Align ribokinase (EC 2.7.1.15) (characterized)
to candidate Pf1N1B4_405 Carbohydrate kinase, PfkB family
Query= BRENDA::A0A0H2UL04 (309 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_405 Length = 309 Score = 110 bits (275), Expect = 4e-29 Identities = 97/318 (30%), Positives = 146/318 (45%), Gaps = 27/318 (8%) Query: 4 MNKLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAARMQADVGFIAC 63 M L+ G V D V+ V P+ G + ++ + GG G N AA R V ++ Sbjct: 1 MPNLLHTGQVMIDLVMAVDKLPQSGGDVLAQSARFEAGG-GFNVMAAARRNGLPVVYLGG 59 Query: 64 VGDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMIQVSDSGENSICISAEANAKLTAA 123 G FG RE+ +GI G+ TG+ + S E + A +LTA Sbjct: 60 HGKGRFGDMAREAMTAEGIRI-GIDQSTERDTGLCVALTEASAERTFISCIGAEGELTAE 118 Query: 124 AIEPDLAAIRD----ARYLLM---QLETPLDGILKAAQEAKTAKTNVILNPAPARELPDE 176 + A D + Y L+ + + ++ +L K V+ +P P + PD Sbjct: 119 DLASVPAEAGDFVYVSGYSLLHGGKAQALVNWVLDLPDGIK-----VVFDPGPLVDSPDA 173 Query: 177 -----LLKCVDLITPNETEAEVLTGITVYDDSSAQQAADAL--HCKGIEIVIITLGSKGV 229 L +DL T N EA TG S +A + L H ++++ GS+G Sbjct: 174 PLMKALFPRIDLWTSNRVEALRFTGA-----SDIAEALNGLADHLPTDALMVVRDGSQGC 228 Query: 230 WLSQNGRGQRIPGFVVKATDTTAAGDTFNGALVTGLLQEMPLESAIKFAHAAAAISVTRF 289 W+SQ+G Q +PGF V A D+ AGD G LV GL Q + A + A+AAAA++VTR+ Sbjct: 229 WISQHGDRQHVPGFKVTAVDSNGAGDAHAGVLVAGLAQGLSAIDAARRANAAAALAVTRW 288 Query: 290 GAQTSIPTRAEVEAFLAE 307 G TS P AE++AF+ + Sbjct: 289 GPATS-PGAAELDAFIRD 305 Lambda K H 0.316 0.132 0.373 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: 224 Number of extensions: 9 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: 309 Length of database: 309 Length adjustment: 27 Effective length of query: 282 Effective length of database: 282 Effective search space: 79524 Effective search space used: 79524 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: 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