GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Pseudomonas simiae WCS417

Align ABC transporter for L-Arginine, putative ATPase component (characterized)
to candidate GFF1259 PS417_06395 amino acid transporter

Query= reanno::BFirm:BPHYT_RS07685
         (263 letters)



>FitnessBrowser__WCS417:GFF1259
          Length = 254

 Score =  361 bits (927), Expect = e-105
 Identities = 183/253 (72%), Positives = 212/253 (83%), Gaps = 1/253 (0%)

Query: 11  KLAVQDIHKRYGDNEVLKGVSLNANKGDVISIIGASGSGKSTFLRCINFLERPNAGQIVV 70
           KL V+ +HK YGDNEVLKGVSL A  GDVIS+IGASGSGKSTFLRCINFLE PN G + +
Sbjct: 3   KLTVEGLHKSYGDNEVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLETPNDGAMTL 62

Query: 71  DGEMVKTKTDRAGNLEVADHKQLQRIRTKLAMVFQHFNLWAHMNVLENIVEAPIHVLGLK 130
           DG+ ++  +DR G + VAD  +LQR+RT+LAMVFQHFNLW+HM+VLENI  AP  VLG  
Sbjct: 63  DGQPIRMVSDRHG-MRVADDAELQRLRTRLAMVFQHFNLWSHMSVLENITMAPRRVLGCS 121

Query: 131 RKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMNPDVMLFDEPTSALD 190
           +K+AEDRAR YL+KVGL  R+  QYP+ LSGGQQQRVAIARALAM P+VMLFDEPTSALD
Sbjct: 122 KKDAEDRARRYLDKVGLPARVADQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALD 181

Query: 191 PELVGEVLKVMQKLAEEGRTMIVVTHEMGFARNVSNHVMFLHQGRTEEEGLPAEVLSAPR 250
           PELVGEVLKV+Q LAEEGRTMI+VTHEM FAR VS+ V+FLHQG  EE+G P EVL  P+
Sbjct: 182 PELVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSSQVLFLHQGLVEEQGPPEEVLGNPK 241

Query: 251 SERLKQFLSGSLK 263
           SERL+QFLSG+LK
Sbjct: 242 SERLQQFLSGNLK 254


Lambda     K      H
   0.318    0.133    0.374 

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: 256
Number of extensions: 5
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: 263
Length of database: 254
Length adjustment: 24
Effective length of query: 239
Effective length of database: 230
Effective search space:    54970
Effective search space used:    54970
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 (21.7 bits)
S2: 47 (22.7 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