Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate N515DRAFT_3133 N515DRAFT_3133 carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-)
Query= uniprot:Q6MNM1 (272 letters) >FitnessBrowser__Dyella79:N515DRAFT_3133 Length = 273 Score = 156 bits (395), Expect = 4e-43 Identities = 86/258 (33%), Positives = 149/258 (57%), Gaps = 2/258 (0%) Query: 15 SLFSIYPILYVLSVSLRPDNAFQTQSLEIIGPNASFKNFVDLFATTDFLIWMRNSLVVSA 74 +L +++P+L++LSVS ++ +A+ N+ +LF ++ NSL VS+ Sbjct: 18 TLVAVFPLLWMLSVSFMRPGEASALPPPLLPTHATLANYHELFERAGMGRYLLNSLGVSS 77 Query: 75 ATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLMLPFYIILSKLRLIDSF 134 A TLL +A + YA A+ RF GR + LL + PA + MLP +++L L L++S+ Sbjct: 78 AITLLSLAFNLMAGYAFAKLRFSGRERLFQVLLGGLVIPAQVAMLPLFLLLKYLGLVNSY 137 Query: 135 WGLFLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGCSKWMIFYKIILPVSSPALVIT 194 + + + A F I+ ++ Y IP +L EAA +DG + IF +I+LP+ P +V Sbjct: 138 AAV--VVPAMATIFGIFLVRQYARGIPDDLMEAARIDGAGELRIFVQIVLPLLKPIMVTL 195 Query: 195 ALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSFQASLATQWGLYAAGALIVSVPVLILF 254 A+F+F+++W++++ + L + YTLP+ L S L AG+++ +PVL+LF Sbjct: 196 AIFTFLTAWNDFMWPLIALTGQEHYTLPIALASLSREHVQDSELMMAGSVVTVLPVLVLF 255 Query: 255 ISISRYLVSGLTMGSVKG 272 +++ RY + GL +GSVKG Sbjct: 256 LALQRYYLQGLLLGSVKG 273 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: 199 Number of extensions: 9 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: 273 Length adjustment: 25 Effective length of query: 247 Effective length of database: 248 Effective search space: 61256 Effective search space used: 61256 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