Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate BWI76_RS00580 BWI76_RS00580 ribokinase
Query= reanno::pseudo1_N1B4:Pf1N1B4_6031 (305 letters) >FitnessBrowser__Koxy:BWI76_RS00580 Length = 403 Score = 198 bits (504), Expect = 2e-55 Identities = 117/291 (40%), Positives = 160/291 (54%), Gaps = 3/291 (1%) Query: 1 MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVG 60 M KV V GS N+D+V + R PRGGE+L+ + GGKGANQA AA++ GAQV V Sbjct: 98 MQGKVCVFGSFNVDIVAKVERFPRGGESLMALGSSLGPGGKGANQATAASKAGAQVHFVA 157 Query: 61 CVGNDAYGEALRGALLAEQIDCQAV--STVEDSSGVALIVVDDNSQNAIVIVAGANGALT 118 VG D + L I + S E + + V +N +N I I +GAN +T Sbjct: 158 KVGKDQFSHLAADHLTRSAIHSYTLYQSESEPTGNAIIYVSQENGENMIAIYSGANTTIT 217 Query: 119 PEVIDRFDAVLQAADVIICQLEVPDATVGHALKRGRELGKTVILNPAPASRPLPVDWYAA 178 I + L ++DV++ QLE +K ELGK VILNPAP S + + Sbjct: 218 YSEIQKIIPELSSSDVLLVQLENNFDATHSLIKIAHELGKQVILNPAPYSAEI-IPSIPF 276 Query: 179 IDYLIPNESEASVLSGLPVDSLSTAETAATRLIAMGAGKVIITLGSQGSLFADGQRFEHF 238 +D + PNE+EAS+LSG+ + TA+ AA R+ +GA KV+IT+GS+G+L D ++F H Sbjct: 277 VDVITPNETEASLLSGIDISDFDTAKEAALRIARLGAKKVLITMGSRGALLLDNRQFSHI 336 Query: 239 PAAKVKAVDTTAAGDTFVGGFAAALAAGKGEADAIRFGQVAAALSVTRAGA 289 A VDTT AGD F G AA+LAAG A + A+L+V GA Sbjct: 337 RAFPAVTVDTTGAGDAFNGALAASLAAGNSLVQAATWASAFASLAVELEGA 387 Lambda K H 0.316 0.132 0.369 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: 253 Number of extensions: 15 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: 305 Length of database: 403 Length adjustment: 29 Effective length of query: 276 Effective length of database: 374 Effective search space: 103224 Effective search space used: 103224 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: 49 (23.5 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