GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF3104
          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 (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