLARGFTNRDKILKFEGCYHGHADCLLVKAGSGA-LTLGQPSSPG-IPEDFAKHT 176

Query: 176 LHGVSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGI 235
           L  V  +  + S++ +F+    P++IA II+EPV G          F++ LRALCDQ+G 
Sbjct: 177 LTAVYNE--LESVKTLFEQ--YPEEIACIILEPVAGNMNCIPPIPGFLEGLRALCDQYGA 232

Query: 236 LLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGG- 294
           LLI DEV TG  R     A    GI PDLTT  K +GGG P+    G+ E+M  IAP G 
Sbjct: 233 LLIIDEVMTGF-RVSKSGAQGHYGITPDLTTLGKVIGGGMPVGAFGGRKEVMQFIAPTGP 291

Query: 295 --LGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGL 352
               GT +G+PIA +A LA ++    E L E   A  +R+  G +    KH +   +  +
Sbjct: 292 VYQAGTLSGNPIAMSAGLAQMEELCAEGLYEELAAKTKRIAEGFKAAANKHGIPLSINYV 351

Query: 353 GSM 355
           G M
Sbjct: 352 GGM 354


Lambda     K      H
   0.319    0.137    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: 475
Number of extensions: 21
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: 426
Length of database: 428
Length adjustment: 32
Effective length of query: 394
Effective length of database: 396
Effective search space:   156024
Effective search space used:   156024
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