GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Synechococcus elongatus PCC 7942

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase

Query= SwissProt::P17328
         (400 letters)



>FitnessBrowser__SynE:Synpcc7942_1406
          Length = 368

 Score =  157 bits (398), Expect = 4e-43
 Identities = 92/229 (40%), Positives = 134/229 (58%), Gaps = 9/229 (3%)

Query: 38  TGLSLGVKD-ASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKIS 96
           +G SL   D  S  +E GEI  ++G SG GK+T++R++        G + + G  +A   
Sbjct: 17  SGSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQ 76

Query: 97  DAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGM-ELAGIAAQERREKALDALRQVGLE 155
            +   E R   + MVFQ +AL PH+TVLDN  FG+ +  G AA  R+  AL     VGLE
Sbjct: 77  RSLPPETR--SVGMVFQDYALFPHLTVLDNVCFGLRDRKGSAAVARQALAL-----VGLE 129

Query: 156 NYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQ 215
                YP ELSGG +QRV LARALA  P ++L+DE  S LD  +R  ++ EL  +  + Q
Sbjct: 130 GLERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQAQ 189

Query: 216 RTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264
            T + ++HD +EA+ I DR+A+M+ G   Q+G P+E+  +PA+ +V  F
Sbjct: 190 ATAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEF 238


Lambda     K      H
   0.319    0.137    0.378 

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: 327
Number of extensions: 16
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: 400
Length of database: 368
Length adjustment: 30
Effective length of query: 370
Effective length of database: 338
Effective search space:   125060
Effective search space used:   125060
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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