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.
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:
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