Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate Echvi_2325 Echvi_2325 6-phosphofructokinase
Query= CharProtDB::CH_024070 (320 letters) >FitnessBrowser__Cola:Echvi_2325 Length = 324 Score = 255 bits (652), Expect = 9e-73 Identities = 139/318 (43%), Positives = 202/318 (63%), Gaps = 8/318 (2%) Query: 2 IKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDM 61 +KKI VLTSGGDAPGMNA IR VVR+ + G+E+ GI GY G+ + +++ ++VS++ Sbjct: 1 MKKIAVLTSGGDAPGMNACIRAVVRTGIFHGMEMYGIMYGYDGMINGEIQKMESHAVSNI 60 Query: 62 INRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGA-MRLTEMGFPC 120 + RGGT L SAR +FR + R +A E L+K GI+ LV IGGDG++ GA + E G P Sbjct: 61 VQRGGTILKSARSEKFRTKEGRKIAYEQLQKHGIEGLVAIGGDGTFTGAKVFYEEYGIPT 120 Query: 121 IGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLA 180 IG PGTIDNDI GTD+TIGF TA++T +EAID++RDT+++H RI +EVMGR G + + Sbjct: 121 IGCPGTIDNDIYGTDFTIGFDTAINTALEAIDKIRDTAAAHDRIFFIEVMGRDSGYIAVE 180 Query: 181 AAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITE-----HMCDVDELAHFI 235 + GG E V+VPE + + ++V ++K G K K +++ + E ++ E I Sbjct: 181 CGLGGGAEMVMVPETKTTLHEVVEKLK-GSRKTKTSSVIVVAEGDEEGSAAEIMEKVKNI 239 Query: 236 EKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNEQLVHH 295 + ++ + T LGHIQRGG+P DR+LASR G A++ L+ G GI ++++V+ Sbjct: 240 INDDTKDFKVTTLGHIQRGGNPTGKDRMLASRCGMAAVEGLMNGQANCMAGIIHDEVVYT 299 Query: 296 DIIDAIENMKRPFKGDWL 313 D I K P D L Sbjct: 300 SFEDCITKSK-PLNKDTL 316 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: 307 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: 324 Length adjustment: 28 Effective length of query: 292 Effective length of database: 296 Effective search space: 86432 Effective search space used: 86432 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