Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_052752467.1 HA49_RS10585 PTS transporter subunit EIIC
Query= TCDB::P08722 (625 letters) >NCBI__GCF_000757425.2:WP_052752467.1 Length = 467 Score = 493 bits (1270), Expect = e-144 Identities = 239/442 (54%), Positives = 327/442 (73%), Gaps = 8/442 (1%) Query: 3 ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62 +LA +IV VGG +NI +++HCATRLRFKL A +K G++ VVESGGQFQVV Sbjct: 6 QLATQIVEAVGGKNNIQTVVHCATRLRFKLASTPLDAASKVKALEGVMAVVESGGQFQVV 65 Query: 63 IGNHVADVFLAVNSVAGLDEKAQQ-----APENDDKGNLLNRFVYVISGIFTPLIGLMAA 117 IGNHV +VF A+ D + +Q AP G LL RF+ ++SGIFTP++G+MAA Sbjct: 66 IGNHVGEVFRAIELFLAGDGEVRQDTDRTAPSKPAAG-LLARFIDLVSGIFTPVLGVMAA 124 Query: 118 TGILKGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVI 177 +G+LKG LALAL +++SGTY I F+ASDALF+FFP++LGYTAGK+FGG+PF M I Sbjct: 125 SGMLKGFLALALALNLLSQESGTYQIWFAASDALFYFFPLVLGYTAGKKFGGSPFLTMAI 184 Query: 178 GGALVHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAW 237 GGALVHP+I++ NG A+ F G+P+T +NYSSSVIPIIF++W C LE++L Sbjct: 185 GGALVHPVIMS-LSNGSDPSAVDT-FFGLPLTFINYSSSVIPIIFASWACCWLEKQLYPR 242 Query: 238 LPSAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFW 297 LPS+I+NF TPL CLMVI P+TFL++GPLST++S+ +A+GY W+Y P AG +G W Sbjct: 243 LPSSIRNFATPLFCLMVIVPLTFLVIGPLSTFLSQCLASGYQWIYDIAPWIAGIFLGSVW 302 Query: 298 QIFVMFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAG 357 QI V+FGLHWGL+P+ INN ++LG+DT++PLL+PA++ Q GAALGVFL ++ + K++AG Sbjct: 303 QICVIFGLHWGLIPVAINNLSMLGFDTIVPLLLPAVLGQTGAALGVFLACKEQKLKMLAG 362 Query: 358 SAALTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQ 417 ++ LFGITEPA+YGV LP + PF++ CI+G +G I+G Q KV+SFGL S+F+F Q Sbjct: 363 TSVTAGLFGITEPAIYGVTLPLRKPFMMGCIAGGIGGGIVGLFQAKVWSFGLVSVFSFTQ 422 Query: 418 TIPSTGIDFTVWASVIGGVIAI 439 IP+ G+D +VW +V+G + A+ Sbjct: 423 MIPAEGVDLSVWGAVVGAITAL 444 Lambda K H 0.324 0.141 0.427 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: 1059 Number of extensions: 65 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: 625 Length of database: 467 Length adjustment: 35 Effective length of query: 590 Effective length of database: 432 Effective search space: 254880 Effective search space used: 254880 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 52 (24.6 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