Align 1-phosphofructokinase; Fructose 1-phosphate kinase; EC 2.7.1.56 (characterized)
to candidate GFF3591 PS417_18385 ribokinase
Query= SwissProt::D4GYE6 (305 letters) >FitnessBrowser__WCS417:GFF3591 Length = 305 Score = 87.4 bits (215), Expect = 4e-22 Identities = 89/273 (32%), Positives = 125/273 (45%), Gaps = 31/273 (11%) Query: 37 GGKGINVAKYASALDADVTASGFLGGH-FGKFVRDRLDADGIASDFV-TVDA-------- 86 GGKG N A ++ L ADV+ G +G +G +R+ L +GI V TVD Sbjct: 39 GGKGANQAVASARLGADVSMIGCVGSDAYGSQLREALLVEGIDCQAVSTVDGSSGVALIV 98 Query: 87 --DTRLNTTVLAADGEYKLNHNGPQ-----IRAADVDELVETAQANEPDTLLVGGSLPPG 139 D+ N V+ A +L Q ++AADV N VG +L G Sbjct: 99 VDDSSQNAIVIVAGSNGELTPASLQAFDAVLQAADVIVCQLEVPMNT-----VGYALKRG 153 Query: 140 MSLSDVDRLARAGDWKIAVDMGGEYLAELDADYYVCKPNRSELAAATGRTVETEADAVEA 199 L L A + + E+ A +D Y + PN SE +A +G TV++ A A Sbjct: 154 RELGKTVILNPA---PASGPLPAEWYASID--YLI--PNESEASALSGVTVDSIDAAKVA 206 Query: 200 AEELHARGFEYVLASLGADGALLVTDDEVLSAPALDVEVVDTVGAGDAVMSGFLAAREHG 259 A +L G V+ +LGA GAL A V+ VDT AGD + GF AA +G Sbjct: 207 ATQLIQAGAGKVIVTLGAQGALFTDGQRFEHLQAPKVKAVDTTAAGDTFVGGFAAALANG 266 Query: 260 LSDADALRMGVLTASRVVGVAGTR--VPDLEDV 290 S+A+A+R G + A+ V AG + +P L DV Sbjct: 267 KSEAEAIRFGQVAAALSVTRAGAQPSIPTLHDV 299 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: 212 Number of extensions: 11 Number of successful extensions: 2 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: 305 Length of database: 305 Length adjustment: 27 Effective length of query: 278 Effective length of database: 278 Effective search space: 77284 Effective search space used: 77284 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