GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylHsa in Pantoea rwandensis LMG 26275

Align Xylose/arabinose import permease protein XylH (characterized, see rationale)
to candidate WP_084931761.1 HA51_RS02830 hypothetical protein

Query= uniprot:Q4J711
         (356 letters)



>NCBI__GCF_002095475.1:WP_084931761.1
          Length = 323

 Score =  147 bits (370), Expect = 5e-40
 Identities = 103/304 (33%), Positives = 160/304 (52%), Gaps = 20/304 (6%)

Query: 19  VIIALFFYFENSAYFSSNNITTIFQYLAEIGIIAIGEAMLMLCGEIDLS--PPALANFVP 76
           +II + F F +  +F+  N+  I Q  +   +IA+G  ++++ G IDLS  P A  + V 
Sbjct: 31  LIIVVTFSFLSPVFFTVPNLLNILQQSSINALIALGMTLVIISGGIDLSVGPTAALSAVL 90

Query: 77  LITLTIYNSIYQAISPTPAIVVSILLSLGLASLIGLMNGLITTKAKVNSLITTVGTLFLF 136
             TL +      A  P P   V+IL +LG+ +L G+ +G++   A +   I T+G L LF
Sbjct: 91  GATLMV------AGVPVP---VAILATLGIGALCGVFSGMLVAYAGLQPFIVTLGGLSLF 141

Query: 137 NGIALIYSGGYPE---SFPYFRFLGGTVSILPVPFIWSLGALVFLILLLHYTKIGVWTIA 193
             IALIY+GG P       +   +   V  +P P I      + L L+++ T +G + +A
Sbjct: 142 RAIALIYTGGNPVFGIPMEFRSIINSDVFGIPTPIIIVAVIALVLWLVMNKTPLGEYILA 201

Query: 194 AGSNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSRVLTIGATNFTADVV--LEGI 251
            G N   A   GVPV R K+  FII   + +L  +I   R   +GA   T   +  L+ I
Sbjct: 202 VGGNEEAARVAGVPVKRTKVTVFIISGTLASLASLILIGR---LGAAEPTIGNLWELDAI 258

Query: 252 AAAVIGGTSLVGGKGSLVGAFLGSVFISELLNGFNILGINAYEFDAILGGAIVVVMVLSY 311
           AAA IGG SL+GGKGS+VG  +G++ +  L NG  +L I A+ +  +  G I+++ +L  
Sbjct: 259 AAAAIGGASLMGGKGSIVGTIIGAIILGALRNGLTLLNIQAF-YQLLATGLIIIIAMLID 317

Query: 312 YAKR 315
            A R
Sbjct: 318 RATR 321


Lambda     K      H
   0.325    0.143    0.404 

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: 354
Number of extensions: 33
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: 356
Length of database: 323
Length adjustment: 28
Effective length of query: 328
Effective length of database: 295
Effective search space:    96760
Effective search space used:    96760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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