Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate 3608216 Dshi_1621 PfkB domain protein (RefSeq)
Query= reanno::psRCH2:GFF3290 (312 letters) >FitnessBrowser__Dino:3608216 Length = 316 Score = 130 bits (328), Expect = 3e-35 Identities = 106/311 (34%), Positives = 148/311 (47%), Gaps = 7/311 (2%) Query: 1 MARVLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGF 60 M R++T+TLNPALD + + R + + A G G+NV++ +A LG Q Sbjct: 1 MTRIVTLTLNPALDSSTDAEHVAPDLKLRCSAPRADAGGGGVNVSRAIAFLGGQSLAALA 60 Query: 61 LGEGNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEAD-GRVTDINGPGLAVSEAQRAE 119 LG G + QL G + VA ETR NL + D G PG ++ Sbjct: 61 LGGGPGERVRQLLRVEGIPVHDLGVAVETRQNLSVIARDTGAQYRFIMPGQTWTDVDVDR 120 Query: 120 LLARLKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALR---DGL 176 L +L A +L+V +GSLP G+ V L N L LGVR+ LDTSGAAL+ G Sbjct: 121 SCEALCKLARAGDLIVPSGSLPPGVGPGDLVALTNRLAVLGVRIVLDTSGAALQAFATGR 180 Query: 177 ATRPWLIKPNEEELAEARGIELSGSSALAAEAQRLQEEG-IEHVVVSQGADG-VSWFSPG 234 A +++ + EE G +L + +A + L + G + V+V++GA+G + S G Sbjct: 181 AKTLHVLRMDLEEAQSLAGRDLDTVADVAQFGRELVDAGAAKSVIVAKGAEGSILVTSRG 240 Query: 235 AALHASPPKVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITD 294 H PPKV VVS GAGDS +AG L +G AA AV + D Sbjct: 241 QGWHVRPPKVNVVSKTGAGDSFVAGFTLALAQGSSDLEATVRGVGAAASAVTTPDTDLCD 300 Query: 295 TAQLAELQAAV 305 A AE AA+ Sbjct: 301 GAS-AERYAAL 310 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: 251 Number of extensions: 17 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: 316 Length adjustment: 27 Effective length of query: 285 Effective length of database: 289 Effective search space: 82365 Effective search space used: 82365 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