Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate BWI76_RS27535 BWI76_RS27535 PTS transporter subunit IIBC
Query= BRENDA::P69786 (477 letters) >FitnessBrowser__Koxy:BWI76_RS27535 Length = 519 Score = 226 bits (576), Expect = 1e-63 Identities = 162/512 (31%), Positives = 256/512 (50%), Gaps = 51/512 (9%) Query: 8 NLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVS-----HVMAEAGGS----VFAN 58 N+QK ++++ V LP+ G++L + S + P ++S H + + G +F N Sbjct: 11 NMQKFSRAMIGAVLFLPVIGLILALSSVLTN--PTLISETSFLHQLGQLLGDTFWPLFGN 68 Query: 59 MPLIFAIGVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKH------ 112 + L+F +G++ G + V IM H AE+I ++ Sbjct: 69 LGLLFCVGISYGLAKDKKTEVALVSVMCFIMFLGANHSWLEHTHGLAEKINGEYYGTGQT 128 Query: 113 ------LADTGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGV 166 + D GV GII G A++ N+ I+LP L + G + + IF + Sbjct: 129 QLLGFVVVDMGVFLGIILGCTIAWVHNKVSTIELPGALSMYGGAKLTLVAMTPVVIFYAI 188 Query: 167 VLSFIWPPIGSAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQM-QIGEY 225 ++ WP + I + + F +YGF E+ L+P GLHH PFQ+ QIG Sbjct: 189 AFTWFWPFMTHGIAALTGFMKNAGVAGVF-VYGFFEKFLIPTGLHHFVWSPFQLTQIGGT 247 Query: 226 TNAAGQVFHGDIPRYMA----GDPT-----AGKLSGGFLFKMYGLPAAAIAIWHSAKPEN 276 + GQV G ++A D T A + S + ++GL A++A +H+AKPE Sbjct: 248 LSVDGQVVSGTQAIFLAYMRHPDLTPVMNEALRFSQQGMTTIFGLAGASLAFYHTAKPEK 307 Query: 277 RAKVGGIMISAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRD-GT 335 + I++ A +TS LTGITEPIEF+F+FV+P+L++IHA L + IC + +R G Sbjct: 308 KMMAKAILLPAIITSMLTGITEPIEFTFLFVSPLLWVIHATLTAASQAICDIFTVRPWGA 367 Query: 336 SFSHGLIDFIV----LSGNSSKLWLFPIVGIGYAIVYYTIFRVLIKALDLKTPGRED--- 388 S GLI+F++ L + ++ + ++GIG VYY IFR L+ L+LKTPGRED Sbjct: 368 S---GLIEFLIYNLPLPVSLTRWPGYVLIGIGQFAVYYVIFRTLVVKLNLKTPGREDDEN 424 Query: 389 ------ATEDAKATGTSEMAPALVAAFGGKENITNLDACITRLRVSVADVSKVDQAGLKK 442 A K + ++ GGKENI ++D C TRLRV++ ++ VD LK Sbjct: 425 VKLYSKADYRKKMGEPQSVTNEIINGLGGKENIISVDNCFTRLRVAIHNMDLVDDTILKS 484 Query: 443 LGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYI 474 GA GVV + VQ I+G K +++ +D ++ Sbjct: 485 TGANGVVRNRNEVQVIYGVKVGQVRSRVDSWL 516 Lambda K H 0.325 0.140 0.422 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: 667 Number of extensions: 45 Number of successful extensions: 7 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: 477 Length of database: 519 Length adjustment: 34 Effective length of query: 443 Effective length of database: 485 Effective search space: 214855 Effective search space used: 214855 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 (21.6 bits) S2: 52 (24.6 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