Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Cola:Echvi_3653 Length = 290 Score = 146 bits (368), Expect = 9e-40 Identities = 76/206 (36%), Positives = 128/206 (62%), Gaps = 5/206 (2%) Query: 46 DASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRR 105 D L I +GE + G SGSGK++ +R+++ L+ P +G + ++G S + R Sbjct: 20 DIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHLSVNGEQWFDASFGKNVSPGR 79 Query: 106 KKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDEL 165 +K+ +FQ ++L P+MTV +N AF ++ NA+++ ++ L +GL + + P L Sbjct: 80 RKLGYLFQDYSLFPNMTVKENIAFALK----NAKDKAY-LMELLESMGLLHLQDTLPKHL 134 Query: 166 SGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDL 225 SGG +QRV LARALA+ PDILL+DE SALDP +R ++Q+ ++ + K+ T + +SHD Sbjct: 135 SGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQEYILAIHRKYALTTILVSHDA 194 Query: 226 DEAMRIGDRIAIMQNGEVVQVGTPDE 251 E +++ DRI + +G+V++ TP E Sbjct: 195 GEIIKLSDRIIELDHGKVLRQCTPKE 220 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: 302 Number of extensions: 14 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: 290 Length adjustment: 28 Effective length of query: 372 Effective length of database: 262 Effective search space: 97464 Effective search space used: 97464 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