GapMind for catabolism of small carbon sources

 

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

Align AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__ANA3:7026050
          Length = 376

 Score =  148 bits (374), Expect = 1e-40
 Identities = 86/247 (34%), Positives = 137/247 (55%), Gaps = 14/247 (5%)

Query: 16  VAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIV 75
           +++ + N++K +G F  L  +NL +  GE I + GPSGSGK+T++R I  LE    G+I 
Sbjct: 1   MSIRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIH 60

Query: 76  VDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVA-- 133
               ++T    ++    R VG VFQ++ LF H+T+ +N       +  +PKKQ    A  
Sbjct: 61  FGNRDVT----QVHVRDRRVGFVFQNYALFRHMTVADNVAFG---LEVIPKKQRPSKAEI 113

Query: 134 ----MHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIK 189
                H L+ V++   A +YP QLSGGQ+QR+A+AR+L   P+++L DEP  ALD ++ K
Sbjct: 114 QKRVSHLLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRK 173

Query: 190 EVLDTMVGLAEE-GMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERT 248
           E+   +  L +E   T + VTH+   A ++++RV+ M  G I + N P   +  P     
Sbjct: 174 ELRRWLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFV 233

Query: 249 KLFLSQI 255
             FL  +
Sbjct: 234 FDFLGNV 240


Lambda     K      H
   0.321    0.135    0.394 

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: 215
Number of extensions: 9
Number of successful extensions: 4
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: 257
Length of database: 376
Length adjustment: 27
Effective length of query: 230
Effective length of database: 349
Effective search space:    80270
Effective search space used:    80270
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 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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