GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Pseudomonas simiae WCS417

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate GFF1168 PS417_05935 polyamine ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF2754
         (331 letters)



>FitnessBrowser__WCS417:GFF1168
          Length = 344

 Score =  239 bits (611), Expect = 6e-68
 Identities = 130/274 (47%), Positives = 178/274 (64%), Gaps = 4/274 (1%)

Query: 3   ALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISI 62
           A+Q T+V + FG V+ +  +++ ++DGEF   +GPSG GK+T LR+I+G E  +AG I I
Sbjct: 4   AVQFTHVSRQFGEVKAVDRVSIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIRI 63

Query: 63  GGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLS 122
            G+     PP +R +  VFQ YAL+PH++VR+N+A  LK +   K E   R  EA  M++
Sbjct: 64  HGEEAAGLPPYQRDVNTVFQDYALFPHMNVRDNVAYGLKVKGVGKTERMNRAEEALGMVA 123

Query: 123 LEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQ 182
           L  Y DR+P +LSGGQRQRVA+ RA+V  P++ L DEPL  LD  LR   + E+ +L RQ
Sbjct: 124 LGGYGDRKPVQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQSELKKLQRQ 183

Query: 183 LSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIG-APAMNF 241
           L  + I+VTHDQ EA++++D++ V   GRIEQV TP  LY  PA  FVAEF+G +  +  
Sbjct: 184 LGITFIFVTHDQTEALSMSDRVAVFNKGRIEQVDTPRNLYMKPATSFVAEFVGTSNVIRG 243

Query: 242 VPAQRLGGNPGQFIGIRPEYARISPVGPL-AGEV 274
             AQRLGG    F  IRPE+ R +  GPL  GEV
Sbjct: 244 ELAQRLGGTAQPF-SIRPEHVRFAE-GPLGTGEV 275


Lambda     K      H
   0.320    0.137    0.391 

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: 321
Number of extensions: 15
Number of successful extensions: 1
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: 331
Length of database: 344
Length adjustment: 28
Effective length of query: 303
Effective length of database: 316
Effective search space:    95748
Effective search space used:    95748
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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