Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate BWI76_RS06705 BWI76_RS06705 binding-protein-dependent transport system inner membrane protein
Query= uniprot:Q6MNM1 (272 letters) >FitnessBrowser__Koxy:BWI76_RS06705 Length = 283 Score = 204 bits (520), Expect = 1e-57 Identities = 102/273 (37%), Positives = 168/273 (61%), Gaps = 4/273 (1%) Query: 2 LKKTFSWISILLFSLFSIYPILYVLSVSLRPDNAFQTQSLEIIGPNASFKNFVDLF-ATT 60 ++ + +W+ ++ S IYP+++ + SL N+ + S II N SF+++ DLF Sbjct: 13 IRLSLTWLVVIFVSTMIIYPLVWTVGASLNAGNSLLSTS--IIPENLSFQHYADLFNGNV 70 Query: 61 DFLIWMRNSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLMLP 120 ++L W NS+ +S T +L + S +AYA +R+RF+GR L L+ QM P ++ Sbjct: 71 NYLTWYWNSMKISFMTMVLTLISVSFTAYAFSRFRFKGRQNGLMLFLLLQMIPQFSALIA 130 Query: 121 FYIILSKLRLIDSFWGLFLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGCSKWMIFY 180 +++ L LI+S L LIY +P W MK Y D IP++L+E+A +DG S + IF+ Sbjct: 131 IFVLSQLLGLINSHLALVLIYVGGMIPMNTWLMKGYLDAIPKDLDESARMDGASSFRIFF 190 Query: 181 KIILPVSSPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSFQA-SLATQWGLY 239 +II+P+S P L + ALFSF ++++++ +L+ P YTLP+GL + A + + Y Sbjct: 191 EIIMPLSKPILAVVALFSFTGPLGDFILSSTILRTPDKYTLPIGLYNLVAQKMGASYTTY 250 Query: 240 AAGALIVSVPVLILFISISRYLVSGLTMGSVKG 272 AAGA++++VPV IL++++ +Y VSGLT GS KG Sbjct: 251 AAGAVLIAVPVAILYLALQKYFVSGLTSGSTKG 283 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: 15 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: 283 Length adjustment: 25 Effective length of query: 247 Effective length of database: 258 Effective search space: 63726 Effective search space used: 63726 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