GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Pseudomonas stutzeri RCH2

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 GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__psRCH2:GFF16
          Length = 278

 Score =  218 bits (556), Expect = 8e-62
 Identities = 120/250 (48%), Positives = 159/250 (63%), Gaps = 12/250 (4%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           V    + K YG+  VL  ++L++  GE++ I GPSGSGKST++R +  LE   +G I VD
Sbjct: 25  VRFAGVTKRYGELTVLDGLDLQIEEGEKVAIIGPSGSGKSTLLRVLMTLEGIDEGVIEVD 84

Query: 78  GTELTN-----------DLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPK 126
           G  LT+           + + +  VR +VGMVFQ FNLFPH+  L+N   AP+ V  + K
Sbjct: 85  GEPLTHMPDASGQLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQVLGLSK 144

Query: 127 KQAEEVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPE 186
            +A   A   L  V + ++   +P QLSGGQQQRVAIAR+L M PK+MLFDE TSALDPE
Sbjct: 145 AEARGRAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVTSALDPE 204

Query: 187 MIKEVLDTMVGLAE-EGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQH 245
           +  EVL+ +  L E   +TML VTH+MGFAR+ A+RV F  QG+I EQ  P   F+NPQ 
Sbjct: 205 LCGEVLNVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDELFNNPQE 264

Query: 246 ERTKLFLSQI 255
           ERT+ FLS +
Sbjct: 265 ERTREFLSAV 274


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: 223
Number of extensions: 11
Number of successful extensions: 3
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: 278
Length adjustment: 25
Effective length of query: 232
Effective length of database: 253
Effective search space:    58696
Effective search space used:    58696
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.

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