GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Lactobacillus silagei IWT126

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_089136612.1 CES79_RS05995 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>NCBI__GCF_002217945.1:WP_089136612.1
          Length = 246

 Score =  229 bits (584), Expect = 4e-65
 Identities = 109/239 (45%), Positives = 170/239 (71%), Gaps = 1/239 (0%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           +++ ++ K+Y   H+L DIN  + +GE + + GPSGSGKST+IRC+N LE +Q G +  +
Sbjct: 6   IKVEHLEKYYQKDHILHDINFSIDQGEVVALLGPSGSGKSTLIRCLNGLEPYQNGTVSFN 65

Query: 78  GTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFL 137
           G ++    K   ++R+++GMVFQ ++LFP+LT+L+N  L P+ V+K  ++ A+  A   L
Sbjct: 66  GDQVVPTEKNWQKLRQKIGMVFQSYDLFPNLTVLDNILLGPVKVQKQSRETAKAAAEKLL 125

Query: 138 KRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVG 197
            +V + E  N YP QLSGGQ+QR+AI R+L +NP++MLFDE T++LDPEM++ VL+ +  
Sbjct: 126 DQVGLREYENVYPRQLSGGQKQRIAIVRALALNPELMLFDEVTASLDPEMVRGVLNIISK 185

Query: 198 LAEEG-MTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQI 255
           LA++  MTM+ VTHEM FA+Q+A+RV+F++ G+I+EQ +   FF  PQ +R K FL  +
Sbjct: 186 LAQDSDMTMIVVTHEMNFAQQIADRVLFLEDGKILEQTKGDQFFKQPQTDRAKEFLESM 244


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: 179
Number of extensions: 5
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: 246
Length adjustment: 24
Effective length of query: 233
Effective length of database: 222
Effective search space:    51726
Effective search space used:    51726
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: 46 (22.3 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