Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate CCNA_01110 CCNA_01110 2-dehydro-3-deoxygluconokinase
Query= reanno::Dyella79:N515DRAFT_1919 (326 letters) >FitnessBrowser__Caulo:CCNA_01110 Length = 308 Score = 99.4 bits (246), Expect = 1e-25 Identities = 82/265 (30%), Positives = 120/265 (45%), Gaps = 15/265 (5%) Query: 5 ILCFGEALIDFHAEGRDAQGFPRSFIPFAGGAPANVSVAVARLGGPAAFAGMLGQ-DMFG 63 I GE +++ E D G P + FAG N ++ +ARLG A+ LGQ D F Sbjct: 4 ITVLGECMVELSPEAGDG-GAPLYRMGFAGDT-FNTAIYMARLGDQVAYCTALGQGDPFS 61 Query: 64 DFLLDSLRRAGVDTAGVARTGEANTALAFVALDSHGERSFSFYRP--PSADLLFRPEHFR 121 + +L ++RR G+DT V + L + LD HGER F ++R P DL H Sbjct: 62 EGVLAAMRREGMDTQLVRQVENRLPGLYAIVLDEHGERKFHYWRERAPIRDLF--SAHTA 119 Query: 122 AESFRGAAVFH-VCSNSMTEPALAEATREGMRR----AHTAGAWVSFDLNLRPALWPNQS 176 + A V + +T + + R +R H+ G V+ D N RPALWP+ Sbjct: 120 DQLIEAAKASDLVYLSGVTLAVIGDIGRARLRDILAYVHSHGVAVALDFNYRPALWPSAE 179 Query: 177 ASHDELWPALHLADVVKLSAEEFHWLAGDEGEEATLDRLWAGRARLLVVTDGSRTLRWFH 236 A+ L + + LS+E+ L G E E+ + WA +V D S + Sbjct: 180 AARAALDGVVPACRYISLSSEDSRPLYGREAEDLAAE--WAAAGAEVVARDESHAVNVHT 237 Query: 237 PDASGEMPVYA-VPTVDSTAAGDAF 260 P+ P A V VD+T AGD+F Sbjct: 238 PEGRTATPAPARVKAVDTTGAGDSF 262 Lambda K H 0.322 0.135 0.418 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: 298 Number of extensions: 24 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: 326 Length of database: 308 Length adjustment: 27 Effective length of query: 299 Effective length of database: 281 Effective search space: 84019 Effective search space used: 84019 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 (22.0 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