GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Pseudomonas simiae WCS417

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF2490 PS417_12700 ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>FitnessBrowser__WCS417:GFF2490
          Length = 367

 Score =  261 bits (668), Expect = 2e-74
 Identities = 156/375 (41%), Positives = 217/375 (57%), Gaps = 24/375 (6%)

Query: 1   MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60
           M  +++ +L K F     +  + L+++D+EF+V VGPSGCGKST LR++AGLE  + G I
Sbjct: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60

Query: 61  YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120
            + G  +    P  RD+AMVFQ YALYPHM+VR+N+ F L+   G      + +V E A 
Sbjct: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLA-GVDKKLVESKVSEAAR 119

Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180
            L +  LL+RKP +LSGGQ+QRVA+GRAIVR+P++FL DEPLSNLDA LR +MR EL  L
Sbjct: 120 ILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARL 179

Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240
             +L  T +YVTH+Q EAMT+AD++ V++ G ++QV SP E YH+P NLFVA F+G P +
Sbjct: 180 HKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKM 239

Query: 241 NLVRG--TRSESTF------VGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPD 292
             ++G  TR ES         G   + PL    + SV       LG+RPE +E+A     
Sbjct: 240 GFLKGKVTRVESQSCEVQLDAGTLINLPLSGATL-SVGSA--VTLGIRPEHLEIASPG-- 294

Query: 293 DAALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIP 352
                   L +   V E  G     H+      +  + L     G      G+ + + + 
Sbjct: 295 -----QTTLTVTADVGERLGSDTFCHVI----TANGEPLTMRIRGDMASQYGETLHLHLD 345

Query: 353 PDKIHLFDAETGTAV 367
           P   HLFD + G AV
Sbjct: 346 PAHCHLFDTD-GVAV 359


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: 319
Number of extensions: 11
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: 383
Length of database: 367
Length adjustment: 30
Effective length of query: 353
Effective length of database: 337
Effective search space:   118961
Effective search space used:   118961
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