Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 154 bits (390), Expect = 3e-42 Identities = 83/222 (37%), Positives = 130/222 (58%), Gaps = 5/222 (2%) Query: 44 VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103 VKD + IEEG + I+G +GSGK+T+++L+ L P +G+++ G I ++ Sbjct: 21 VKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKGEIVFSGQTI--VNGKSALPA 78 Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPD 163 ++++ ++FQ +AL P MT+L+N + NA R+ A+D+L GLE+ +YP Sbjct: 79 NQREVGVIFQEYALFPQMTLLENVREALHQESRNA---RQIAMDSLALAGLEDSFSAYPH 135 Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223 +LS G RQR LARALA P +LL+D+ F +LD + E+ +++ + T + SH Sbjct: 136 QLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISEDIRDIVKATGITAIVASH 195 Query: 224 DLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFF 265 +A+ + D IAI+ G + QVGTP EI PAN YV FF Sbjct: 196 HAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANFF 237 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: 334 Number of extensions: 12 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: 345 Length adjustment: 30 Effective length of query: 370 Effective length of database: 315 Effective search space: 116550 Effective search space used: 116550 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.
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