GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Synechococcus elongatus PCC 7942

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 Synpcc7942_1414 Synpcc7942_1414 ATPase

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__SynE:Synpcc7942_1414
          Length = 241

 Score =  132 bits (333), Expect = 5e-36
 Identities = 83/224 (37%), Positives = 132/224 (58%), Gaps = 8/224 (3%)

Query: 18  VEIVNMNKWYGD----FHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGK 73
           ++  +++K YG+       L  ++ +V  GE   I G SGSGKST +  I  L+    G+
Sbjct: 9   IQFEHVSKIYGEGETTVRALDHVDFQVRAGEYCAIMGASGSGKSTAMNLIGCLDRPTAGR 68

Query: 74  IVVDGTELTN-DLKKIDEVR-REVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEE 131
             +DGT++ + D   +  VR R++G VFQ F+L P L+ +EN  L  I+   + +++  +
Sbjct: 69  YYLDGTDVADLDDDALAAVRNRKIGFVFQQFHLLPQLSAVENVMLPMIYAG-ISQQERRD 127

Query: 132 VAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEV 191
            A+  L +V + ++ +  P QLSGGQQQRVAIAR++   P ++L DEPT ALD +  +EV
Sbjct: 128 RAVAALTQVGLAQRLDNKPNQLSGGQQQRVAIARAIVNQPVLLLADEPTGALDSQTTEEV 187

Query: 192 LDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNE 235
           L+    L + G+T++ VTHE   A + A RVI+   GQI  + +
Sbjct: 188 LNIFDQLHQRGITIVIVTHEAEVADR-AERVIWFRDGQIQRETQ 230


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: 155
Number of extensions: 9
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: 241
Length adjustment: 24
Effective length of query: 233
Effective length of database: 217
Effective search space:    50561
Effective search space used:    50561
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.

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