Align Inner-membrane translocator (characterized, see rationale)
to candidate H281DRAFT_02175 H281DRAFT_02175 monosaccharide ABC transporter membrane protein, CUT2 family
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__Burk376:H281DRAFT_02175 Length = 353 Score = 201 bits (512), Expect = 2e-56 Identities = 136/369 (36%), Positives = 205/369 (55%), Gaps = 27/369 (7%) Query: 2 KSSAETLSSTRMSADLISPQMNASEAHSSERQPRMQESHKTMVQEKNARYQAGKSTSMGR 61 K AE+L S + PQ + +S +Q Q S T V+ + +M R Sbjct: 4 KLDAESLQSEPQAGQEARPQPGSE---ASPQQASSQASQATGVRN-------WRRLAMQR 53 Query: 62 YLWPLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATG 121 + LLA+ +L NL F+++ + L + + ++ IGM+LV+ATG Sbjct: 54 EVIVLLAM---VLFNLIFTPHFWSLQTFNVNL--------TQVVTIVIVGIGMTLVVATG 102 Query: 122 GIDLSVGAVMAIAGAVCANLLL---VPD-ISLVTVIAAGLIVGLLAGCINGGLVSFLGIQ 177 GIDLSVGA MAI+GA+ L L VP I+L V+ ++ L G NG LV+ L +Q Sbjct: 103 GIDLSVGASMAISGALAPMLFLNIPVPGGIALAFVLP--VLAAALCGVFNGLLVTRLAVQ 160 Query: 178 PIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLL 237 PIVATL+L +AGRG+AQ++ G + F P F I +G+ G+P V +++ ++ + Sbjct: 161 PIVATLVLFIAGRGIAQVVTDGSLQAFNTPAFQWIALGKVAGVPFQVLLMLALVVAFAWV 220 Query: 238 LRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANN 297 +RKT G ++ G N KA+ G+ S+KL AY + A LAG+IS + SDAN Sbjct: 221 VRKTLFGQYLLITGGNEKAAYLSGVPTASVKLIAYTLCAALAGLAGLISISVNSSSDANV 280 Query: 298 AGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAI 357 GL +ELDA+ AV +GG ALTGG+ + ++VGALIIQ L T++ G+P L++KA Sbjct: 281 VGLGIELDAIAAVAVGGTALTGGKAFIGGTLVGALIIQLLRYTLLAHGIPDAAALVVKAG 340 Query: 358 VILTVLLLQ 366 +I+ + +Q Sbjct: 341 IIVAAVYVQ 349 Lambda K H 0.323 0.136 0.379 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: 331 Number of extensions: 17 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: 405 Length of database: 353 Length adjustment: 30 Effective length of query: 375 Effective length of database: 323 Effective search space: 121125 Effective search space used: 121125 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 50 (23.9 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