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_1680 Synpcc7942_1680 Sulphate transport system permease protein 1

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__SynE:Synpcc7942_1680
          Length = 338

 Score =  162 bits (411), Expect = 6e-45
 Identities = 83/229 (36%), Positives = 143/229 (62%), Gaps = 6/229 (2%)

Query: 16  VAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIV 75
           V +++  ++K +G F  ++D++L V  G  + + GPSGSGKST++R I  LE+   G+I 
Sbjct: 1   VGIQVSQVSKQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIF 60

Query: 76  VDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMH 135
           + G + TN+  +     R++G VFQH+ LF HLT+ +N     + +RK  K++       
Sbjct: 61  LTGRDATNESVR----DRQIGFVFQHYALFKHLTVRKNIAFG-LELRKHTKEKVRARVEE 115

Query: 136 FLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTM 195
            L+ V++    ++YP QLSGGQ+QRVA+AR+L + P+++L DEP  ALD ++ K++   +
Sbjct: 116 LLELVQLTGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSWL 175

Query: 196 VGLAEE-GMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNP 243
             L +E  +T + VTH+   A +VA++++ M+ G++ +   PA  +DNP
Sbjct: 176 RKLHDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNP 224


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: 213
Number of extensions: 10
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: 338
Length adjustment: 26
Effective length of query: 231
Effective length of database: 312
Effective search space:    72072
Effective search space used:    72072
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: 48 (23.1 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