GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17595 in Pseudomonas simiae WCS417

Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate GFF4244 PS417_21740 ABC transporter

Query= uniprot:A0A1N7UBU2
         (233 letters)



>FitnessBrowser__WCS417:GFF4244
          Length = 229

 Score =  230 bits (587), Expect = 2e-65
 Identities = 111/224 (49%), Positives = 159/224 (70%), Gaps = 1/224 (0%)

Query: 7   LHGYGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPD 66
           L GYG ++  GAW+TL+LA  ++AL++ LGLI  A +LS  +WL     LY+T+IR +PD
Sbjct: 2   LKGYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPVRWLAWLGDLYSTVIRGIPD 61

Query: 67  LVLILLIFYSLQLWLNDLSEVFGWD-YFEIDPFTAGVITLGFIYGAYFTENFRGAILSVP 125
           LVLILLIFY  Q  LN ++ + G+D Y +++P  AG+ TLGFI+GAY +E FRGA +++P
Sbjct: 62  LVLILLIFYGGQDLLNRVAPMLGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIP 121

Query: 126 VGQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAA 185
            GQ EA  AYG+S +Q F  V+ PQ++R A+PG  NNWLVL K+TAL+S++GL D++  A
Sbjct: 122 KGQAEAGLAYGMSSFQVFFRVMVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKA 181

Query: 186 QNAGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLGIK 229
           + A   T EP  F +    MYLVIT++S   L+ LE+RY++G++
Sbjct: 182 KQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVR 225


Lambda     K      H
   0.327    0.141    0.428 

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: 194
Number of extensions: 10
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: 233
Length of database: 229
Length adjustment: 23
Effective length of query: 210
Effective length of database: 206
Effective search space:    43260
Effective search space used:    43260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 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