GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_1962 Various polyols ABC transporter, permease component 1

Query= TCDB::Q72H67
         (291 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1962
          Length = 280

 Score =  124 bits (312), Expect = 2e-33
 Identities = 94/280 (33%), Positives = 144/280 (51%), Gaps = 12/280 (4%)

Query: 14  VLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPDFRQALWNTL 73
           V P++ +++L    PLA   Y+S  + ++      EFVGLEN+AY   D  F     NTL
Sbjct: 1   VSPSVALLLLWMIVPLAMTVYFSVIRYNLLNPGENEFVGLENFAYFVTDSGFLPGALNTL 60

Query: 74  KFTVVSVSLETVLGLAIALIIH-SNFRGRGLVRTAILIPWAI-PTVVSAKMWQWMLNDVY 131
                 + +  + G+ IA ++  S F GRG+VR  ++ P+ I PTV S      + + V 
Sbjct: 61  ILVGSVLLISVIFGVLIAALLEASEFFGRGIVRVLLISPFFIMPTVGSLIFKNLIFHPVS 120

Query: 132 GVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQMIPEELYEA 191
           G++  +    G  +Q V +LA   L   SII +  W+  PF  LLL+  +Q + +E  EA
Sbjct: 121 GILAAVWKFFG--AQPVDWLAHYPLF--SIIVIVSWQWLPFAILLLMTAMQSLDQEQKEA 176

Query: 192 ASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNP--ATRTLA-- 247
           A +DGA     FW +TLP L   + V ++  T+  L VF  +F  +   P  A+  LA  
Sbjct: 177 ARLDGAGALAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGPGFASTNLAYL 236

Query: 248 VYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMRTVGK 287
           +YN Q LV F D+G  SA  +  +VI     ++ +R +GK
Sbjct: 237 IYN-QALVQF-DVGMASAGGLIAVVIANIAAIVLVRMIGK 274


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: 203
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: 280
Length adjustment: 26
Effective length of query: 265
Effective length of database: 254
Effective search space:    67310
Effective search space used:    67310
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: 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