Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate 18060 b4032 maltose transporter subunit (NCBI)
Query= uniprot:Q6MNM1 (272 letters) >FitnessBrowser__Keio:18060 Length = 296 Score = 154 bits (388), Expect = 3e-42 Identities = 96/282 (34%), Positives = 157/282 (55%), Gaps = 25/282 (8%) Query: 11 ILLFSLFSIYPILYVLSVSLRPDNAFQTQSLEIIGPNASFKNFVDLFATT---------- 60 +LLF ++P+L V+++SLR N F T SL I S+ ++ + Sbjct: 20 LLLFIAAIMFPLLMVVAISLRQGN-FATGSL--IPEQISWDHWKLALGFSVEQADGRITP 76 Query: 61 ---DFLIWMRNSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATML 117 L+W+ NS+ V+ + + VAL++T AYA AR RF G+ +L +L+ QMFPA + Sbjct: 77 PPFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPAVLS 136 Query: 118 MLPFYIILSKLRLIDSFWGL-------FLIYSSTALPFCIWQMKAYYDTIPRELEEAALL 170 ++ Y + +L F GL F AL +W +K Y++TI LEEAA L Sbjct: 137 LVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIALH--VWTIKGYFETIDSSLEEAAAL 194 Query: 171 DGCSKWMIFYKIILPVSSPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSFQA 230 DG + W F ++LP+S P L + + SF+++ +E +A+++L+D YTL +G++ + Sbjct: 195 DGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYLN 254 Query: 231 SLATQWGLYAAGALIVSVPVLILFISISRYLVSGLTMGSVKG 272 WG +AA A++ ++P+ I+F+ R+LV+GLT G VKG Sbjct: 255 PQNYLWGDFAAAAVMSALPITIVFLLAQRWLVNGLTAGGVKG 296 Lambda K H 0.329 0.139 0.421 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: 216 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 272 Length of database: 296 Length adjustment: 26 Effective length of query: 246 Effective length of database: 270 Effective search space: 66420 Effective search space used: 66420 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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