Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate CA265_RS20980 CA265_RS20980 6-phosphofructokinase
Query= CharProtDB::CH_024070 (320 letters) >FitnessBrowser__Pedo557:CA265_RS20980 Length = 327 Score = 253 bits (647), Expect = 3e-72 Identities = 138/306 (45%), Positives = 200/306 (65%), Gaps = 3/306 (0%) Query: 2 IKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDM 61 IK IGVLTSGGD+PGMNAAIR VVR ++ +EV G GY GL + + +DR SV+++ Sbjct: 4 IKNIGVLTSGGDSPGMNAAIRAVVRGSIYYDIEVTGFMRGYEGLINNDFIPMDRKSVANI 63 Query: 62 INRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLT-EMGFPC 120 I RGGT L +AR F+ R A ENLK GIDALVVIGGDG++ GA + E FP Sbjct: 64 IQRGGTILKTARSEAFKTVEGRKKAYENLKANGIDALVVIGGDGTFTGANIFSKEFDFPI 123 Query: 121 IGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLA 180 +GLPGTIDND+ GTD+TIG+ +A++TV++A+D++RDT+ SH R+ +VEVMGR G + L Sbjct: 124 VGLPGTIDNDLAGTDFTIGYDSAINTVIDAVDKIRDTAESHDRLFIVEVMGRDSGLIALR 183 Query: 181 AAIAGGCEFVVVPEVEFSREDLVNEIK-AGIAKGKKHAIVAITEHMCDVDELAHFIE-KE 238 + I G E +++PE + +D++++++ + K K IVA + ++ ++ K Sbjct: 184 SGIGVGAEAIMIPEANMNADDILHKLEHSRKDKASKIIIVAEGDDTGGAFKVGEILQAKY 243 Query: 239 TGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNEQLVHHDII 298 +T+ +VLGHIQRGG P DR+LASR+G A++ L+ G G G N ++V Sbjct: 244 PHYDTKVSVLGHIQRGGKPTCMDRVLASRLGVAAVEGLINGESGVMAGQINREIVFTPFD 303 Query: 299 DAIENM 304 AI+++ Sbjct: 304 HAIKHI 309 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: 337 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: 327 Length adjustment: 28 Effective length of query: 292 Effective length of database: 299 Effective search space: 87308 Effective search space used: 87308 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