Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate Synpcc7942_0949 Synpcc7942_0949 permease protein of sugar ABC transporter
Query= reanno::Koxy:BWI76_RS01825 (514 letters) >FitnessBrowser__SynE:Synpcc7942_0949 Length = 292 Score = 110 bits (274), Expect = 9e-29 Identities = 82/258 (31%), Positives = 127/258 (49%), Gaps = 20/258 (7%) Query: 257 VTIGWDNFTRVFQDEGIQKPFFAIFVWTVVFSVLTVILTVAVGMVLACLVQWEALKGKAI 316 V IG N+ R++ D F T VF+V +V L + +G+ +A L+ + + + Sbjct: 44 VFIGLANYQRLWGDSRFWGDLFN----TTVFTVTSVSLELVLGLAIALLLH-QPSRWRGP 98 Query: 317 YRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFGIKPA--WFSDPTTARTMIII 374 R + +LP+ +P+ + L + +FN +G N L L I W +P A ++ Sbjct: 99 LRTIALLPWVLPTAVMALGWAWIFNDPYGVWNDWLQQLGWIAAPINWLGNPRWAWLTLVA 158 Query: 375 VNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGATPFQNFFKITLPLLIKPLTPLMIASF 434 + W P++ IL + +AIP+DLYEA ++GAT +Q+F++ITLPLL L ++ Sbjct: 159 ADVWKTTPFVAILLLAGRQAIPEDLYEAHCLEGATAWQSFWQITLPLLRPQLAIALLFRS 218 Query: 435 AFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVSYTYRIAFEGGGGQDFGLAA--AIAT 492 A F F L++++T GG PA T+ L Y Y A DFG A AI T Sbjct: 219 AQAFGLFDLVKVMTGGG--------PANSTETLALYAYTTALR---YLDFGYGATLAIVT 267 Query: 493 LIFLLVGLLAIVNLKATR 510 L GL I L +R Sbjct: 268 AAILAAGLGLIWGLGRSR 285 Lambda K H 0.325 0.140 0.426 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: 415 Number of extensions: 21 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: 514 Length of database: 292 Length adjustment: 30 Effective length of query: 484 Effective length of database: 262 Effective search space: 126808 Effective search space used: 126808 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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