GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araH in Sinorhizobium meliloti 1021

Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate SM_b20506 SM_b20506 L-arabinose transporter permease

Query= CharProtDB::CH_014278
         (328 letters)



>FitnessBrowser__Smeli:SM_b20506
          Length = 317

 Score =  330 bits (845), Expect = 4e-95
 Identities = 173/303 (57%), Positives = 214/303 (70%)

Query: 24  QYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVAS 83
           + G+LV+FA  F+  A+ VPNF T  NM GL  ++   G+VAC M+FCLAS DFDLSV S
Sbjct: 12  EQGLLVIFAAAFVVVALTVPNFLTERNMLGLLQSVVTIGVVACTMMFCLASRDFDLSVGS 71

Query: 84  VIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIVR 143
            +A +G+   +  N T S+ +G+ A L  G + GL NG VIA+ +INALITTLATMQIVR
Sbjct: 72  TVAFSGMVAVMASNATGSIVLGLLAALACGGIVGLANGIVIARFRINALITTLATMQIVR 131

Query: 144 GLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLAI 203
           G A I SDG+AVGI D  F+ L  + +  +P PIW+     I+FG LLN+T FG+NTLAI
Sbjct: 132 GFALIASDGRAVGINDPVFYQLSLSKFLTVPTPIWVMALFFIVFGFLLNRTVFGKNTLAI 191

Query: 204 GGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISACV 263
           GGN EA+RLAGV V R +I IF L GLV A+AG++LASR+TSGQP  + G EL VISACV
Sbjct: 192 GGNPEASRLAGVDVARMRIWIFALQGLVCAVAGVLLASRITSGQPNAATGLELSVISACV 251

Query: 264 LGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYKQK 323
           LGGVSL GG   ++ VV G+LI+G  EN MNLLNI  F QYVVRGLILL AV+ D  +  
Sbjct: 252 LGGVSLAGGRATMTGVVVGVLIMGIAENVMNLLNIQAFYQYVVRGLILLIAVLLDNMRSV 311

Query: 324 AKR 326
           A R
Sbjct: 312 AGR 314


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: 402
Number of extensions: 19
Number of successful extensions: 1
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: 317
Length adjustment: 28
Effective length of query: 300
Effective length of database: 289
Effective search space:    86700
Effective search space used:    86700
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: 48 (23.1 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