GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Shewanella sp. ANA-3

Align Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized)
to candidate 7026373 Shewana3_3515 ABC transporter related (RefSeq)

Query= SwissProt::P0AAF6
         (242 letters)



>FitnessBrowser__ANA3:7026373
          Length = 349

 Score =  142 bits (359), Expect = 7e-39
 Identities = 88/241 (36%), Positives = 137/241 (56%), Gaps = 9/241 (3%)

Query: 2   SIQLNGINCFYGAHQALFDITLDCPQGETLVLLGPSGAGKSSLLRVLNLLEMPRSGTLNI 61
           ++ L+ ++  Y   Q L  + L   QGE L LLGPSG GK++LLR +  L+    G + I
Sbjct: 4   TLNLHQVHSDYQGQQVLKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQI 63

Query: 62  AGNHFDFTKTPSDKAIRDLRRNVGMVFQQYNLWPHLTVQQNLIEAPCRVLGLSKDQALAR 121
            G     T + + + +   +R +GM+FQ Y L+PHLTV +N++     V  L+  Q  AR
Sbjct: 64  NGK----TVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFG---VAKLTPAQRKAR 116

Query: 122 AEKLLERLRLKPYSDRYPLHLSGGQQQRVAIARALMMEPQVLLFDEPTAALDPEITAQIV 181
            + +L  ++L+  + RYP  LSGGQQQRV+IARAL  EPQ+LL DEP + +D ++   ++
Sbjct: 117 LDDMLALVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMM 176

Query: 182 SIIRE-LAETNITQVIVTHEVEVARKTASRVVYMENGHIVEQGDA-SCFTEPQTEAFKNY 239
           + IR  L + N++ V VTH  + A   A  +     G IV+ G A + +  P +    ++
Sbjct: 177 AEIRSILKQRNVSAVFVTHSKDEAFVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADF 236

Query: 240 L 240
           L
Sbjct: 237 L 237


Lambda     K      H
   0.320    0.135    0.391 

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: 181
Number of extensions: 6
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: 242
Length of database: 349
Length adjustment: 26
Effective length of query: 216
Effective length of database: 323
Effective search space:    69768
Effective search space used:    69768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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