Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate WP_011337406.1 RSPH17029_RS05145 1-phosphofructokinase family hexose kinase
Query= reanno::psRCH2:GFF3290 (312 letters) >NCBI__GCF_000015985.1:WP_011337406.1 Length = 314 Score = 126 bits (317), Expect = 6e-34 Identities = 107/315 (33%), Positives = 152/315 (48%), Gaps = 14/315 (4%) Query: 1 MARVLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGF 60 M +LT+TLNPA+DL +P + G R +V G GLNV++ + LG + T Sbjct: 1 MIPILTLTLNPAIDLAADVPQVLPGIKLRCTEPRVDPGGGGLNVSRAIRILGGRSTAFVA 60 Query: 61 LGEGNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAE-ADGRVTDINGPGLAVSEAQRAE 119 LG L +A G GETR +L + E A GR PG A +A+R E Sbjct: 61 LGGNIGGRLAALVAAAGIEIVAFSGPGETRESLTVTETATGRQFRFMLPG-AAWDAERVE 119 Query: 120 L-LARLKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRD---G 175 LAR+ R VP +VV++GSLP G+ + F +++ + R+ +DTSGA L G Sbjct: 120 AALARIDRAVPEGGMVVLSGSLPPGVPAD-FPAMVSRVLGKRARLLVDTSGAPLAHLAAG 178 Query: 176 LATRPWLIKPNEEELAEARGIELSGSSALAAEAQRLQEEGI-EHVVVSQGADGVSWFSPG 234 +++ ++ E A G L+ +S A A L G+ E V+V++GADG Sbjct: 179 GVPDLDILRMDDGEAASLAGRPLACASETADFASSLVARGVAECVIVARGADGSVLADAR 238 Query: 235 AALHASPPKVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITD 294 HA V VVS VGAGD+ + + L G P E L H A AA AV +T+ Sbjct: 239 GRWHARSEPVEVVSAVGAGDTFVGAFVLALSRGAPPEEALAHGVAGAAAAV------LTE 292 Query: 295 TAQLAELQAAVRLQP 309 +L + RL P Sbjct: 293 ATELCHPEDVARLLP 307 Lambda K H 0.316 0.132 0.371 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: 241 Number of extensions: 12 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: 312 Length of database: 314 Length adjustment: 27 Effective length of query: 285 Effective length of database: 287 Effective search space: 81795 Effective search space used: 81795 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 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