GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate AO353_07265 AO353_07265 spermidine/putrescine ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc04256
         (361 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_07265
          Length = 374

 Score =  217 bits (553), Expect = 4e-61
 Identities = 126/289 (43%), Positives = 175/289 (60%), Gaps = 4/289 (1%)

Query: 4   VSVRDLSLNF-GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFI 62
           VS R +  ++ G   ++  LNL+I  GEFL LLG SG GK+T L  +AG    + G+I +
Sbjct: 15  VSFRGVQKSYDGENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILL 74

Query: 63  KDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQ 122
             R +    P  R IGMVFQ+YAL+P MTV +NL+F L V  +  +++  RVKR   ++Q
Sbjct: 75  AGRAINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRGLNKSDVSDRVKRVLSMVQ 134

Query: 123 IQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQS 182
           +    +R P++LSGGQ+QRVA+ RALV +  + L DEPL  LD +LR  +++EIK LHQ 
Sbjct: 135 LDAFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQR 194

Query: 183 LKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFF 242
           L  T++YVTHDQ EALT++DR+AV   G IQQ+A P  +Y  P+N FVA FIG    N  
Sbjct: 195 LGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAPPRELYEKPKNTFVANFIG--ENNRL 252

Query: 243 RGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVD 291
            G +    G   V   G    V A   +   + G+ V L +RPE V ++
Sbjct: 253 NGRLHSHTGDRCVVELGRGEKVEALAVNVG-KTGEPVTLSIRPERVSLN 300


Lambda     K      H
   0.320    0.137    0.392 

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: 400
Number of extensions: 15
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: 361
Length of database: 374
Length adjustment: 30
Effective length of query: 331
Effective length of database: 344
Effective search space:   113864
Effective search space used:   113864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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