GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Marinobacter adhaerens HP15

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 GFF2976 HP15_2920 amino acid ABC transporter, ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__Marino:GFF2976
          Length = 248

 Score =  288 bits (738), Expect = 6e-83
 Identities = 147/242 (60%), Positives = 186/242 (76%), Gaps = 3/242 (1%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           V++  MNK++G  HVL+DI+L V +GE +VI G SGSGKST+IRC+N LEE++ G + VD
Sbjct: 5   VKMKGMNKYFGKLHVLKDIDLTVEQGEVVVIIGASGSGKSTLIRCVNGLEEYESGTLEVD 64

Query: 78  GTEL---TNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAM 134
           G +L   + + K + E+R+EVGMVFQ FNLFPHLT+  N  LAP  V++ P+  A   A 
Sbjct: 65  GQQLAPKSGNPKALAEIRKEVGMVFQQFNLFPHLTVKRNIMLAPKKVKETPETVANATAE 124

Query: 135 HFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDT 194
             L RV I  QA+KYP QLSGGQQQRVAIAR+L M P++MLFDEPTSALDPEMI EVLD 
Sbjct: 125 RLLNRVGIGNQADKYPSQLSGGQQQRVAIARALAMEPRLMLFDEPTSALDPEMIGEVLDV 184

Query: 195 MVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQ 254
           M  LA+EGMTM+ VTHEMGFAR+VA+RVI++ +G IVEQ +P   FDNPQ+ERT+ FLS+
Sbjct: 185 MRELAKEGMTMMVVTHEMGFAREVADRVIYIHEGAIVEQGKPDDVFDNPQNERTQAFLSR 244

Query: 255 IL 256
           +L
Sbjct: 245 VL 246


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: 236
Number of extensions: 6
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: 248
Length adjustment: 24
Effective length of query: 233
Effective length of database: 224
Effective search space:    52192
Effective search space used:    52192
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 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