GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24015 in Stutzerimonas stutzeri A1501

Align ABC transporter related (characterized, see rationale)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

Query= uniprot:B2TBJ9
         (263 letters)



>NCBI__GCF_000013785.1:WP_011911265.1
          Length = 279

 Score =  258 bits (658), Expect = 1e-73
 Identities = 138/259 (53%), Positives = 182/259 (70%), Gaps = 3/259 (1%)

Query: 1   MNATAPVALSVK--NIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLE 58
           M A AP    V+  ++ K +G+  VL+G+ LD  +G+ ++I+G SGSGKST LR L  LE
Sbjct: 16  MAAAAPAQPMVRFASVTKRYGELTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLRVLMTLE 75

Query: 59  TPDDGSVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIE 118
             DDG + + GE L     G G+L P++ R + RVR ++GMVFQ+FNL+ HM  L+N++E
Sbjct: 76  GIDDGLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVME 135

Query: 119 GPMRVQKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLF 178
            P++V   S+ E+ E AE LLA VGL +K  H+PA LSGGQQQRVAIARALAM PKVMLF
Sbjct: 136 APVQVLGLSKREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLF 195

Query: 179 DEPTSALDPELVGEVLRVMRSLAE-EGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGT 237
           DE TSALDPEL GEVL V+R L E    TML+VTH+MGFAR  ++RV F HQG++   G+
Sbjct: 196 DEVTSALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGS 255

Query: 238 PDEVFVECKSDRFRQFVSS 256
           PD +F   + DR R+F+S+
Sbjct: 256 PDALFNNPQEDRTREFLSA 274


Lambda     K      H
   0.318    0.133    0.377 

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: 228
Number of extensions: 9
Number of successful extensions: 2
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: 263
Length of database: 279
Length adjustment: 25
Effective length of query: 238
Effective length of database: 254
Effective search space:    60452
Effective search space used:    60452
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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