Align ribokinase (EC 2.7.1.15) (characterized)
to candidate BPHYT_RS09175 BPHYT_RS09175 2-dehydro-3-deoxygluconokinase
Query= BRENDA::A0A0H2UL04 (309 letters) >FitnessBrowser__BFirm:BPHYT_RS09175 Length = 312 Score = 106 bits (265), Expect = 6e-28 Identities = 86/287 (29%), Positives = 138/287 (48%), Gaps = 21/287 (7%) Query: 35 NYQVIPGGKGANQAVAAARMQADVGFIACVGDDSFGINIRESFKLDGINTAGVKLQPNCP 94 NY GG +N +AAAR A GF++ VG D FG + + ++ + ++T+ V++ P Sbjct: 31 NYLQGFGGDTSNFCIAAARQGAQTGFVSAVGADHFGRLLVDLWEREQVDTSLVRVDPQAS 90 Query: 95 TGIAMIQVSDSGENSICISAEANAKLTAAAIEPDLAAIRDARYL------LMQLETPLDG 148 TG+ + +G + A + A A P L AI A+ + L + D Sbjct: 91 TGVYFVSHGPNGHAFDYLRAGSAASRYAPHDLP-LDAIAAAKVIHLSGISLAISLSACDA 149 Query: 149 ILKAAQEAK------TAKTNVILNPAP---ARELPDELLKCVDLITPNETEAEVLTGITV 199 L+A A+ + TN+ L P AR + E ++ D+ P+ + LTG+T Sbjct: 150 ALEAIAHARANGVRVSFDTNLRLKLWPLARARAVMLEAIRQTDICLPSWDDVTDLTGLTG 209 Query: 200 YDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFVVKATDTTAAGDTFNG 259 D+ D L G +V + LG +G +++ + +PG VV A D T AGD F G Sbjct: 210 RDE-----IVDFLLSHGPSVVALKLGKEGSYIATPNERRVVPGHVVNAVDATGAGDCFGG 264 Query: 260 ALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAEVEAFLA 306 A + ++ +A ++A+ AAA+S +GA IP+RA VE LA Sbjct: 265 AFIARIVAGDDPFTAARYANVAAALSTQGYGAVAPIPSRATVEQLLA 311 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: 191 Number of extensions: 5 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: 312 Length adjustment: 27 Effective length of query: 282 Effective length of database: 285 Effective search space: 80370 Effective search space used: 80370 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