Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_034281372.1 BA81_RS07465 PTS transporter subunit EIIC
Query= TCDB::P08722 (625 letters) >NCBI__GCF_000691165.1:WP_034281372.1 Length = 635 Score = 462 bits (1189), Expect = e-134 Identities = 253/628 (40%), Positives = 379/628 (60%), Gaps = 23/628 (3%) Query: 3 ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62 + A++++ VGG N+ + HC TRLRF L DESKA E L+ T G++ V +SGGQ+ V+ Sbjct: 5 QTAKEVLELVGGEKNVKQVTHCMTRLRFNLYDESKADKEKLQSTDGVMGVNQSGGQYHVI 64 Query: 63 IGNHVADVFLAVNSVAGLDEKAQQA-PENDDKGNLLNRFVYVISGIFTPLIGLMAATGIL 121 IGN V++V+ A+ + +GL + E K N++++ ISG+FTP++ +A G++ Sbjct: 65 IGNDVSNVYQAMIADSGLSSDVKSGGTEEASKQNVISKLFDFISGVFTPILPAIAGAGMI 124 Query: 122 KGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGAL 181 KG+LAL LTFQW +++S TY IL + D F+F PI+L + K+ G N + A I A Sbjct: 125 KGILALMLTFQWISDKSSTYAILTAIGDGAFYFLPILLAVSVAKKIGTNQYIAAAIAAAA 184 Query: 182 VHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPSA 241 +HP + G +FLG+PV + YSSSVIPI+ + WL S +ER + P + Sbjct: 185 LHPQLTALLGAGNT------EFLGLPVVAVVYSSSVIPILLTIWLGSYVERFAEKYSPKS 238 Query: 242 IKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIFV 301 +K P + L+V+ PV + VGPL I ++ G L++ AG ++GGF + Sbjct: 239 LKIILVPTVTLLVVVPVMLIAVGPLGGIIGSGLSGGIDLLFKHAGLLAGLLIGGFMSPLI 298 Query: 302 MFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAAL 361 + G+H+ L+P+ INN T+ G+D ++P++ A MAQ GAA GVFL ++ K +A S ++ Sbjct: 299 ITGMHYALLPIMINNITLNGFDFILPMMFVANMAQAGAAFGVFLRSKNKTFKSLAMSTSI 358 Query: 362 TSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVY----SFGLPSIFTFMQ 417 T+L GITEPA+YGVN+ K PF+ A I A G + + K Y S GLP + TF Sbjct: 359 TALMGITEPAMYGVNMRLKKPFLAALIGAAAGGVFMSIFKVKSYVISGSAGLPGLPTF-- 416 Query: 418 TIPSTGIDFTVWASVIGGVIAIGCAFVGTVMLHF--ITAKRQPAQGAPQEKTPEVITPPE 475 I T S+IG VIA A + T++L F + K P+EK E Sbjct: 417 ------IGPTFVYSIIGLVIAFVVATIMTLVLGFKDVPVKDDTKADKPEEKKDTAALQNE 470 Query: 476 QGGICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAIG 535 + SP+ G++ PL V D TF++ ++GKG AI+P+VG V +P G++ ++F T HAIG Sbjct: 471 V--VQSPLEGQLKPLNQVNDATFSNEIMGKGAAIVPTVGRVVAPFNGKVETIFHTKHAIG 528 Query: 536 IESDDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTTPV 595 ++S+ G E+LIHVGIDTVKLDGK+F++HV GD + GD LI FDI I++ G+D+TTPV Sbjct: 529 LKSEQGTELLIHVGIDTVKLDGKYFTSHVQSGDLIQAGDVLIDFDIEGIQQEGYDVTTPV 588 Query: 596 LISNSDDFTDVLPHGTAQISAGEPLLSI 623 +++N++DF V I+ E LL++ Sbjct: 589 IVTNTNDFAQVDAKTDGTITVKETLLTV 616 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: 1124 Number of extensions: 65 Number of successful extensions: 6 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: 635 Length adjustment: 38 Effective length of query: 587 Effective length of database: 597 Effective search space: 350439 Effective search space used: 350439 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