Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate 352883 BT3356 6-phosphofructokinase (NCBI ptt file)
Query= CharProtDB::CH_024070 (320 letters) >FitnessBrowser__Btheta:352883 Length = 336 Score = 239 bits (610), Expect = 7e-68 Identities = 125/302 (41%), Positives = 196/302 (64%), Gaps = 13/302 (4%) Query: 4 KIGVLTSGGDAPGMNAAIRGVVRSALTE-GLEVMGIYDGYLGLYEDRMVQLDRYSVSDMI 62 +IG+LTSGGD PG+NA IRGV ++A+ G+EV+GI+ G+ GL + S+S ++ Sbjct: 2 RIGILTSGGDCPGINATIRGVCKTAINHYGMEVIGIHSGFQGLLTKDIESFTDKSLSGLL 61 Query: 63 NRGGTFLGSARFPEFR------DENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTEM 116 N+GGT LG++R F+ D + A+ ++N+++ G+D +V IGG+G+ A + M Sbjct: 62 NQGGTMLGTSREKPFKKGGVVSDVDKPALILQNIQEMGLDCVVCIGGNGTQKTAAKFAAM 121 Query: 117 GFPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGD 176 G + +P TIDNDI GTD + GF +A+S +AIDRL T+SSH+R+ V+EVMG G Sbjct: 122 GVNIVSVPKTIDNDIWGTDISFGFDSAVSIATDAIDRLHSTASSHKRVMVIEVMGHKAGW 181 Query: 177 LTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCD------VDE 230 + L + +AGG + ++VPE+ ++ +++ N I + KGK ++IV + E + + Sbjct: 182 IALYSGMAGGGDVILVPEIPYNIKNIGNTILERLKKGKPYSIVVVAEGILTDGRKRAAEY 241 Query: 231 LAHFIEKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNE 290 +A IE ETG ETR TVLG+IQRGGSP P+DR L++RMG +A +L+ G GR + ++ + Sbjct: 242 IAQEIEYETGIETRETVLGYIQRGGSPTPFDRNLSTRMGGHATELIANGQFGRMIALKGD 301 Query: 291 QL 292 + Sbjct: 302 DI 303 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: 373 Number of extensions: 26 Number of successful extensions: 4 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: 336 Length adjustment: 28 Effective length of query: 292 Effective length of database: 308 Effective search space: 89936 Effective search space used: 89936 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: 49 (23.5 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