Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate GFF851 Psest_0865 ABC-type maltose transport systems, permease component
Query= uniprot:Q6MNM1 (272 letters) >FitnessBrowser__psRCH2:GFF851 Length = 296 Score = 153 bits (387), Expect = 4e-42 Identities = 90/279 (32%), Positives = 154/279 (55%), Gaps = 17/279 (6%) Query: 10 SILLFSLFSIYPILYVLSVSLRPDNAFQTQSLEIIGPNASFKNFVDLFATTD-------- 61 ++L F ++P+L V+S+S R N F T SL P + T Sbjct: 19 ALLAFVAAILFPLLMVISISFREGN-FATGSLFPENPTLEHWSLALGIPYTHADGSVTQP 77 Query: 62 ---FLIWMRNSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLM 118 L+W+ NS+ ++ +++L + L++TSAYA AR RF G+ +L S+L+ QMFP + + Sbjct: 78 PFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIFQMFPPVLSL 137 Query: 119 LPFYIILSKLRLIDSFWGL-----FLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGC 173 + Y + +L S+ G+ ++ S + IW +K Y+++I LEEAA++DG Sbjct: 138 VAIYALFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDASLEEAAIVDGA 197 Query: 174 SKWMIFYKIILPVSSPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSFQASLA 233 + W F+ I+LP+S P L + + +F++S +EY IA+V+L D TL +G + + Sbjct: 198 TTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSVGAQQYLYPQN 257 Query: 234 TQWGLYAAGALIVSVPVLILFISISRYLVSGLTMGSVKG 272 WG +AA A++ +P+ +F+ +++V GLT G VKG Sbjct: 258 YLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVKG 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: 227 Number of extensions: 19 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: 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