Align 1-phosphofructokinase; Fructose 1-phosphate kinase; EC 2.7.1.56 (characterized)
to candidate Pf1N1B4_6031 Ribokinase (EC 2.7.1.15)
Query= SwissProt::D4GYE6 (305 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6031 Length = 305 Score = 83.6 bits (205), Expect = 5e-21 Identities = 89/284 (31%), Positives = 121/284 (42%), Gaps = 51/284 (17%) Query: 36 AGGKGINVAKYASALDADVTASGFLGGH-FGKFVRDRL--------------DADGIASD 80 +GGKG N A A+ L A V+ G +G +G+ +R L D+ G+A Sbjct: 38 SGGKGANQAVAAARLGAQVSMVGCVGNDAYGEALRGALLAEQIDCQAVSTVEDSSGVA-- 95 Query: 81 FVTVDADTRLNTTVLAADGEYKLNHN-----GPQIRAADVDELVETAQANEPDTLLVGGS 135 + VD D N V+ A L ++AADV Q PD VG + Sbjct: 96 LIVVD-DNSQNAIVIVAGANGALTPEVIDRFDAVLQAADVI----ICQLEVPDAT-VGHA 149 Query: 136 LPPGMSLSDVDRLARAG-------DWKIAVDMGGEYLAELDADYYVCKPNRSELAAATGR 188 L G L L A DW A+D YL PN SE + +G Sbjct: 150 LKRGRELGKTVILNPAPASRPLPVDWYAAID----YLI----------PNESEASVLSGL 195 Query: 189 TVETEADAVEAAEELHARGFEYVLASLGADGALLVTDDEVLSAPALDVEVVDTVGAGDAV 248 V++ + A AA L A G V+ +LG+ G+L PA V+ VDT AGD Sbjct: 196 PVDSLSTAETAATRLIAMGAGKVIITLGSQGSLFADGQRFEHFPAAKVKAVDTTAAGDTF 255 Query: 249 MSGFLAAREHGLSDADALRMGVLTASRVVGVAGTR--VPDLEDV 290 + GF AA G +ADA+R G + A+ V AG + +P L DV Sbjct: 256 VGGFAAALAAGKGEADAIRFGQVAAALSVTRAGAQPSIPTLSDV 299 Lambda K H 0.315 0.133 0.375 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: 231 Number of extensions: 13 Number of successful extensions: 2 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: 305 Length of database: 305 Length adjustment: 27 Effective length of query: 278 Effective length of database: 278 Effective search space: 77284 Effective search space used: 77284 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 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