Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_034283128.1 BA81_RS14345 PTS transporter subunit EIIC
Query= TCDB::P08722 (625 letters) >NCBI__GCF_000691165.1:WP_034283128.1 Length = 618 Score = 497 bits (1279), Expect = e-145 Identities = 260/632 (41%), Positives = 394/632 (62%), Gaps = 28/632 (4%) Query: 3 ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62 +LA I+ +G N+ SL+HCATRLRF L D SKA ++K G++ V+ESGGQFQVV Sbjct: 5 QLAEDIIKHIGTEKNVHSLVHCATRLRFTLNDRSKADKAAIEKLNGVVTVMESGGQFQVV 64 Query: 63 IGNHVADVFLAVNSVAGL--DEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGI 120 IGN V +V+ + L D A A ++ +L +FV ++SGIFTPL+G+MA GI Sbjct: 65 IGNTVPEVYREIGEFTNLLEDSAASSAKSGEESTSLFGKFVDIVSGIFTPLLGVMAGAGI 124 Query: 121 LKGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGA 180 LKG+L + + +W + + +Y ILF+ASD+LF+F P++L +T+ ++F NPF A+ I GA Sbjct: 125 LKGLLGICINAKWLSPEDTSYQILFAASDSLFYFLPLLLAFTSARKFKANPFVAVTIAGA 184 Query: 181 LVHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPS 240 L++P I + G + F GIPV L++Y+S+VIPII + ++ +ER N + Sbjct: 185 LIYPTIQELSKGGGD-----VTFFGIPVVLMSYTSTVIPIILAVFVMGYIERFFNKVIHE 239 Query: 241 AIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIF 300 ++KNF TPL+ L+ + P+T ++ GP + IAA L ++ P AGA++ WQI Sbjct: 240 SVKNFITPLILLVTVVPLTLIVFGPFGVYAGNGIAAVLLKVFSFSPTLAGALIAMAWQIL 299 Query: 301 VMFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAA 360 V+FG+HWGLVP+ +NN V G D + P PA+ +Q GA++GV L ++ + K +AGS A Sbjct: 300 VIFGIHWGLVPVILNNIAVHGKDHIKPATAPAVFSQAGASIGVMLKTKNKKLKSLAGSTA 359 Query: 361 LTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQTIP 420 ++++FGITEPAVYGV L K PF+ A IS +G IIGY+Q+ + GLPS+ T+P Sbjct: 360 VSAVFGITEPAVYGVTLRLKKPFIAAVISAGVGGAIIGYSQSIAIASGLPSLL----TLP 415 Query: 421 -STGIDFTVWASVIGGVIAIGCAFVGTVMLHFITAKRQPAQGAPQEKTPEVITP------ 473 G FT G +I I +FV +++L ++ + P +++TP P Sbjct: 416 IFYGQGFT------GFIIGISVSFVLSIILTYLIGFKDPVD---EDETPAASAPVIENEH 466 Query: 474 -PEQGGICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLH 532 + + SP+ GE++ L V D F+SG LGKG AI+PS G++ +PV+G + ++F T H Sbjct: 467 GVKAAHVKSPLKGEVIKLEEVQDKAFSSGALGKGAAIIPSEGKLFAPVSGVVTTVFPTGH 526 Query: 533 AIGIESDDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLT 592 A G+ S+ G E+LIH+G+DTV+L GK F+ V G + G+ L FDI AI+ AG +T Sbjct: 527 AYGLTSESGAEVLIHIGLDTVQLGGKHFTPKVVQGQTITEGELLAEFDIEAIQAAGLSVT 586 Query: 593 TPVLISNSDDFTDVLPHGTAQISAGEPLLSII 624 TPV+I+NS +F+D++ QI+ G+ L ++ Sbjct: 587 TPVIITNSGEFSDIIETEEKQITPGQSFLHLV 618 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: 1181 Number of extensions: 73 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: 618 Length adjustment: 37 Effective length of query: 588 Effective length of database: 581 Effective search space: 341628 Effective search space used: 341628 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