Align 6-phosphofructokinase (EC 2.7.1.11) (characterized)
to candidate 3608216 Dshi_1621 PfkB domain protein (RefSeq)
Query= BRENDA::P06999 (309 letters) >FitnessBrowser__Dino:3608216 Length = 316 Score = 192 bits (489), Expect = 7e-54 Identities = 129/314 (41%), Positives = 176/314 (56%), Gaps = 9/314 (2%) Query: 1 MVRIYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFP 60 M RI TLTL P+LDS+T + P+ KLRC+AP + GGGG+NV+RAIA LGG + A Sbjct: 1 MTRIVTLTLNPALDSSTDAEHVAPDLKLRCSAPRADAGGGGVNVSRAIAFLGGQSLAALA 60 Query: 61 AGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNE-DEFR 119 GG GE + LL E +PV + TRQNL V +G QYRF+MPG + D R Sbjct: 61 LGGGPGERVRQLLRVEGIPVHDLGVAVETRQNLSVIARDTGAQYRFIMPGQTWTDVDVDR 120 Query: 120 QLEEQVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIG 179 E +G ++V SGSLPPGV L L + G+R ++D+SG AL A A G Sbjct: 121 SCEALCKLARAGDLIVPSGSLPPGVGPGDLVALTNRLAVLGVRIVLDTSGAALQ-AFATG 179 Query: 180 ---NIELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSE 236 + +++ + +E +L R+L DV + +E+V++G AK V+V+ G +G++ V S Sbjct: 180 RAKTLHVLRMDLEEAQSLAGRDLDTVADVAQFGRELVDAGAAKSVIVAKGAEGSILVTSR 239 Query: 237 -NCIQVVPPPVKSQSTVGAGDSMVGAMTLKLAENAS-LEEMVRFGVAAGSAATLNQGTRL 294 V PP V S GAGDS V TL LA+ +S LE VR GV A ++A T L Sbjct: 240 GQGWHVRPPKVNVVSKTGAGDSFVAGFTLALAQGSSDLEATVR-GVGAAASAVTTPDTDL 298 Query: 295 CSHDDTQKIYAYLS 308 C ++ YA LS Sbjct: 299 CDGASAER-YAALS 311 Lambda K H 0.314 0.131 0.363 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: 283 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: 309 Length of database: 316 Length adjustment: 27 Effective length of query: 282 Effective length of database: 289 Effective search space: 81498 Effective search space used: 81498 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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