GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Pseudomonas simiae WCS417

Align Maltose transport system permease protein malF aka TT_C1628, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate GFF2492 PS417_12710 sugar ABC transporter permease

Query= TCDB::Q72H67
         (291 letters)



>FitnessBrowser__WCS417:GFF2492
          Length = 297

 Score =  134 bits (338), Expect = 2e-36
 Identities = 96/283 (33%), Positives = 148/283 (52%), Gaps = 12/283 (4%)

Query: 11  WILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPDFRQALW 70
           W LV P++ +++L    PL    Y+S  + ++ +    EFVGLEN+ Y   D  F     
Sbjct: 15  WFLVSPSVALLLLWMIVPLGMTLYFSLIRYNLLYPGENEFVGLENFTYFITDSGFLPGAT 74

Query: 71  NTLKFTVVSVSLETVLGLAI-ALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMWQWML-N 128
           NTL      + +  V G+ I AL+  S F GRGLVR  ++ P+ I   V A +W+ ++ +
Sbjct: 75  NTLLLVGSVLLISVVFGVLISALLEASEFLGRGLVRVLLISPFFIMPTVGALIWKNLIFH 134

Query: 129 DVYGVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQMIPEEL 188
            V G++  +    G  ++ V +LA   LL  SII +  W+  PF  LLL+  +Q + +E 
Sbjct: 135 PVSGILAAVWKFFG--AEPVDWLAHYPLL--SIIIIVSWQWLPFAILLLMTAMQSLDQEQ 190

Query: 189 YEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNP--ATRTL 246
            EAA +DGA     FW +TLP L   + V ++  T+  L VF  +F  +   P  A+  L
Sbjct: 191 KEAARLDGAGAIAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGPGYASTNL 250

Query: 247 A--VYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMRTVGK 287
           A  +YN Q LV F D+G  SA  +  +VI     ++ +R +GK
Sbjct: 251 AYLIYN-QALVQF-DVGMASAGGLIAVVIANIAAIILVRMIGK 291


Lambda     K      H
   0.329    0.142    0.433 

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: 226
Number of extensions: 13
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: 291
Length of database: 297
Length adjustment: 26
Effective length of query: 265
Effective length of database: 271
Effective search space:    71815
Effective search space used:    71815
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 (21.8 bits)
S2: 48 (23.1 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