GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araH in Halomonas xinjiangensis TRM 0175

Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate WP_052384031.1 JH15_RS10185 ABC transporter permease

Query= CharProtDB::CH_014278
         (328 letters)



>NCBI__GCF_000759345.1:WP_052384031.1
          Length = 331

 Score =  183 bits (465), Expect = 4e-51
 Identities = 100/294 (34%), Positives = 165/294 (56%), Gaps = 5/294 (1%)

Query: 28  LVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVASVIAC 87
           L+   +LF+  +     F    N+  +   +S +G++A GM F + +G  DLSV S++A 
Sbjct: 31  LLALLILFVLSSFASEYFLNARNITNVLRQVSYTGIIAIGMTFVIIAGGIDLSVGSMVAL 90

Query: 88  AGVTTAVVINLT----ESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIVR 143
            GV    V+N      +++ +G+ A ++ G L GL NG ++ + ++ A + TLATM I R
Sbjct: 91  VGVLLLYVVNAIADPIQAVLLGMLAAVVAGSLFGLFNGLLVTRGRMAAFVVTLATMSIFR 150

Query: 144 GLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLAI 203
            LA  ++D   V   +  F ++G    FG+P P+W      +   +LL  T FGR+  A+
Sbjct: 151 SLALYLTDAGEVTTRNPLFSSIGGGYLFGIPIPVWAFFGLALAAHVLLAHTPFGRHVCAV 210

Query: 204 GGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPM-TSIGYELIVISAC 262
           G N + AR +G+ V R  +  F+++G+   ++ I+L+SR+ S  P      YEL  I+A 
Sbjct: 211 GANSQVARYSGIRVERVVLSTFIIAGICVGLSAIMLSSRLNSVSPSDAGYFYELDAIAAV 270

Query: 263 VLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVI 316
           V+GG +L GG G +   V G LILG + N +NL  +SP+ Q +V+G ++L AV+
Sbjct: 271 VIGGTALSGGRGSVWGTVIGALILGIINNMLNLTGVSPYLQGLVKGAVILLAVL 324


Lambda     K      H
   0.327    0.141    0.414 

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: 300
Number of extensions: 23
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: 328
Length of database: 331
Length adjustment: 28
Effective length of query: 300
Effective length of database: 303
Effective search space:    90900
Effective search space used:    90900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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