GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Synechococcus elongatus PCC 7942

Align Histidine transport system permease protein HisQ (characterized)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine

Query= SwissProt::P0A2I9
         (228 letters)



>FitnessBrowser__SynE:Synpcc7942_0248
          Length = 396

 Score = 82.0 bits (201), Expect = 1e-20
 Identities = 53/166 (31%), Positives = 92/166 (55%), Gaps = 8/166 (4%)

Query: 12  GAIVTLELALSSVVLAVLIGLVGAGAKLSQNRVTGLIFEGYTTLIRGVPDLVLMLLIFYG 71
           G ++TL  AL S+V ++ +G++ A  + S       +   Y  L RG+P   L+ ++F+G
Sbjct: 190 GLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLP---LVTILFFG 246

Query: 72  LQIALNVVTDSLGIDQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPKGHIEAATAFG 131
            Q+ + ++ DS    +  ID ++  I+ L     AY  ET RG   A+P+G  EAA A G
Sbjct: 247 -QVMVPLMLDS----EWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALG 301

Query: 132 FTHGQTFRRIMFPAMMRYALPGIGNNWQVILKATALVSLLGLEDVV 177
               QT+R I+ P  +R ++P I   +  +L+ T L+S++GL +++
Sbjct: 302 LNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELL 347


Lambda     K      H
   0.328    0.144    0.422 

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: 225
Number of extensions: 21
Number of successful extensions: 1
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: 228
Length of database: 396
Length adjustment: 27
Effective length of query: 201
Effective length of database: 369
Effective search space:    74169
Effective search space used:    74169
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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