GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Synechococcus elongatus PCC 7942

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__SynE:Synpcc7942_1680
          Length = 338

 Score =  196 bits (498), Expect = 7e-55
 Identities = 113/289 (39%), Positives = 178/289 (61%), Gaps = 15/289 (5%)

Query: 2   VRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61
           V I V  VSK F  G   A+ +V++ +E G    +LGPSG+GK+T +R+IAGL+ P +G 
Sbjct: 1   VGIQVSQVSKQF--GSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGR 58

Query: 62  LYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRV 121
           ++   R  A+N  +     DR+IG VFQ +AL+ +LT  +NIAF L   K +KE++R RV
Sbjct: 59  IFLTGR-DATNESV----RDRQIGFVFQHYALFKHLTVRKNIAFGLELRKHTKEKVRARV 113

Query: 122 EEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARA 181
           EE+ +++ +  + + +P +LSGGQ+QRVALARAL   P +LLLDEPF  LDA++R   R+
Sbjct: 114 EELLELVQLTGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRS 173

Query: 182 LVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLI 241
            ++++   + VT + V+HD  +   +AD++ V+  GK+ Q+G P ++YDNP +  V S I
Sbjct: 174 WLRKLHDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFI 233

Query: 242 GEINELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKD 290
           G +N L    ++     G L  P         + +RP D++++ D I +
Sbjct: 234 GPVNVLPN--SSHIFQAGGLDTP------HPEVFLRPHDIEIAIDPIPE 274


Lambda     K      H
   0.319    0.139    0.390 

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: 338
Number of extensions: 15
Number of successful extensions: 2
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: 353
Length of database: 338
Length adjustment: 29
Effective length of query: 324
Effective length of database: 309
Effective search space:   100116
Effective search space used:   100116
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 (21.7 bits)
S2: 49 (23.5 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