GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Pseudomonas stutzeri RCH2

Align ABC transporter permease (characterized, see rationale)
to candidate GFF561 Psest_0566 urea ABC transporter, permease protein UrtB

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__psRCH2:GFF561
          Length = 523

 Score =  114 bits (286), Expect = 4e-30
 Identities = 94/308 (30%), Positives = 148/308 (48%), Gaps = 15/308 (4%)

Query: 4   LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63
           LL Q  +GL LGS+  L ALG  + +G++ +IN AHGE+LM+GA T++    +M    P 
Sbjct: 227 LLGQAFSGLSLGSILLLAALGLAITFGLLGVINMAHGEMLMLGAYTTYMVQVLMARLAPE 286

Query: 64  APGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMS-ILLQTLAMII 122
           A  +   L+A  +A  V A +   +E+   R L   P L  L+   G+S IL+Q + ++ 
Sbjct: 287 ALAF-YPLVALPVAFFVTAAIGMALERTVIRHLYGRP-LETLLATWGISLILIQLVRVLF 344

Query: 123 WKPNYKPYPTMLPSSPFEIGGAFITP-TQILILGVTAVALASLVYLVNHTNLGRAMRATA 181
              N +       S   ++    + P  +++I+G     +     L+N T LG  +RA  
Sbjct: 345 GAQNVEVANPAWLSGGLQVLPNLVLPYNRMVIIGFALFVVLLTWLLLNKTRLGLNVRAVT 404

Query: 182 ENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVF 241
           +N  +A+  GV    +    F +G+ +A + G+   S  G     +G    + +F   V 
Sbjct: 405 QNRNMAACCGVPTGRIDMLAFGLGSGIAGLGGVA-LSQIGNVGPDLGQSYIIDSFLVVVL 463

Query: 242 GGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL- 300
           GG+G LAG++     LG+   I    IG + G +L      I A I+L I    RP GL 
Sbjct: 464 GGVGQLAGSIFAAFGLGIANKILEPQIGAVLGKIL------ILALIILFI--QKRPQGLF 515

Query: 301 -LGERVAD 307
            L  RV D
Sbjct: 516 ALKGRVID 523


Lambda     K      H
   0.327    0.142    0.419 

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: 294
Number of extensions: 11
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: 309
Length of database: 523
Length adjustment: 31
Effective length of query: 278
Effective length of database: 492
Effective search space:   136776
Effective search space used:   136776
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 (21.7 bits)
S2: 50 (23.9 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