GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaA in Shewanella amazonensis SB2B

Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate 6938535 Sama_2638 putative oxidoreductase (RefSeq)

Query= metacyc::G1G01-5614-MONOMER
         (432 letters)



>FitnessBrowser__SB2B:6938535
          Length = 428

 Score =  142 bits (359), Expect = 2e-38
 Identities = 122/400 (30%), Positives = 182/400 (45%), Gaps = 12/400 (3%)

Query: 30  EH-KADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVGLVNAGTWIRPDD 88
           EH + DVCVIG G TGLS+A+HLLE G  V+VLEA +IG G SGRN G +        D 
Sbjct: 26  EHLETDVCVIGAGYTGLSSALHLLESGFKVVVLEAARIGWGASGRNGGQIVNSYSRDIDV 85

Query: 89  VEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLHMAHNATGIADLEARHE 148
           +E T+G+++G    ++  E    +   I +  IDC  ++ G +  A N   +  L+A+  
Sbjct: 86  IEKTVGKEKGKLFGEMAFEGGRIIRDRIAKYNIDCDLKN-GGVFAALNQKQMGHLKAQKA 144

Query: 149 QWRRRG--ADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAAAVTRLGGKI 206
            W   G    +E+L  A  +    T++    +LD+  G I+P+    G A AV  LGGKI
Sbjct: 145 LWEAHGHTNQLEILDEAGIRNVVNTERYVGGMLDKSGGHIHPLNLALGEARAVESLGGKI 204

Query: 207 FQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSNLQKQFFRGYYYQVASK 266
           F+ S+V  +  EG+   VKT  G V+A  VV++  AY       L  +        + ++
Sbjct: 205 FEDSAVLDVV-EGEPAIVKTEFGQVKARFVVVAGNAYLGKLMPELMAKSMPCGTQVITTE 263

Query: 267 PLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDNKPAWFVRSWADRIQS 326
           PL    A+ +LP      D   +L   R     RL+ G       +    ++S       
Sbjct: 264 PLSDEMANSLLPQDYCVEDCNYLLDYFRLSGDKRLIYGGGVVYGARDPDNIKSIILPKML 323

Query: 327 HYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGRGNTTGTVIGRAFAEF 386
             +P+L  V  +  WTG    T   L ++      +    G +G G T   + G+  AE 
Sbjct: 324 ETFPQLKGVRIDYTWTGNFLLTLSRLPQVGRIGKNIYYSQGCSGHGVTYTHLAGKLIAE- 382

Query: 387 LLKGEADSLPI----PFSPMSGVSAPSLRTAFYESGFSLY 422
           +L G+A    +    P  P  G  A  LR  F   G   Y
Sbjct: 383 VLNGQATRFDVFAELPHYPFPGGHA--LRVPFSAIGAWYY 420


Lambda     K      H
   0.319    0.135    0.419 

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: 441
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: 432
Length of database: 428
Length adjustment: 32
Effective length of query: 400
Effective length of database: 396
Effective search space:   158400
Effective search space used:   158400
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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