Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_007681145.1 BN137_RS01325 PTS transporter subunit EIIC
Query= TCDB::P08722 (625 letters) >NCBI__GCF_000319285.1:WP_007681145.1 Length = 622 Score = 424 bits (1090), Expect = e-123 Identities = 238/625 (38%), Positives = 362/625 (57%), Gaps = 16/625 (2%) Query: 3 ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62 + R+I+ +GG NI+SL HC TRLRF L D +K L+ G++ V SG QFQV+ Sbjct: 5 QTGRQIIEHLGGEANILSLYHCITRLRFALVDLNKVNRTALENLDGVMGVNLSGDQFQVI 64 Query: 63 IGNHVADVFLAVNS-VAGLDEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGIL 121 IGN VA + A+ + + LD K +P + N ++ + ++GIF+P+I +A GIL Sbjct: 65 IGNEVAPLCQAILAQLPNLDAKKATSPPK--RRNPISVVLEGLAGIFSPIIPAIAGAGIL 122 Query: 122 KGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGAL 181 KG+L+L L W + TY IL S SD +F+F P++L ++AG +FG NP+ A+ + L Sbjct: 123 KGVLSLCLALGWVQADNQTYQILMSISDGVFFFMPLVLAFSAGNKFGANPYVAVALAATL 182 Query: 182 VHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPSA 241 HP + ++G + FLG+PV ++Y+SSVIPI+ + L S +ER ++ ++P+A Sbjct: 183 FHPTLTALLKSGGP-----VAFLGVPVASVSYASSVIPILLAVLLLSYVERFIDRFMPAA 237 Query: 242 IKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIFV 301 +K F PLL L+++ PVT + +GP + ++ G LWL + AG ++GG + + Sbjct: 238 LKTMFVPLLSLVIVAPVTLIAIGPAGIFFGNTLSGGILWLVANMGWLAGVIVGGTLSLMI 297 Query: 302 MFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAAL 361 + G+H+ LVP+ INN + LGYD L A M Q GAA GVFL R+ + K +A S + Sbjct: 298 ITGMHYVLVPIVINNISKLGYDPFKILFYVANMGQAGAAFGVFLRARNKKLKTLALSTSF 357 Query: 362 TSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQTIPS 421 ++ GITEPA+YGVN+ K PF A I GA G K Y+F L I IP+ Sbjct: 358 SAAMGITEPAMYGVNIRFKRPFAAALIGGACGGAFAMALGVKTYAFALSGI----PGIPA 413 Query: 422 TGIDFTVWASVIGGVIAIGCAFVGTVMLHFITAKRQPAQGAPQEKTPEVITP---PEQGG 478 +WA + IA A + TV+L F + PAQ A + ++P + Sbjct: 414 LVGPTFLWA-MASLAIAFCTAALMTVILGFEEPAQTPAQPAAPPEVVAGVSPVALAREEQ 472 Query: 479 ICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAIGIES 538 + +P++G + PL ++D FA + GKGIAI+P GE+ SPV GRI S+F + HA+ + S Sbjct: 473 LFAPVSGRLTPLASLSDPVFADEIFGKGIAIVPQSGELLSPVNGRIDSVFDSNHALTLIS 532 Query: 539 DDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTTPVLIS 598 D+G E+LIH+GIDTVKL G+ F+ HV G V G LISFD+ A++ D + V+++ Sbjct: 533 DNGAEVLIHIGIDTVKLGGQHFTRHVESGAFVEAGQPLISFDLDALKALNIDPSVIVIVT 592 Query: 599 NSDDFTDVLPHGTAQISAGEPLLSI 623 N++ + D+ P ++ E L + Sbjct: 593 NTEHYGDISPLKQGDVAPREAFLKL 617 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: 1174 Number of extensions: 73 Number of successful extensions: 4 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: 622 Length adjustment: 37 Effective length of query: 588 Effective length of database: 585 Effective search space: 343980 Effective search space used: 343980 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: 54 (25.4 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