GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Pseudomonas stutzeri RCH2

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit

Query= uniprot:D4GP38
         (383 letters)



>FitnessBrowser__psRCH2:GFF3591
          Length = 369

 Score =  221 bits (564), Expect = 2e-62
 Identities = 113/224 (50%), Positives = 155/224 (69%), Gaps = 1/224 (0%)

Query: 14  GDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMNYRVPQ 73
           G+++ V DL+LDI   EFL L+GPSG GK+T+L MLAG ETPT+G+I + G  +N   P 
Sbjct: 22  GESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLDGRAINNVPPH 81

Query: 74  NRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRKPD 133
            RD+ MVFQ+YAL+PHMTV +N+ F L    G    +  ERV      + +    +R P 
Sbjct: 82  KRDMGMVFQNYALFPHMTVSENLAFPLSVR-GMAKPDIKERVKRALAMVQLEGFRNRYPA 140

Query: 134 ELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYVTH 193
           +LSGGQQQRVAL RA+V +P++ LMDEPL  LD +LR +M+ E+++L ++L VT VYVTH
Sbjct: 141 QLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHERLGVTVVYVTH 200

Query: 194 NQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGE 237
           +Q EA+TM+DR+AV   G++QQ+  P   Y +P N FVA F+GE
Sbjct: 201 DQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLGE 244


Lambda     K      H
   0.317    0.135    0.386 

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: 345
Number of extensions: 7
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: 383
Length of database: 369
Length adjustment: 30
Effective length of query: 353
Effective length of database: 339
Effective search space:   119667
Effective search space used:   119667
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: 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 (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