GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Shewanella loihica PV-4

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 5209222 Shew_1700 phosphate ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__PV4:5209222
          Length = 272

 Score =  137 bits (345), Expect = 2e-37
 Identities = 82/252 (32%), Positives = 145/252 (57%), Gaps = 11/252 (4%)

Query: 11  VSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEE-- 68
           +S+ + A+EI N++  YGD   L D+++K+ + +     GPSG GKST++RCINR+ +  
Sbjct: 19  LSSEQTALEIRNLDLKYGDKQALFDVSMKIPKKKVTAFIGPSGCGKSTLLRCINRMNDLV 78

Query: 69  ---HQKGKIVVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMP 125
              +  G+I++ G  + +    +  +RR VGMVFQ  N FP  +I EN            
Sbjct: 79  DNCNIDGEILLHGQNIYDKKVDVASLRRNVGMVFQRPNPFPK-SIYENVVYGLRLQGINN 137

Query: 126 KKQAEEVAMHFLKRV----KIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTS 181
           ++Q +E A   L+      ++ ++ +     LSGGQQQR+ IAR++ + P+++L DEPTS
Sbjct: 138 RRQLDEAAERSLRGAAIWDEVKDRLHDNAFGLSGGQQQRLVIARAIAIEPEVLLLDEPTS 197

Query: 182 ALDPEMIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFD 241
           ALDP +    ++ ++   +   T++ VTH M  A +V+++  FM  G++VE  +    F 
Sbjct: 198 ALDP-ISTLTIEELITELKAKYTVVIVTHNMQQAARVSDQTAFMYMGELVEYADTNTIFT 256

Query: 242 NPQHERTKLFLS 253
            P+ ++T+ +++
Sbjct: 257 TPKKKKTEDYIT 268


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: 168
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: 272
Length adjustment: 25
Effective length of query: 232
Effective length of database: 247
Effective search space:    57304
Effective search space used:    57304
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 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