Align D-chiro-inositol 1-dehydrogenase (EC 1.1.1.369) (characterized)
to candidate BWI76_RS10220 BWI76_RS10220 dehydrogenase
Query= BRENDA::Q9WYP5 (334 letters) >FitnessBrowser__Koxy:BWI76_RS10220 Length = 335 Score = 226 bits (576), Expect = 6e-64 Identities = 132/337 (39%), Positives = 193/337 (57%), Gaps = 16/337 (4%) Query: 1 MRIGVIGLGRIGTIHAENL-KMIDDAILYAISDVREDRLREMKEKLGVEKAYKDPHELIE 59 +R+G+IG GR+GT H E++ + I A L A++D E+ +LG +K+Y DP EL+ Sbjct: 7 VRVGLIGAGRMGTFHGESVAQRIPGATLVAVADPVPGAAEELSARLGAKKSYTDPQELLN 66 Query: 60 DPNVDAVLVCSSTNTHSELVIACAKAKKHVFCEKPLSLNLADVDRMIEETKKADVILFTG 119 DP +DAV++ S TH+ELV+A AKA K +FCEKP+++ L D D+ I KKA V L G Sbjct: 67 DPEIDAVVIASPARTHAELVVAAAKAGKAIFCEKPMAVTLEDADKAINAAKKAGVALQVG 126 Query: 120 FNRRFDRNFKKLKEAVENGTIGKPHVLRITSRDPA---PPPLDYIRVSGGIFLDMTIHDF 176 FNRRF F E ++ G IG P +LR T+RDP P P+ + IFL+ IHDF Sbjct: 127 FNRRFVSGFSAAYEEIKAGKIGVPQLLRSTTRDPGLGDPTPIPH----WTIFLETLIHDF 182 Query: 177 DMARYI-MGEEVEEVFADGSVLVDEEIGKAGDVDTAVVVLRFKSGALGVIDNSRRAVYGY 235 D+ ++ G + V+A LV + G +DTAVV + F +GA + + +AVYGY Sbjct: 183 DILLHLNPGAKPTRVYAVADALVRPDFKDRGLLDTAVVNICFDNGAFATAEANFQAVYGY 242 Query: 236 DQRIEVFGSKGRIFADNVRETTVVLTDEQG---DRGSRYLYFFLERYRDSYLEELKTFIK 292 D R EVFGSKG + A N+ V G D R + D+Y+ E+ F++ Sbjct: 243 DVRGEVFGSKGMLQAGNINVNNCVRYTADGISIDTARR----DTDLLHDAYVAEVTDFVR 298 Query: 293 NVKSGEPPAVSGEDGKMALLLGYAAKKSLEEKRSVKL 329 V +G+ P +GED + AL + A S+++ + +KL Sbjct: 299 CVATGDTPKATGEDARNALEVALACIASVQQSQPIKL 335 Lambda K H 0.319 0.139 0.390 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: 301 Number of extensions: 12 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: 334 Length of database: 335 Length adjustment: 28 Effective length of query: 306 Effective length of database: 307 Effective search space: 93942 Effective search space used: 93942 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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