Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_057507836.1 ABB28_RS06360 ribokinase
Query= reanno::Koxy:BWI76_RS00290 (309 letters) >NCBI__GCF_001431535.1:WP_057507836.1 Length = 320 Score = 185 bits (470), Expect = 1e-51 Identities = 122/314 (38%), Positives = 175/314 (55%), Gaps = 25/314 (7%) Query: 4 AGKLVVLGSINADHILNLDAFPTPGETVTGHHYQVAFGGKGANQAVAAGRSGANISFIAC 63 + +VV+GS N DH+ +A P PG T+ G Y GGKG NQAVAA R+GA +F+ Sbjct: 2 SSNVVVVGSFNVDHVWRCEALPAPGATIAGR-YSTGPGGKGFNQAVAARRAGAQTTFVCA 60 Query: 64 TGDDDIGERVRRQLESDNIDVAPVRAVAGESTGVALIFVNAEGENTIGIHAGANAALCVA 123 G+D G R D ++ + E TG I+V+A G NTI I GANAAL + Sbjct: 61 LGEDAGGAMARGLAAQDGFTLSAEAST--EPTGTGGIYVDARGRNTIVIGPGANAALSIG 118 Query: 124 QVDAEKERIASAQALLMQLESPLESVLAAAKIAHQNQTSVILNPAPARELPDE--LLTLV 181 V ++ +A A+ +L+QLESP+E++ AA +A + + +LN APA + P LL L Sbjct: 119 FVQQQQALLAGAKVVLVQLESPVETIEAALAVAREAGVTTVLNAAPA-DAPSSIGLLKLA 177 Query: 182 DIITPNETEAEKL----TGVRVENDEDAAKAAKVLHD-----KGIGTVIITLGSRGVWAS 232 D+ITPNETE L G RV+ ++ AA LH G GTV++TLG+ GV+ S Sbjct: 178 DVITPNETEFAALLSRHVGERVDPNDVAALDGASLHALCRKLVGSGTVVVTLGAVGVFVS 237 Query: 233 SE-----GNGR---RVPGFKVQAVDTIAAGDTFNGALVTALLEGRE--LAEAIRFAHAAA 282 + G+ + RV +V A+DT AGD FNGALV ++ + A +RFA+ A Sbjct: 238 HDEDTLRGDSQPYYRVGAEQVHAIDTTGAGDAFNGALVASIAHSPDAPFARHVRFANQFA 297 Query: 283 AIAVTRKGAQPSVP 296 + ++GA ++P Sbjct: 298 GRSTEKEGAAAAMP 311 Lambda K H 0.315 0.131 0.366 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: 287 Number of extensions: 18 Number of successful extensions: 7 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: 309 Length of database: 320 Length adjustment: 27 Effective length of query: 282 Effective length of database: 293 Effective search space: 82626 Effective search space used: 82626 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 (21.5 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