Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate Synpcc7942_0948 Synpcc7942_0948 permease protein of sugar ABC transporter
Query= uniprot:Q6MNM1 (272 letters) >FitnessBrowser__SynE:Synpcc7942_0948 Length = 275 Score = 134 bits (336), Expect = 3e-36 Identities = 87/276 (31%), Positives = 154/276 (55%), Gaps = 6/276 (2%) Query: 2 LKKTFSW-ISILLFSLFSIYPILYVLSVSLRPDNAFQTQSLEIIGPNA-SFKNFVDLFAT 59 +K F W I+ L SLFS+ PIL+ L S++ NA I P + +++ L+ Sbjct: 1 MKPRFRWAIAALALSLFSLAPILWQLLTSIKV-NADIAAIPTIYWPRQWTVEHYQALWQQ 59 Query: 60 TD-FLIWMRNSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLM 118 T F ++ NS VVSA TL + + + AYA+AR R R +++ SLL+ +FP +L Sbjct: 60 TPAFGRYLLNSAVVSAIATLAALLIGTPCAYAIARRRDRSSQVLVGSLLLVTLFPYVLLF 119 Query: 119 LPFYIILSKLRLIDSFWGLFLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGCSKWMI 178 ++ L+ +++ L + Y++ LP I ++++++ +P ELEEAA +DG S Sbjct: 120 QGLLEVVRWLQWGNNYAALVVPYTALNLPLVILLLRSFFEQLPPELEEAAQIDGLSLGQR 179 Query: 179 FYKIILPVSSPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSFQ--ASLATQW 236 + I++P+++PALV + +F+ SW+EYV+A + L T+P+ + + + Sbjct: 180 LWLILVPLTAPALVTAGILAFIFSWNEYVLALSFISQQALKTVPIAVAEIGGISIFDVPY 239 Query: 237 GLYAAGALIVSVPVLILFISISRYLVSGLTMGSVKG 272 G AA ++ ++P++ L + R ++ GLT G+VKG Sbjct: 240 GDIAAATVVATLPLIGLVLVAQRRILEGLTAGAVKG 275 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: 225 Number of extensions: 15 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: 275 Length adjustment: 25 Effective length of query: 247 Effective length of database: 250 Effective search space: 61750 Effective search space used: 61750 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