GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natF in Pseudomonas stutzeri RCH2

Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate GFF3104 Psest_3163 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain

Query= uniprot:Q31RP1
         (359 letters)



>lcl|FitnessBrowser__psRCH2:GFF3104 Psest_3163 ABC-type amino acid
           transport/signal transduction systems, periplasmic
           component/domain
          Length = 342

 Score =  327 bits (837), Expect = 4e-94
 Identities = 158/321 (49%), Positives = 219/321 (68%), Gaps = 3/321 (0%)

Query: 40  ESNSRLNQVQARGKLLCGVEGRLPGFSFLDSQGNYSGLDVDICKAIAAALFNDPKAIEYR 99
           ++ + L+ VQ +G + CG+   LPGFSF D++G Y G+DVDIC+A+AAA+F D   ++Y 
Sbjct: 24  QAGATLDAVQKKGFVQCGISDGLPGFSFADAKGKYQGIDVDICRAVAAAVFGDASKVKYS 83

Query: 100 SLDSVERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAPTTFYDGQGLMVRRNSGIQS 159
            L + ERF AL SGEVD+LSRNTTWT SRDA  G  L F   T+YDGQG +V +  G+ S
Sbjct: 84  PLTAKERFTALQSGEVDVLSRNTTWTSSRDAAMG--LNFTGVTYYDGQGFLVNKELGVSS 141

Query: 160 LQDFQGKSICVETGTTSELNLADTMRELGVQYQEIKFPNSDANYAAYAQGRCEGVTSDRS 219
            ++  G ++C++ GTT+ELNL+D  R  G +Y  I +  SD +  +   GRC+ +TSD+S
Sbjct: 142 AKELDGATVCIQAGTTTELNLSDYFRANGHKYTPITYDTSDESAKSLESGRCDVLTSDQS 201

Query: 220 QLAARRTTLSDADQHQLLDAVISKEPLSPATLNNDSPWFDVVKWVVNATIQAEEFGITQA 279
           QL A+R  L+    + +L  VISKEPL PA    D  WFD+V+W + A + AEE G+T A
Sbjct: 202 QLYAQRIKLAKPADYVVLPEVISKEPLGPAVRQGDEEWFDIVRWTLFAMLNAEELGVTSA 261

Query: 280 NIDQF-KTSKNPEIRRFLGLEGELGQQLGLSNDFAYRAIKAVGNYGEIYERNVGQQSPLK 338
           N+++  K++KNP++ R LG EGE G+ L L  D+A + +K VGNYGEI++RNVG  S LK
Sbjct: 262 NVEEMAKSTKNPDVARLLGAEGEYGKDLKLPKDWAVQIVKQVGNYGEIFDRNVGAGSELK 321

Query: 339 LNRGLNQLYKNGGLLYSPPFR 359
           + RGLN L+ NGGL Y+PP R
Sbjct: 322 IERGLNALWNNGGLQYAPPVR 342


Lambda     K      H
   0.317    0.134    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: 319
Number of extensions: 16
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: 359
Length of database: 342
Length adjustment: 29
Effective length of query: 330
Effective length of database: 313
Effective search space:   103290
Effective search space used:   103290
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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