Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)
Query= BRENDA::P69786 (477 letters) >FitnessBrowser__SB2B:6936959 Length = 485 Score = 435 bits (1118), Expect = e-126 Identities = 210/469 (44%), Positives = 307/469 (65%), Gaps = 7/469 (1%) Query: 6 FANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPLIFAI 65 F Q++ ++L++P+++LP AG+++G+ + ++P V + +M G +F MP++FAI Sbjct: 20 FRFAQRLSQTLLIPIAILPAAGVMIGIATNPLPFIPDVANVLMLSVGKLIFDIMPMLFAI 79 Query: 66 GVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLGGIISG 125 VA+GF + G++A +A YG+++ T+A A V HLP+ + DTG+ GG++ G Sbjct: 80 AVAIGFCRDQGIAAFSAAFGYGVLLSTLAAAAK-VYHLPSHIVWGTPTIDTGIAGGMLVG 138 Query: 126 AIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQTFSQW 185 I +++LP FF G+R P+I + V+L+FIWPP+ +I+ S W Sbjct: 139 GITCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVMLAFIWPPLALSIERLSDW 198 Query: 186 AAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYMAGDP 245 A YQ P +AFG YG +ER L+P GLHHIWN PF +++G+Y + G++ G++ RY AGDP Sbjct: 199 AVYQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYAHD-GEIVRGEMARYFAGDP 257 Query: 246 TAGKLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFM 305 +AG L+GG+L KM+GLPAAA+AIW A R +V G+M+SAA S+LTG+TEPIEF+F+ Sbjct: 258 SAGNLAGGYLIKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTGVTEPIEFAFL 317 Query: 306 FVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIVGIGYA 365 FVAP+LY+ HA+L GLA+ I ILL M FSHGL+DF++L SS +G Sbjct: 318 FVAPLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLFPQSSNTHWIWFLGPLTF 377 Query: 366 IVYYTIFRVLIKALDLKTPGREDATEDAKATGTSEMAPALVAAFGGKENITNLDACITRL 425 ++YY +FR I A +LKTPGR +A TG A+V+A GG NI +L AC+TRL Sbjct: 378 VIYYILFRASILAFNLKTPGRFEAD-----TGQKRNLIAIVSALGGGGNIADLSACLTRL 432 Query: 426 RVSVADVSKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYI 474 R+SVAD S+VD+ L LGA GV+V GSGVQ +FGTK++ L+ + Y+ Sbjct: 433 RISVADPSQVDRQRLMSLGAKGVIVVGSGVQLVFGTKAETLRKLLQRYL 481 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: 690 Number of extensions: 30 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: 477 Length of database: 485 Length adjustment: 34 Effective length of query: 443 Effective length of database: 451 Effective search space: 199793 Effective search space used: 199793 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: 51 (24.3 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