Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate AO353_15980 AO353_15980 trehalose permease IIC protein
Query= TCDB::P08722 (625 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15980 Length = 480 Score = 214 bits (546), Expect = 5e-60 Identities = 139/465 (29%), Positives = 236/465 (50%), Gaps = 29/465 (6%) Query: 4 LARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVVI 63 +A +++ +GGADN+ HC TRLR LKD + + L + + +GG FQVVI Sbjct: 8 IASELLHSLGGADNLEQAAHCVTRLRLALKDPQRVDSATLNQIDLVKGSFFTGGLFQVVI 67 Query: 64 G-NHVADVFLAVNSVAGLDEK--AQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGI 120 G V V+ A+ GL A + DK N + R V V S +F P++ + G+ Sbjct: 68 GPGEVEKVYAALRQQTGLAASTIADVKQKGADKTNAMQRLVRVFSDVFMPILPALIIAGL 127 Query: 121 L---------KGMLALALTF-QWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGN 170 L KGM T + G + ++ ++ F F P ++G++A KRFGG+ Sbjct: 128 LMGVNNLIGAKGMFIAGKTLLEAYPTLDGVWSLINLMANTSFVFLPALVGWSAAKRFGGS 187 Query: 171 PFTAMVIGGALVHPLILTAFENGQKADALGLDFLGIP---------VTLLNYSSSVIPII 221 +V+G LVHP +L A+ G+ GLD +P + + Y ++PI+ Sbjct: 188 EILGIVLGLMLVHPDLLNAWNYGKAV--AGLDGQSLPYFDIFGWFKIEKVGYQGQILPIL 245 Query: 222 FSAWLCSILERRLNAWLPSAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWL 281 +A++ S++E+ L A +P+AI+ P+ ++V + ++GP++ + LI G + L Sbjct: 246 MAAYVMSVIEKWLRARVPNAIQLLVVPITTIVVTGVLALAVIGPVTRHLGILITEGVVTL 305 Query: 282 YQAVPAFAGAVMGGFWQIFVMFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAAL 341 + P GA+ G + V+ G+H + + + + G + P+++ + +AQ AAL Sbjct: 306 FDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQGSAAL 365 Query: 342 GVFLCERDAQKKVVAGSAALTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQ 401 GVF R A+ K +A ++A+++ FGITEPA++GVNL K+PF A ALG + + Sbjct: 366 GVFYMTRSARDKSMASTSAISAYFGITEPAMFGVNLRYKFPFYAALSGSALGCMFLSLNK 425 Query: 402 TKVYSFGLPSIFTFMQTIPSTGIDFTVWASVIGGVIAIGCAFVGT 446 + + G+ + F+ IP + ++G VIA+ FV T Sbjct: 426 VQASAIGVGGLPGFISIIPQ-----FIPMFIVGMVIAMVVPFVLT 465 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: 881 Number of extensions: 53 Number of successful extensions: 5 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: 480 Length adjustment: 36 Effective length of query: 589 Effective length of database: 444 Effective search space: 261516 Effective search space used: 261516 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: 53 (25.0 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