GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Herbaspirillum seropedicae SmR1

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate HSERO_RS00895 HSERO_RS00895 ABC transporter

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__HerbieS:HSERO_RS00895
          Length = 255

 Score =  198 bits (503), Expect = 1e-55
 Identities = 119/259 (45%), Positives = 164/259 (63%), Gaps = 12/259 (4%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           LL +  ++ RFGGL A+N V  +   G+I  +IGPNGAGKTT FN ITG Y P  G   L
Sbjct: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64

Query: 71  RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130
              DGK +       + ++ KA +ARTFQNIRLFG M+VLEN++V  H +  +    ++ 
Sbjct: 65  ---DGKPY--SPSAPHEVA-KAGIARTFQNIRLFGEMTVLENVMVGCHVRTRQ----NVF 114

Query: 131 GLLGLPSYTRTEREAV-DLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVM 189
           G +      R E  A+ + ++  LD V + +FA   A +L YG QRRLEIARA+ T+P +
Sbjct: 115 GAVFRHKAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQL 174

Query: 190 LCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKIS 249
           L LDEPAAG+N  E   L +LL  I+ E K  +LLIEHD+ ++M + + + VLDYG+ I+
Sbjct: 175 LALDEPAAGMNATEKLGLRELLVKIQAEGKT-ILLIEHDVKLMMGLCNRITVLDYGKPIA 233

Query: 250 DGDPAFVKNDPAVIRAYLG 268
           +G PA V+ +PAVI AYLG
Sbjct: 234 EGVPADVQKNPAVIEAYLG 252


Lambda     K      H
   0.319    0.137    0.397 

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: 201
Number of extensions: 9
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: 294
Length of database: 255
Length adjustment: 25
Effective length of query: 269
Effective length of database: 230
Effective search space:    61870
Effective search space used:    61870
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: 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