GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livH in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter permease (characterized, see rationale)
to candidate Pf6N2E2_3548 Urea ABC transporter, permease protein UrtB

Query= uniprot:A0A165KC95
         (309 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3548 Urea ABC transporter,
           permease protein UrtB
          Length = 500

 Score =  112 bits (280), Expect = 2e-29
 Identities = 92/308 (29%), Positives = 149/308 (48%), Gaps = 15/308 (4%)

Query: 4   LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63
           LL Q  +G+ LGS+  L ALG  + +G++ +IN AHGE+LM+GA +++    + Q   P 
Sbjct: 204 LLGQAFSGMSLGSILLLAALGLAITFGLLGVINMAHGEMLMLGAYSTYVVQMLFQRFAPN 263

Query: 64  APGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSI-LLQTLAMII 122
           A  +   L+A  +A  + A +   +E+   R L   P L  L+   G+S+ L+Q + ++ 
Sbjct: 264 AIEF-YPLIALPVAFFITAAIGMALERTVIRHLYGRP-LETLLATWGISLMLIQLVRLVF 321

Query: 123 WKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVY-LVNHTNLGRAMRATA 181
              N +       S   ++    + P   +++   A+ +  L + L+N T LG  +RA  
Sbjct: 322 GAQNVEVANPAWLSGGIQVLPNLVLPYNRIVIIAFALFVVVLTWLLLNKTRLGLNVRAVT 381

Query: 182 ENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVF 241
           +N  +A+  GV    V    F +G+ +A + G+   S  G     +G    + +F   V 
Sbjct: 382 QNRNMAACCGVPTGRVDMLAFGLGSGIAGLGGVA-LSQIGNVGPDLGQSYIIDSFLVVVL 440

Query: 242 GGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL- 300
           GG+G LAG+V     LG+   I    IG + G +L      I A I+L I    RP GL 
Sbjct: 441 GGVGQLAGSVFAAFGLGIANKILEPQIGAVLGKIL------ILALIILFI--QKRPQGLF 492

Query: 301 -LGERVAD 307
            L  RV D
Sbjct: 493 ALKGRVID 500


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: 292
Number of extensions: 9
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: 309
Length of database: 500
Length adjustment: 31
Effective length of query: 278
Effective length of database: 469
Effective search space:   130382
Effective search space used:   130382
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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