Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_010960275.1 MCA_RS04760 carbohydrate kinase
Query= reanno::pseudo5_N2C3_1:AO356_00950 (304 letters) >NCBI__GCF_000008325.1:WP_010960275.1 Length = 314 Score = 122 bits (305), Expect = 1e-32 Identities = 97/300 (32%), Positives = 144/300 (48%), Gaps = 13/300 (4%) Query: 2 PAKVVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVGC 61 P V+ IG + DLV P P E ++ ++ GG AN AV ARLG + G Sbjct: 13 PLDVLCIGHASFDLVFSVPHHPAADEKIVADALLACGGGPAANAAVTVARLGRKAGFAGY 72 Query: 62 VGDDAYGEQLRGALLAEGIDCQAVRVEQGSSGVALIVVDDNSQNAIVIVAGANGALTAEV 121 +G D YGE+ L A GID +AV + +++++V + + A+V G L + Sbjct: 73 LGMDLYGERHLEELRAAGIDTRAVVRGSSPTPLSVVLVKPDGRRALVNHKGDTRPLPPQA 132 Query: 122 LDGVDDVLQSADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADWYAC-ID 180 A I+ PD + AL R +L+ A + H ++W + Sbjct: 133 FV---PPATPARCILFDGHEPDLSEP-ALAWARTHDAATVLD-AGSLHG-GSEWLMFRVG 186 Query: 181 YLIPNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGASFEHFPA 240 +L+ +E AA L + E A AA +A + V++TLG GL++ GA PA Sbjct: 187 HLVASEKFAA--QWLGKNDPERALAA----LAERSPCVVITLGEHGLIWRRGAESGRLPA 240 Query: 241 PRVKAVDTTAAGDTFVGGFAAALACGKSEVDAIRFGQVAAALSVTRAGAQPSIPTLLEVQ 300 V+AVDTT AGD F G +AA LA G + +R+ A AL TR GA+P IP+ +V+ Sbjct: 241 FPVEAVDTTGAGDVFHGAYAAGLAAGMDWPEMLRYASAAGALCCTRLGARPGIPSGADVE 300 Lambda K H 0.318 0.133 0.377 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: 247 Number of extensions: 16 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: 304 Length of database: 314 Length adjustment: 27 Effective length of query: 277 Effective length of database: 287 Effective search space: 79499 Effective search space used: 79499 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 (21.7 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