Align mannose permease IIC component (characterized)
to candidate WP_027699770.1 TT13_RS09610 mannose/fructose/sorbose family PTS transporter subunit IIC
Query= CharProtDB::CH_088330 (266 letters) >NCBI__GCF_000691805.2:WP_027699770.1 Length = 270 Score = 215 bits (547), Expect = 9e-61 Identities = 113/244 (46%), Positives = 165/244 (67%), Gaps = 6/244 (2%) Query: 3 ITTLQIVLVFIVACIAGMGSILDEFQFHRPLIACTLVGIVLGDMKTGIIIGGTLEMIALG 62 ++ + + V I A +AG+ ILD++Q H+P+IA +L+G+ G + GII+GG L++IALG Sbjct: 1 MSAISVFFVLIFAFLAGLEGILDQWQLHQPIIASSLIGLATGHLAAGIILGGFLQLIALG 60 Query: 63 WMNIGAAVAPDAALASIISTILVI-AGHQSI----GAGIALAIPLAAAGQVLTIIVRTIT 117 W N+GAAVAPDAALAS+ S IL++ +G+ S+ G I AI LA AG VLT +VR + Sbjct: 61 WANVGAAVAPDAALASVASAILMVQSGNFSVENIKGIIIPAAILLATAGLVLTTLVRFFS 120 Query: 118 VAFQHAADKAADNGNLTAISWIHVSSLFLQAMRVAIPAVIVALSVGTSEVQNMLNAIPEV 177 VA H AD A+ G+ +++ H+ +L +Q +R+AIPA ++ L V V + L +IP V Sbjct: 121 VAIVHLADAQAEKGSYRGVAFWHIVALVMQGLRIAIPAGLL-LIVPQQVVMHALQSIPPV 179 Query: 178 VTNGLNIAGGMIVVVGYAMVINMMRAGYLMPFFYLGFVTAAFTNFNLVALGVIGTVMAVL 237 ++ GL I GGM+VVVGY MVIN+M L PFF+LGF A L+A+G+IG V+A++ Sbjct: 180 ISGGLTIGGGMVVVVGYGMVINLMATRELWPFFFLGFAIAPINQLTLIAIGIIGVVIALV 239 Query: 238 YIQL 241 Y+ L Sbjct: 240 YLTL 243 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: 237 Number of extensions: 11 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: 266 Length of database: 270 Length adjustment: 25 Effective length of query: 241 Effective length of database: 245 Effective search space: 59045 Effective search space used: 59045 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 Sep 24 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