Align 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178) (characterized)
to candidate BPHYT_RS11300 BPHYT_RS11300 2-dehydro-3-deoxygluconokinase
Query= BRENDA::Q97U29 (313 letters) >FitnessBrowser__BFirm:BPHYT_RS11300 Length = 327 Score = 140 bits (354), Expect = 3e-38 Identities = 102/307 (33%), Positives = 150/307 (48%), Gaps = 14/307 (4%) Query: 2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEF 61 +DVI GE + F + GPL V F K VAG++LN I + R ++RVGND F Sbjct: 8 LDVITYGEAMAMFVAAETGPLAGVGQFTKRVAGADLNVAIGLSRLGFKVGWMSRVGNDSF 67 Query: 62 GKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDI 121 G+ + + +GID + D TG + ++ + Y+RKGSA S LS D Sbjct: 68 GQYVRDTLTKEGIDQGCVTTDERYPTG-FQLKSKNDDGSDPAIEYFRKGSAASHLSLADY 126 Query: 122 NENYVRNSRLVHSTGITLAISDNAKEAVIKAFELA-------KSRSLDTNIRPKLWSSLE 174 +YV +R +H TG+ AIS +++E AF LA K+ S D N+RP LW S Sbjct: 127 AADYVLQARHLHLTGVAPAISASSREL---AFHLAREMRAAGKTISFDPNLRPTLWPSRA 183 Query: 175 KAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGA-I 233 E + ++ D ++ + +IL T PD+ + Y E G + ++ KLG++GA Sbjct: 184 AMVEGLNALAALAD--WVLPGIGEGEILTGYTQPDDIAKFYLEQGARGVIIKLGAQGAYF 241 Query: 234 AYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRG 293 D+ V D GAGD A VS L+GK + ++A G L I V G Sbjct: 242 RTADDAAMIAGQPVAKVVDTVGAGDGFAVGVVSALLEGKSLPQAVARGNRIGALAIQVIG 301 Query: 294 DNELTPT 300 D+E P+ Sbjct: 302 DSEGLPS 308 Lambda K H 0.317 0.136 0.383 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: 227 Number of extensions: 10 Number of successful extensions: 5 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: 313 Length of database: 327 Length adjustment: 28 Effective length of query: 285 Effective length of database: 299 Effective search space: 85215 Effective search space used: 85215 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