GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Pseudomonas fluorescens FW300-N2E3

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 AO353_25885 AO353_25885 sugar ABC transporter permease

Query= TCDB::Q72H67
         (291 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25885
          Length = 308

 Score =  134 bits (337), Expect = 3e-36
 Identities = 99/293 (33%), Positives = 154/293 (52%), Gaps = 15/293 (5%)

Query: 4   LRQVRLA---WILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLF 60
           LR+ RLA   W LV P++ +++L    PL    Y+S  + ++ +     FVGLEN++Y  
Sbjct: 16  LRKSRLANPGWFLVSPSVALLLLWMIVPLGMTLYFSLIRYNLLYPGDNAFVGLENFSYFL 75

Query: 61  QDPDFRQALWNTLKFTVVSVSLETVLGLAI-ALIIHSNFRGRGLVRTAILIPWAIPTVVS 119
            D  F     NTL      + +  V G+ I AL+  S F GRG+VR  ++ P+ I   V 
Sbjct: 76  TDSGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFLGRGIVRVMLISPFFIMPTVG 135

Query: 120 AKMWQWML-NDVYGVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLL 178
           A +W+ ++ + V G++  +    G  +Q V +LA   LL  SII +  W+  PF  L+L+
Sbjct: 136 ALIWKNLIFHPVSGILAAVWKLFG--AQPVDWLAHYPLL--SIIIIVSWQWLPFAILILM 191

Query: 179 AGLQMIPEELYEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSG 238
             +Q + +E  EAA +DGA     FW +TLP L   + V ++  T+  L VF  +F  + 
Sbjct: 192 TAMQSLDQEQKEAARLDGAGPIAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTN 251

Query: 239 VNP--ATRTLA--VYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMRTVGK 287
             P  A+  LA  +YN Q LV F D+G  SA  +  +VI     ++ +R +GK
Sbjct: 252 GGPGYASTNLAYLIYN-QALVQF-DVGMASAGGLIAVVIANIAAIILVRMLGK 302


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: 228
Number of extensions: 12
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: 308
Length adjustment: 27
Effective length of query: 264
Effective length of database: 281
Effective search space:    74184
Effective search space used:    74184
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