GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Marinomonas arctica 328

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 WP_111607903.1 DK187_RS13615 ATP-binding cassette domain-containing protein

Query= TCDB::Q52815
         (257 letters)



>NCBI__GCF_003259225.1:WP_111607903.1
          Length = 255

 Score =  254 bits (648), Expect = 2e-72
 Identities = 127/249 (51%), Positives = 176/249 (70%), Gaps = 10/249 (4%)

Query: 17  AVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVV 76
           A+E+++++K +GD  VL+ I+LK   G+ I I G SGSGKST +RCIN LE   +G+IV 
Sbjct: 6   ALELIDIHKTFGDIEVLKGISLKAYDGDVISILGSSGSGKSTFLRCINMLENPTRGEIVF 65

Query: 77  DGTEL----------TNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPK 126
           +G +L           N++K++ ++R+++G VFQ FNL+PH+TIL+N    P+ V K PK
Sbjct: 66  NGNKLDLVQGESDLVANNMKQLTQMRQQIGFVFQSFNLWPHMTILQNVMEGPLHVLKRPK 125

Query: 127 KQAEEVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPE 186
            +  E A H L++V I E+ N YP QLSGGQQQRVAIAR+L M+P+++LFDEPTSALDPE
Sbjct: 126 HEVAEYAEHLLRKVGIAEKKNMYPNQLSGGQQQRVAIARTLAMDPQVILFDEPTSALDPE 185

Query: 187 MIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHE 246
           ++ EVL  M  LAEEG TML VTHEM FAR+V++ V+F+ QG + E+  P+  F  P+ E
Sbjct: 186 LVGEVLGVMRNLAEEGRTMLIVTHEMNFAREVSSDVVFLHQGVVEEKGTPSQVFSAPKSE 245

Query: 247 RTKLFLSQI 255
           R K FLS +
Sbjct: 246 RCKAFLSSV 254


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: 214
Number of extensions: 7
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: 257
Length of database: 255
Length adjustment: 24
Effective length of query: 233
Effective length of database: 231
Effective search space:    53823
Effective search space used:    53823
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: 47 (22.7 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