GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Synechococcus elongatus PCC 7942

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

Query= uniprot:Q31RN9
         (396 letters)



>FitnessBrowser__SynE:Synpcc7942_0248
          Length = 396

 Score =  797 bits (2059), Expect = 0.0
 Identities = 396/396 (100%), Positives = 396/396 (100%)

Query: 1   MMRSPQGITPQQTPIAWLRQNLFSSWLNSAITLLLVVIIVTVVGRLGLWITTEARWTVLV 60
           MMRSPQGITPQQTPIAWLRQNLFSSWLNSAITLLLVVIIVTVVGRLGLWITTEARWTVLV
Sbjct: 1   MMRSPQGITPQQTPIAWLRQNLFSSWLNSAITLLLVVIIVTVVGRLGLWITTEARWTVLV 60

Query: 61  DNWTLFFVGRYPAAEQWRLWLWLGLLSPTLGLTWGCLATGSHRWQRRSLWGWAGLAAAIA 120
           DNWTLFFVGRYPAAEQWRLWLWLGLLSPTLGLTWGCLATGSHRWQRRSLWGWAGLAAAIA
Sbjct: 61  DNWTLFFVGRYPAAEQWRLWLWLGLLSPTLGLTWGCLATGSHRWQRRSLWGWAGLAAAIA 120

Query: 121 GIPLPWFPHKLGLAAIAATVPAASWLAQRCRGQAWLRFLPTLWGVLFLVGLWLLQGGLGL 180
           GIPLPWFPHKLGLAAIAATVPAASWLAQRCRGQAWLRFLPTLWGVLFLVGLWLLQGGLGL
Sbjct: 121 GIPLPWFPHKLGLAAIAATVPAASWLAQRCRGQAWLRFLPTLWGVLFLVGLWLLQGGLGL 180

Query: 181 RPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLV 240
           RPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLV
Sbjct: 181 RPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLV 240

Query: 241 TILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAAL 300
           TILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAAL
Sbjct: 241 TILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAAL 300

Query: 301 GLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYL 360
           GLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYL
Sbjct: 301 GLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYL 360

Query: 361 GRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRLTPQR 396
           GRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRLTPQR
Sbjct: 361 GRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRLTPQR 396


Lambda     K      H
   0.329    0.142    0.471 

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: 779
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: 396
Length of database: 396
Length adjustment: 31
Effective length of query: 365
Effective length of database: 365
Effective search space:   133225
Effective search space used:   133225
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 (21.8 bits)
S2: 50 (23.9 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