Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate WP_103233592.1 C1634_RS09815 6-phosphofructokinase
Query= CharProtDB::CH_024070 (320 letters) >NCBI__GCF_002899945.2:WP_103233592.1 Length = 328 Score = 239 bits (609), Expect = 9e-68 Identities = 137/305 (44%), Positives = 193/305 (63%), Gaps = 4/305 (1%) Query: 2 IKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDM 61 +KKI VLTSGGD+PGMNAA+R VVR+A +E G+ +GY GL D +++ SV ++ Sbjct: 6 VKKIAVLTSGGDSPGMNAALRAVVRTANYYNIECYGVREGYNGLINDDFLKMGARSVKNI 65 Query: 62 INRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLT-EMGFPC 120 IN+GGT L SAR EFR + R A +N K GID LV IGGDG++ GA E G Sbjct: 66 INQGGTILKSARSAEFRTKEGRQKAYDNCVKLGIDGLVCIGGDGTFTGAKIFNEEFGIRV 125 Query: 121 IGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLA 180 IG+PGTIDNDI GTD TIG+ TAL+T ++AID++RDT++SH R+ VEVMGR G + L Sbjct: 126 IGIPGTIDNDIFGTDNTIGYDTALNTAMDAIDKIRDTATSHNRVFFVEVMGRDAGFIALN 185 Query: 181 AAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAIT--EHMCDVDELAHFIEKE 238 + +A G +++PE + S ++L + + GK +IV + E + +V ELA + Sbjct: 186 SGLATGALDILIPEKKDSIDELFAKFRNAEKTGKSSSIVVVAEGEKLANVYELAEKTKLT 245 Query: 239 -TGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNEQLVHHDI 297 + R +LGH+QRGGSP DR+LASR+G A+ L+ G G+++ L + I Sbjct: 246 FPDYDIRVAILGHMQRGGSPSCADRVLASRLGYGAVVGLMDGQSNVMAGMRSNDLTYTPI 305 Query: 298 IDAIE 302 +AI+ Sbjct: 306 EEAIK 310 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: 319 Number of extensions: 15 Number of successful extensions: 3 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: 328 Length adjustment: 28 Effective length of query: 292 Effective length of database: 300 Effective search space: 87600 Effective search space used: 87600 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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