GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Streptomyces kebangsaanensis SUK12

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_079189056.1 RH94_RS16015 ABC transporter ATP-binding protein

Query= CharProtDB::CH_088321
         (255 letters)



>NCBI__GCF_001906585.1:WP_079189056.1
          Length = 305

 Score =  179 bits (454), Expect = 6e-50
 Identities = 100/249 (40%), Positives = 144/249 (57%), Gaps = 3/249 (1%)

Query: 2   TLRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFL 61
           TL  + ++V+     +++ VSL++  G++  L+GPNG GKSTLL    R L P SG V L
Sbjct: 37  TLDIDGVSVTVDGRTLVDRVSLTVSPGEVVGLVGPNGAGKSTLLRTVYRALRPTSGRVLL 96

Query: 62  GDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNV 121
               +  +  ++LAR L+ + Q H     +TV E+V+ GR P    +    A D A V  
Sbjct: 97  DGADVWRMPGKRLARHLAAVLQEHAGDFELTVYEVVAMGRTPHKRPFAGDDAGDRAVVTA 156

Query: 122 AMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLM 181
           A+ +  +  LA      LSGG++QR  +A  LAQ    ++LDEPT +LD+ HQ+D +RL 
Sbjct: 157 ALTELDVAGLADAPFDRLSGGEKQRVLIARALAQRAGTMVLDEPTNHLDLRHQLDALRL- 215

Query: 182 GELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEI 241
             +R  G T V  LHDLN A+ +CD+L V+  G V+A GTP +V+TP LL  V+ VEA +
Sbjct: 216 --VRRLGVTAVVALHDLNLAASFCDRLCVLETGRVVAHGTPRDVLTPALLAEVYRVEAYV 273

Query: 242 HPEPVSGRP 250
              P SG P
Sbjct: 274 TEHPRSGAP 282


Lambda     K      H
   0.320    0.134    0.393 

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: 236
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: 255
Length of database: 305
Length adjustment: 26
Effective length of query: 229
Effective length of database: 279
Effective search space:    63891
Effective search space used:    63891
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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