GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Azospirillum brasilense Sp245

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate AZOBR_RS31205 AZOBR_RS31205 sugar ABC transporter permease

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__azobra:AZOBR_RS31205
          Length = 354

 Score =  162 bits (409), Expect = 2e-44
 Identities = 103/286 (36%), Positives = 164/286 (57%), Gaps = 6/286 (2%)

Query: 46  FSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSL 105
           FS+  ++   + +L  +  + +   +LA GMT VI T G+DLSVG++++IS  VA   + 
Sbjct: 33  FSIRLQDGRLFGSLIDVLNRGAPVALLAIGMTMVIATRGVDLSVGAVMAISGAVA---AT 89

Query: 106 MPQLGMLSVP---AALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGLARLVGNDST 162
           + Q G    P   A+L  GLL G+ NG LVA +++ P + TL  + A RG+A+LV     
Sbjct: 90  LTQAGWGLTPVLAASLAAGLLCGLWNGLLVAVLRIQPIVATLILMVAGRGIAQLVTEGQI 149

Query: 163 IYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSG 222
           +     G  FIG+G  L VP  V+I   ++ V+  ++R T LGL I AVG +  ++  +G
Sbjct: 150 VTFTSPGLTFIGSGSFLTVPMPVVITAVLLGVTALLVRMTALGLMIEAVGVSRLSSAGAG 209

Query: 223 IKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGT 282
           +   VVL+ VY   GL A + G++ +A +  A+    G   ELDAI AV++GGTS +GG 
Sbjct: 210 VNTPVVLVAVYVWCGLCAAVAGLVVAADIRGADANNAGLWLELDAILAVVVGGTSLLGGR 269

Query: 283 GSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDS 328
             ++ ++VGAL I  ++ G++L G    +  I+K  V++  + L S
Sbjct: 270 FGLLLSVVGALTIQAMNTGILLSGFKPEFNLIVKAGVLMVVLLLQS 315


Lambda     K      H
   0.325    0.141    0.409 

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: 338
Number of extensions: 17
Number of successful extensions: 3
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: 337
Length of database: 354
Length adjustment: 29
Effective length of query: 308
Effective length of database: 325
Effective search space:   100100
Effective search space used:   100100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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