Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate RR42_RS18605 RR42_RS18605 sugar ABC transporter permease
Query= uniprot:Q6MNM1 (272 letters) >FitnessBrowser__Cup4G11:RR42_RS18605 Length = 295 Score = 166 bits (419), Expect = 7e-46 Identities = 85/268 (31%), Positives = 150/268 (55%), Gaps = 7/268 (2%) Query: 8 WISILLFSLFSIYPILYVLSVSLRPDNAFQTQSLE---IIGPNASFKNFVDLFATTDFLI 64 +I + +F ++P ++ + +PD +S ++ P +F +F L T + Sbjct: 30 YIPLGIFVFVLLFPFYWMAITAFKPDGELLMRSANPFWVMAP--TFAHFKKLLFDTPYPE 87 Query: 65 WMRNSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLMLPFYII 124 W+ N+++VS +T +A + +AYA+ R RF+G + ++ + + P ++L +P I Sbjct: 88 WLLNTVIVSTISTFASLAASVLAAYAIERLRFQGAKQVGLAVFLAYLIPPSILFIPLASI 147 Query: 125 LSKLRLIDSFWGLFLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGCSKWMIFYKIIL 184 + +L L D+ W L L Y + +PFC W + Y+ +IP ELEE AL+DG ++W I KIIL Sbjct: 148 VFQLGLFDTRWALILTYPTFLIPFCTWLLMGYFRSIPYELEECALIDGATRWEILVKIIL 207 Query: 185 PVSSPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGL-RSFQASLATQWGLYAAGA 243 P++ P L+ +F+F SW+E++ A + ++ T+P+G+ WG AGA Sbjct: 208 PLAVPGLISAGIFAFTLSWNEFIYALTFISSSEVKTVPVGIVTELIEGDVYHWGALMAGA 267 Query: 244 LIVSVPVLILFISISRYLVSGLTMGSVK 271 L+ S+PV +++ Y VSG+T G+VK Sbjct: 268 LLGSLPVALVYSFFVEYYVSGMT-GAVK 294 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: 259 Number of extensions: 10 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: 272 Length of database: 295 Length adjustment: 26 Effective length of query: 246 Effective length of database: 269 Effective search space: 66174 Effective search space used: 66174 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