Align mannose permease IIC component (characterized)
to candidate BWI76_RS01730 BWI76_RS01730 PTS mannose/fructose/sorbose transporter subunit IIC
Query= CharProtDB::CH_088330 (266 letters) >FitnessBrowser__Koxy:BWI76_RS01730 Length = 265 Score = 334 bits (857), Expect = 1e-96 Identities = 165/266 (62%), Positives = 213/266 (80%), Gaps = 2/266 (0%) Query: 1 MEITTLQIVLVFIVACIAGMGSILDEFQFHRPLIACTLVGIVLGDMKTGIIIGGTLEMIA 60 MEI+TLQI+ +FI +CIAGMGS+LDEFQ HRPLIACT++G++LGD+KTGI++GGTLE+IA Sbjct: 1 MEISTLQIIAIFIFSCIAGMGSVLDEFQTHRPLIACTVIGLILGDLKTGIMLGGTLELIA 60 Query: 61 LGWMNIGAAVAPDAALASIISTILVIAGHQSIGAGIALAIPLAAAGQVLTIIVRTITVAF 120 LGWMN+GAA +PD+ALASIIS ILVI G QSI GIA+A+P+AAAGQVLT+ RT+TV F Sbjct: 61 LGWMNVGAAQSPDSALASIISAILVIVGQQSIATGIAIALPVAAAGQVLTVFARTLTVVF 120 Query: 121 QHAADKAADNGNLTAISWIHVSSLFLQAMRVAIPAVIVALSVGTSEVQNMLNAIPEVVTN 180 QHAADKAA+ I +HVS+L +QA+RVAIPA+IV+L V V NMLNAIPE VT Sbjct: 121 QHAADKAAEEARFGTIDLLHVSALGVQALRVAIPALIVSLFVSADMVSNMLNAIPEFVTR 180 Query: 181 GLNIAGGMIVVVGYAMVINMMRAGYLMPFFYLGFVTAAFTNFNLVALGVIGTVMAVLYIQ 240 GL IAGG IVVVGYAMV+ MM YLMPFF+LGF+ + +F+L+A G +G ++A++YIQ Sbjct: 181 GLQIAGGFIVVVGYAMVLRMMGVKYLMPFFFLGFLAGGYLDFSLLAFGGVGVIIALIYIQ 240 Query: 241 LSPKYNRVAGAPAQAAGNNDLDNELD 266 L+P++ + P AA ++ ++LD Sbjct: 241 LNPQWRK--SEPQAAATSSTALDQLD 264 Lambda K H 0.326 0.139 0.397 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: 267 Number of extensions: 11 Number of successful extensions: 1 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: 266 Length of database: 265 Length adjustment: 25 Effective length of query: 241 Effective length of database: 240 Effective search space: 57840 Effective search space used: 57840 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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