Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate Synpcc7942_0592 Synpcc7942_0592 6-phosphofructokinase
Query= CharProtDB::CH_024070 (320 letters) >FitnessBrowser__SynE:Synpcc7942_0592 Length = 360 Score = 184 bits (468), Expect = 2e-51 Identities = 120/314 (38%), Positives = 183/314 (58%), Gaps = 26/314 (8%) Query: 2 IKKIGVLTSGGDAPGMNAAIRGVVRSALTE-GLEVMGIYDGYLGLYEDRMVQL-----DR 55 ++K+GVLTSGGD PG+NA IR + R A+ G E+ GI GL + + + L DR Sbjct: 3 VRKLGVLTSGGDCPGLNAVIRAIARHAVGNYGWELWGIAYATQGLLKRQAIALSPHHFDR 62 Query: 56 YSVSDMINRGGTFLGSARFPEFRDENI--RAVAIENLKKRGIDALVVIGGDGSYMGAMRL 113 S+ ++ GGT LGS R + + +A + ++ G+DAL+ IGGDGS +L Sbjct: 63 QSLDPLLCSGGTILGSIN----RGDTLAHQAEILAGYQELGLDALIGIGGDGSLAILRQL 118 Query: 114 TEMG-FPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGR 172 E G + IG+P TIDND+ T+ IGF TA+ TV EA+ L T++SH RI + EVMGR Sbjct: 119 AEAGRWQFIGIPKTIDNDVALTERAIGFDTAIHTVAEALLSLGSTAASHDRIMIAEVMGR 178 Query: 173 YCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAK-GKKHAIVAI---TEHMCDV 228 G L L IAGG + +++PE+ + +L + ++ + +++A++AI T H +V Sbjct: 179 QSGHLALQGGIAGGADVILLPEIPYRLLELCHYLQQLRDRWQRRYAVIAIAEGTHHPPEV 238 Query: 229 --------DELAHFI-EKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAG 279 ++L I ++ + R TVLGH+QRGG+PV DR+LA++MG A++ L AG Sbjct: 239 TQGPGSLGEQLVQAITAQDPTLDARVTVLGHVQRGGNPVASDRLLATQMGYAAVERLAAG 298 Query: 280 YGGRCVGIQNEQLV 293 G + Q ++V Sbjct: 299 ASGEMMAWQGGRVV 312 Lambda K H 0.322 0.141 0.413 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: 344 Number of extensions: 18 Number of successful extensions: 5 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: 320 Length of database: 360 Length adjustment: 28 Effective length of query: 292 Effective length of database: 332 Effective search space: 96944 Effective search space used: 96944 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 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