Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_022947540.1 H035_RS17985 carbohydrate kinase
Query= reanno::Dyella79:N515DRAFT_1919 (326 letters) >NCBI__GCF_000421465.1:WP_022947540.1 Length = 309 Score = 92.4 bits (228), Expect = 1e-23 Identities = 94/325 (28%), Positives = 138/325 (42%), Gaps = 44/325 (13%) Query: 4 NILCFGEALIDF-----HAEGRDAQGFPRSFIPFAGGAPANVSVAVARLGGPAAFAGMLG 58 +++C G A D H G D + I GG AN SV V+RLG AAFAG LG Sbjct: 5 DVICIGHAAYDLVFSVPHHPGPDEKCTATGLIACGGGPAANASVTVSRLGCRAAFAGYLG 64 Query: 59 QDMFGDFLLDSLRRAGVDTAGVARTGEANTALAFVALDSHGERSFSFYRPPSADLLFRPE 118 +D++G+ L + GVD + R G++ T L+ + + G R+ YR + RP Sbjct: 65 RDLYGEAHRRELIQDGVDDNWICR-GDSPTPLSTILVKPDGRRALVNYRGAT-----RPL 118 Query: 119 HFRAESFRGAAVFHVCSNSMTEPALAEATREGMRRAHTAGAWVSFDLNLRPALWPNQSAS 178 A G V + EP H + W+ + A + + Sbjct: 119 AADAVDLSGLDAKVVLFDGH-EP-------------HVSCHWLPHFRDRGAATVLDAGSL 164 Query: 179 HDELWPALHLADVVKLSAEEF--HWLAGDEGEEATLDRLWAGRARLLVVTDGSRTLRWFH 236 H+ + D + +++ +F WL DE A L+ L A ++ V+T G L W Sbjct: 165 HEGTRRLMFEVDYL-IASRKFAAQWLGCDEPRRA-LEEL-AAKSPAAVITLGEEGLIWQR 221 Query: 237 PDASGEMPVYAVPTVDSTAAGDAFVGGLLHRLATVEKGADQLDHLVAELPRLHAMLRFAA 296 + GEM V+ V VD+T AGD F G V +G D LRFA+ Sbjct: 222 GNEYGEMSVFPVDAVDTTGAGDTFHGAF---AVAVTEGVPWAD-----------ALRFAS 267 Query: 297 ACGALTVTRLGSFAAMPDEAEVLAF 321 A AL T++G+ +P V AF Sbjct: 268 AAAALCCTQMGARPGIPGREAVKAF 292 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: 286 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 326 Length of database: 309 Length adjustment: 27 Effective length of query: 299 Effective length of database: 282 Effective search space: 84318 Effective search space used: 84318 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 24 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