GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Dechlorosoma suillum PS

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_0627 Dsui_0627 ABC-type branched-chain amino acid transport systems, ATPase component

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__PS:Dsui_0627
          Length = 267

 Score =  203 bits (516), Expect = 4e-57
 Identities = 120/270 (44%), Positives = 161/270 (59%), Gaps = 12/270 (4%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           LL+   ++  FGG+ A+   S   + G+I  LIGPNGAGKTT FNC+TG Y P  G I F
Sbjct: 7   LLEASDVAKHFGGVKALRGVSLTIREGEIYGLIGPNGAGKTTFFNCLTGLYVPNGGRIVF 66

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
              +G +  L+     ++     +ARTFQNIRLF+ +T LEN++V +H +        + 
Sbjct: 67  ---AGAE--LDTSAPHKVAARG-IARTFQNIRLFAHMTALENVMVGRHQRTRAG----VF 116

Query: 134 GLIGVGPYKREAAEAIEL-ARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPEL 192
           G I   P  R    AI+  A   L    + DRA D A  L YG QRRLEIARA+ T P+L
Sbjct: 117 GAIFRTPGTRAEEAAIQRRAEELLHYVGIADRAHDLAKHLSYGDQRRLEIARALATEPKL 176

Query: 193 LCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKIS 252
           L LDEPAAG+N  E+  L  L++ IR + G ++LLIEHD+ +VM + D V VL+YG+KI 
Sbjct: 177 LALDEPAAGMNASETGELRTLIEGIRKD-GITVLLIEHDVKLVMGLCDRVAVLDYGEKIC 235

Query: 253 DGTPDHVKNDPRVIAAYLGVEDEEVEEVIA 282
           +  P  V+ DPRVI AYLG E +     +A
Sbjct: 236 EDVPAVVQKDPRVITAYLGAEAQPAGSEVA 265


Lambda     K      H
   0.318    0.136    0.386 

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: 204
Number of extensions: 11
Number of successful extensions: 4
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: 292
Length of database: 267
Length adjustment: 26
Effective length of query: 266
Effective length of database: 241
Effective search space:    64106
Effective search space used:    64106
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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