GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araH in Paraburkholderia bryophila 376MFSha3.1

Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family

Query= CharProtDB::CH_014278
         (328 letters)



>FitnessBrowser__Burk376:H281DRAFT_02703
          Length = 333

 Score =  201 bits (510), Expect = 3e-56
 Identities = 115/309 (37%), Positives = 178/309 (57%), Gaps = 8/309 (2%)

Query: 26  GMLVVFAVLFIAC---AIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVA 82
           G+  +FA L I C   +I  P F T   +  + + +S+ G+ A G  F + +   DLSV 
Sbjct: 25  GIGPLFAALVIICIALSIASPEFLTTSTLTNIMVQVSVVGIAAVGGTFVIITSGIDLSVG 84

Query: 83  SVIACAGVTTAVVI--NLTESLWIGVA---AGLLLGVLCGLVNGFVIAKLKINALITTLA 137
           S++A  G+  A V+  +   ++ +G+A   A L +G   G +NG  +A L++   I TLA
Sbjct: 85  SLVALTGMVAATVMAGSSPGAIGLGIAGLCAALAVGAAAGALNGLAVAWLRLVPFIVTLA 144

Query: 138 TMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFG 197
            M + RGL   ISDG+       +F A G     GLP P+ + +   +I  +LL KTTFG
Sbjct: 145 MMAMARGLTLAISDGRTKFDFPNAFTAFGAKTVAGLPMPMIVMLVIFVIGHVLLRKTTFG 204

Query: 198 RNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELI 257
               A+GGN+EAARLAG+PV R   + ++L+G+ +AIAGI+LA R+ S  P  + G EL 
Sbjct: 205 HQVFAVGGNQEAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGRLNSALPSAANGLELQ 264

Query: 258 VISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIF 317
           VI+A V+GG SL GG G I     G++++G +   ++LL ++PF    ++G ++ AAV+ 
Sbjct: 265 VIAAVVIGGTSLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFWTQFIQGGVIFAAVLL 324

Query: 318 DRYKQKAKR 326
           D   Q+ K+
Sbjct: 325 DALSQRRKQ 333


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: 345
Number of extensions: 16
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: 333
Length adjustment: 28
Effective length of query: 300
Effective length of database: 305
Effective search space:    91500
Effective search space used:    91500
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 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