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_043529964.1 JH15_RS10345 L-arabinose ABC transporter permease AraH

Query= CharProtDB::CH_014278
         (328 letters)



>NCBI__GCF_000759345.1:WP_043529964.1
          Length = 338

 Score =  322 bits (825), Expect = 8e-93
 Identities = 168/304 (55%), Positives = 218/304 (71%)

Query: 23  DQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVA 82
           D  G++ +F +LFIA A+F+P+F T  NM GL L+I++ G +A  M+  LA G+ DLSVA
Sbjct: 33  DTSGLIGIFLILFIALALFIPDFLTGRNMVGLLLSITVIGTIATTMMMVLALGEVDLSVA 92

Query: 83  SVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIV 142
           S++A AGV  AVV + + S++IGV  G+  G   G  NGFV+AK  IN+LI TLA M+ V
Sbjct: 93  SIVAFAGVVAAVVTSTSGSVFIGVVGGVAAGGAVGAFNGFVVAKFGINSLIATLAAMEFV 152

Query: 143 RGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLA 202
           RGLAYI S G AV I    FF LG A++ GL  P+W  +AC +IFG+LLN T+FGRN LA
Sbjct: 153 RGLAYITSGGDAVMITVPGFFDLGSASFLGLTLPVWTMIACFVIFGILLNMTSFGRNVLA 212

Query: 203 IGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISAC 262
            GGN EAA LAGV V R KII+F L G+V+ IAG++L SRM  G P T++G EL VISAC
Sbjct: 213 TGGNAEAAALAGVNVKRLKIIVFGLQGVVAGIAGVLLTSRMGLGDPNTALGLELAVISAC 272

Query: 263 VLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYKQ 322
           VLGGV+L GG+  I+ V+ G+LI+G V+NAM LLN+  F QY+VRG ILL AV+FDR+KQ
Sbjct: 273 VLGGVALSGGVATITGVLVGVLIMGCVQNAMGLLNVPTFYQYLVRGAILLLAVMFDRWKQ 332

Query: 323 KAKR 326
             ++
Sbjct: 333 TRRQ 336


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: 394
Number of extensions: 21
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: 328
Length of database: 338
Length adjustment: 28
Effective length of query: 300
Effective length of database: 310
Effective search space:    93000
Effective search space used:    93000
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