Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate WP_212636784.1 B9A12_RS01450 6-phosphofructokinase
Query= CharProtDB::CH_024070 (320 letters) >NCBI__GCF_900176285.1:WP_212636784.1 Length = 743 Score = 240 bits (612), Expect = 9e-68 Identities = 146/342 (42%), Positives = 197/342 (57%), Gaps = 37/342 (10%) Query: 1 MIKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYE--DRMVQLDRYSV 58 M++ + V+TSGGDAPGMNA +R VVR AL G++V G++ GY GL D + L V Sbjct: 1 MVRTMAVMTSGGDAPGMNAGVRAVVRRALDGGMDVYGVFSGYEGLVAGGDAIRPLGWNDV 60 Query: 59 SDMINRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTE--- 115 ++ RGGTFLG+AR FR R A++NL +RGI ALVVIGGDGS MGA L E Sbjct: 61 GGILPRGGTFLGTARSERFRTVEGRRQAVKNLCERGIQALVVIGGDGSLMGARVLAEEWQ 120 Query: 116 ---------------MGFP----CIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRD 156 G P +GLPG+IDND+ GTD +IG TAL+ +V AID L Sbjct: 121 MHCAELGQEAPAEGRAGMPERLHVVGLPGSIDNDLYGTDMSIGADTALNHIVHAIDDLTS 180 Query: 157 TSSSHQRISVVEVMGRYCGDLTLAAAIAGGCEFVVVPEVEFS---REDLVNEIKAGIAKG 213 T++SHQR +VE MGR+CG L L A+ GG +V+VPE E E + I+ A G Sbjct: 181 TAASHQRTFIVETMGRHCGYLALMGALGGGASWVLVPEEELDLRWHEKMSRAIERARAIG 240 Query: 214 KKHAIVAITEHMCDVD-------ELAHFIEKETGRETRATVLGHIQRGGSPVPYDRILAS 266 + H +V + E D EL + + G + R TVLGH+QRGG P +DRILA+ Sbjct: 241 RPHQMVVVAEGARHPDGLPIRTEELKRILAERLGIDVRVTVLGHVQRGGPPSAFDRILAT 300 Query: 267 RMGAYAIDLLL-AGYGGRC--VGIQNEQLVHHDIIDAIENMK 305 R+G A++LL+ AG C VG+Q ++ + + +E + Sbjct: 301 RLGVAAVELLMGAGPEPLCHMVGLQKNRVTTTSLSEVVEKSR 342 Score = 174 bits (440), Expect = 8e-48 Identities = 105/283 (37%), Positives = 160/283 (56%), Gaps = 17/283 (6%) Query: 5 IGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDMINR 64 + +LT G DAPGMN A+ R L +G V+G+ D + GL L+ V+ +NR Sbjct: 389 VAILTGGADAPGMNTAVSIAARCLLNDGYAVLGVRDAFRGLIAADFQPLEWNQVTGWVNR 448 Query: 65 GGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTE-------MG 117 + LG+AR E ++ +A N++ I L+ +GG G+Y+ A RL E + Sbjct: 449 PSSELGTARH-ELSGSDLERIA-RNIQAHHIRGLIAVGGLGAYLNAKRLMEGASSHPALA 506 Query: 118 FPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDL 177 P + +P TIDN++ T++TIG TAL+ +V+A+D++R T+ +++R VVEVMGR G L Sbjct: 507 LPLVLIPATIDNNLPCTEFTIGCDTALNNIVQALDKIRHTAGANRRAFVVEVMGRQSGFL 566 Query: 178 TLAAAIAGGCEFVVVPEVEFSREDLVNEIKA---GIAKGKKHAIVAITEHMC---DVDEL 231 LA A+A G E +PE S +L +++A GK+ I E+ D + Sbjct: 567 ALAGALASGAEKAYLPERGISLAELNTDVEALRESFRCGKRMVIYLRNENASRHYTTDFI 626 Query: 232 AHFIEKETG--RETRATVLGHIQRGGSPVPYDRILASRMGAYA 272 A +E+E+ + R +LGH+QRGGSP +DRILA RMG+ A Sbjct: 627 ARLLEEESRGLYQVRTAILGHLQRGGSPTAFDRILACRMGSAA 669 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: 683 Number of extensions: 37 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 320 Length of database: 743 Length adjustment: 34 Effective length of query: 286 Effective length of database: 709 Effective search space: 202774 Effective search space used: 202774 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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