Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate WP_011384698.1 AMB_RS11635 ATP-dependent 6-phosphofructokinase
Query= CharProtDB::CH_024070 (320 letters) >NCBI__GCF_000009985.1:WP_011384698.1 Length = 361 Score = 216 bits (551), Expect = 5e-61 Identities = 135/331 (40%), Positives = 185/331 (55%), Gaps = 35/331 (10%) Query: 3 KKIGVLTSGGDAPGMNAAIRGVVRSALTE-GLEVMGIYDGYLGLYEDRM--VQLDRYSVS 59 K+IG+LTSGGD G+NAA+R VV A+ G +V GI DG LGL + V+ D SV Sbjct: 4 KRIGILTSGGDCAGLNAALRAVVHRAIRNYGWKVFGIRDGSLGLMNRPLNYVEFDLKSVG 63 Query: 60 D-MINRGGTFLGSAR--------FPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGA 110 D M+ GGT LG+ P+ ++ ++ K+ GI+ALVVIGGDGS Sbjct: 64 DDMLRLGGTILGTINKGDPFAYPMPDGSKKDRSQDFVDGYKELGIEALVVIGGDGSMRIL 123 Query: 111 MRLTEMG-FPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEV 169 L G P +G+P TIDND+ TDY IGF TAL+ EA+DRL T++SH R+ ++EV Sbjct: 124 NELCRKGGIPMVGIPKTIDNDVAQTDYAIGFATALNVAGEAMDRLAPTAASHHRVMILEV 183 Query: 170 MGRYCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCDVD 229 MGR G + L A IAGG + V++PE+ ++ E + +I +G+ HA++ + E C + Sbjct: 184 MGRDVGHIALNAGIAGGADVVLIPEIPYTLEGIAKKIAEVRDEGRNHALMVVAEG-CKTE 242 Query: 230 E---------------------LAHFIEKETGRETRATVLGHIQRGGSPVPYDRILASRM 268 LA + + ETR TVLGH+QRGG P DRI+AS Sbjct: 243 TGESVTTLQSGGQARYGGIGQYLAARLAETVEAETRVTVLGHVQRGGMPAMRDRIIASAF 302 Query: 269 GAYAIDLLLAGYGGRCVGIQNEQLVHHDIID 299 G YA+DL+ G GR V Q+ Q+V I D Sbjct: 303 GVYAVDLIAQGKLGRMVAWQHGQVVDVPITD 333 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: 358 Number of extensions: 14 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: 361 Length adjustment: 28 Effective length of query: 292 Effective length of database: 333 Effective search space: 97236 Effective search space used: 97236 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