Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate Echvi_2380 Echvi_2380 6-phosphofructokinase
Query= CharProtDB::CH_024070 (320 letters) >FitnessBrowser__Cola:Echvi_2380 Length = 328 Score = 253 bits (646), Expect = 4e-72 Identities = 149/316 (47%), Positives = 199/316 (62%), Gaps = 6/316 (1%) Query: 2 IKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDM 61 I KIGVLTSGGDAPGMNAAIR VVR A LEV GIY GY G+ ++ + QL+ ++ + Sbjct: 6 ITKIGVLTSGGDAPGMNAAIRAVVRCAFYYNLEVYGIYRGYEGMIQNDIRQLNSSDIAYV 65 Query: 62 INRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGA-MRLTEMGFPC 120 + RGGTFL SAR EFR R A ENL++ GI+ LVVIGGDGS GA + E G P Sbjct: 66 LERGGTFLKSARSAEFRTPEGRKKAYENLQQHGINGLVVIGGDGSLTGAHLFYKEFGIPA 125 Query: 121 IGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLA 180 IGLPGTIDND+ GTD TIGF TA +T +EAID++RDT++SH R+ VEVMGR G + + Sbjct: 126 IGLPGTIDNDLSGTDNTIGFDTACNTAIEAIDKIRDTATSHDRLFFVEVMGRDSGFIAIN 185 Query: 181 AAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHA---IVAITEHMCDVDELAHFIEK 237 A I ++PE + E L++ + AK KK A IVA E++ ++K Sbjct: 186 AGIGSAAAATLIPEKKMPVEALIDRLNTR-AKAKKQANVVIVAEGGKSGGALEISKKVKK 244 Query: 238 E-TGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNEQLVHHD 296 + + T+LGH+QRGGSP YDR+LAS++G A++ L+ G G+ N ++V+ Sbjct: 245 YLPNYDIKVTILGHLQRGGSPTSYDRVLASKLGVSAVEGLMQGKCDVMAGVINNKVVYTP 304 Query: 297 IIDAIENMKRPFKGDW 312 I AI + K + D+ Sbjct: 305 IKRAIVDDKEVDEEDF 320 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: 345 Number of extensions: 17 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 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