Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate 351590 BT2062 6-phosphofructokinase (NCBI ptt file)
Query= CharProtDB::CH_024070 (320 letters) >FitnessBrowser__Btheta:351590 Length = 326 Score = 278 bits (711), Expect = 1e-79 Identities = 153/323 (47%), Positives = 209/323 (64%), Gaps = 7/323 (2%) Query: 2 IKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDM 61 +K IG+LTSGGDAPGMNAAIR V R+A+ GL+V GIY GY GL + + +VS++ Sbjct: 4 VKCIGILTSGGDAPGMNAAIRAVTRAAIYNGLQVKGIYRGYKGLVTGEIKEFKSQNVSNI 63 Query: 62 INRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGA-MRLTEMGFPC 120 I GGT L +AR EF R +A +N+K+ GIDALV+IGGDGS GA + E PC Sbjct: 64 IQLGGTILKTARCKEFTTPEGRQLAYDNMKREGIDALVIIGGDGSLTGARIFAQEFDVPC 123 Query: 121 IGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLA 180 IGLPGTIDND+ GTD TIG+ TAL+T+++A+D++RDT++SH+R+ VEVMGR G L L Sbjct: 124 IGLPGTIDNDLYGTDTTIGYDTALNTILDAVDKIRDTATSHERLFFVEVMGRDAGFLALN 183 Query: 181 AAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCDVDELAHFIEKETG 240 AIA G E ++PE + L IK G K K +IV + E + H+ E+ Sbjct: 184 GAIASGAEAAIIPEFSTEVDQLEEFIKNGFRKSKNSSIVLVAESELTGGAM-HYAERVKN 242 Query: 241 R----ETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNEQLVHHD 296 + R T+LGH+QRGGSP +DRILASR+GA AID ++ +GI+++++V+ Sbjct: 243 EYPQYDVRVTILGHLQRGGSPTAHDRILASRLGAAAIDAIMEDQRNVMIGIEHDEIVYVP 302 Query: 297 IIDAIENMKRPFKGDWLDCAKKL 319 AI+N K P K D ++ K+L Sbjct: 303 FSKAIKNDK-PVKRDLVNVLKEL 324 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: 350 Number of extensions: 14 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: 326 Length adjustment: 28 Effective length of query: 292 Effective length of database: 298 Effective search space: 87016 Effective search space used: 87016 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 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