Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate BWI76_RS11130 BWI76_RS11130 PTS glucose transporter subunit IIBC
Query= CharProtDB::CH_001857 (699 letters) >FitnessBrowser__Koxy:BWI76_RS11130 Length = 477 Score = 440 bits (1132), Expect = e-128 Identities = 243/514 (47%), Positives = 335/514 (65%), Gaps = 40/514 (7%) Query: 1 MFKALFGVLQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVM 60 MFK F LQK+G++LMLPV++LP AGILL +G+A N + + V+ VM Sbjct: 1 MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSA--NFSWLPAV----------VSHVM 48 Query: 61 ESAGQIVFDNLPLLFAVGVAIGLANGDGVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSV 120 AG VF N+PL+FA+GVA+G N DGV+ +A+++ Y +M +MS V +P++ + Sbjct: 49 AEAGGSVFANMPLIFAIGVALGFTNNDGVSALASVVAYGIMVKTMSVVAPLVLHLPAEEI 108 Query: 121 ERAKFFTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRF 180 AK + TGV GGII G +AA +FNRFY I+LP+YLGFFAGKRF Sbjct: 109 A-AKHLAD---------------TGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRF 152 Query: 181 VPIVTSISALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHH 240 VPI++ ++A+ G+I+ IWPPI + FS NP +A I+G IER L+PFGLHH Sbjct: 153 VPIISGLAAIFTGVILSFIWPPIGTAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHH 212 Query: 241 IFYSPFWYEFFSYKSAAGEIIRGDQRIFMAQIKDGVQLTAGTFMTGKYPFMMFGLPAAAL 300 I+ PF + Y +AAG++ GD +MA TAG ++G + F M+GLPAAA+ Sbjct: 213 IWNVPFQMQIGEYTNAAGQVFHGDIPRYMAG-----DPTAGK-LSGGFLFKMYGLPAAAI 266 Query: 301 AIYHEAKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSFMVM 360 AI+H AKP+N+ V GIM SAALTSFLTGITEP+EFSF+FVAP+L+ IH + AGL+F + Sbjct: 267 AIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGLAFPIC 326 Query: 361 QLLNVKIGMTFSGGLIDYFLFGILPNRTAWWLVIPVGLGLAVIYYFGFRFAIRKFNLKTP 420 LL ++ G +FS GLID+ + + N + WL VG+ A++YY FR I+ +LKTP Sbjct: 327 ILLGMRDGTSFSHGLIDFIV--LSGNSSKLWLFPIVGICYAIVYYVVFRVLIKALDLKTP 384 Query: 421 GREDAAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKDRL 480 GREDA E++ K G ++ ++ A G +ENI +LDACITRLRV+V D KVD+ L Sbjct: 385 GREDATEDS----KAGATSEMAPALIAAFGGKENITNLDACITRLRVSVADVAKVDQAGL 440 Query: 481 KQLGASGVLEVGNNIQAIFGPRSDGLKTQMQDII 514 K+LGA+GV+ G+ +QAIFG +SD LKT+M + I Sbjct: 441 KKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYI 474 Lambda K H 0.323 0.141 0.412 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: 925 Number of extensions: 41 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: 699 Length of database: 477 Length adjustment: 36 Effective length of query: 663 Effective length of database: 441 Effective search space: 292383 Effective search space used: 292383 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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