Align 1-phosphofructokinase; Fructose 1-phosphate kinase; EC 2.7.1.56 (characterized)
to candidate BPHYT_RS20695 BPHYT_RS20695 ribokinase
Query= SwissProt::D4GYE6 (305 letters) >FitnessBrowser__BFirm:BPHYT_RS20695 Length = 310 Score = 62.8 bits (151), Expect = 1e-14 Identities = 80/270 (29%), Positives = 111/270 (41%), Gaps = 41/270 (15%) Query: 36 AGGKGINVAKYASALDADVTASGFLG--GHFGKFVRDRLDADGIASDFVTVD-------- 85 AGGKG N A A+ + A V G +G + + V+D L+A+GI + V Sbjct: 43 AGGKGGNQAVAAARIGAQVAMVGCVGKDANGAQRVKD-LEAEGIDCSGIEVHPGQPTGVA 101 Query: 86 ----ADTRLNTTVLAADGEYKLN-----HNGPQIRAADVDEL-VETAQANEPDTLLVGGS 135 +D NT V+ A +L + I+A DV +ET + TL + Sbjct: 102 MVTVSDDGQNTIVVVAGSNGELTPESVARHEAAIKACDVVVCQLETPWDSVHATLALARR 161 Query: 136 LPPGMSLSDVDRLARA-GDWKIAVDMGGEYLAELDADYYVCKPNRSELAAATGRTVETEA 194 L L+ +W VD YL PN E A G VE+++ Sbjct: 162 LGKITVLNPAPATGPLPAEWLPLVD----YLV----------PNEVEAAILAGLPVESQS 207 Query: 195 DAVEAAEELHARGFEYVLASLGADGA-LLVTDDEVLSAPALDVEVVDTVGAGDAVMSGFL 253 A AA EL G V+ +LGA GA LLV E + PA V+ VDT AGD + F Sbjct: 208 GARRAATELQQGGARNVIVTLGAQGAYLLVEGGEGMHFPAPQVQAVDTTAAGDTFIGVFA 267 Query: 254 AAREHGLSDADALRMGVLTASRVVGVAGTR 283 A L+ L + A R ++ TR Sbjct: 268 AQ----LASRQPLESAISLAQRAASISVTR 293 Lambda K H 0.315 0.133 0.375 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: 213 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 305 Length of database: 310 Length adjustment: 27 Effective length of query: 278 Effective length of database: 283 Effective search space: 78674 Effective search space used: 78674 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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