Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate CCNA_01892 CCNA_01892 short chain dehydrogenase
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__Caulo:CCNA_01892 Length = 546 Score = 169 bits (429), Expect = 9e-47 Identities = 109/254 (42%), Positives = 145/254 (57%), Gaps = 19/254 (7%) Query: 15 RLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFERLNVTDA 74 + R LVTGGA GIG+ + A+AG +V +AD N + A L G D Sbjct: 29 KAQSRVVLVTGGADGIGWAACQRFARAGDQVLVADRNVERARERADSL-GPDHHAIAMDV 87 Query: 75 DAVAD-------LARRLPDVDVLVNNAGIVRNAPAE--DTPDDDWRAVLSVNLDGVFWCC 125 + A L R +DVLVNNAG+ P D ++ + ++N+ G F Sbjct: 88 SSEAQIREGFEQLHREFGRLDVLVNNAGVTDPQPTATLDQTAEEVARLQAINVTGAFLAA 147 Query: 126 REFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRV 185 RE GR M+ +G GAI++ AS +GL++ + +Y+ASKAAVI LTR+LA EWA++GVRV Sbjct: 148 REAGRLMIEQGHGAIINLASGAGLVAL--AKRTSYSASKAAVISLTRTLACEWAAKGVRV 205 Query: 186 NAVAPGYTATPLTR----RGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFV 241 NAV PGYT T + + GL P L PLGR+ EP E+A +LASDAAS+V Sbjct: 206 NAVLPGYTRTQMVQDQIDAGLLDPS---IVLSRIPLGRMGEPEEMAEGAFFLASDAASYV 262 Query: 242 TGHTLVVDGGYTVW 255 G TLVVDGGYTV+ Sbjct: 263 VGATLVVDGGYTVY 276 Score = 122 bits (305), Expect = 2e-32 Identities = 90/246 (36%), Positives = 135/246 (54%), Gaps = 14/246 (5%) Query: 19 RHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAAREL--DGTFERLNVTDADA 76 R + +TGG +GIG + AG R+ + + + + + A L + + ++TD A Sbjct: 296 RVSAITGGGRGIGRCVVDLFHAAGDRLLVIERDAEGAKALAEALGDEHIVVQADITDVAA 355 Query: 77 V----ADLARRLPDVDVLVNNAGIVRN-APAEDTPDDDWRAVLSVNLDGVFWCCREFGRT 131 V A R +DVL+NNAG P+ + D+ +V +N G + R Sbjct: 356 VEAAFAQAQARWGRLDVLINNAGAADVFKPSLEQTAQDFTSVYDLNFSGPLATAKAAARL 415 Query: 132 MLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAVAPG 191 M ++G G IV+ S++GL PQ + AY A+KAAV ++RSLA EWAS G+RVN VAPG Sbjct: 416 M-SQG-GVIVNLGSIAGL-GALPQ-RNAYCAAKAAVTMMSRSLACEWASAGIRVNTVAPG 471 Query: 192 YTATP--LTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLVVD 249 Y TP L + ++ + + P+GRL +P E+A + +LAS AAS+V G TL VD Sbjct: 472 YIETPAVLALKSAGRAQF-DKIRRRAPIGRLGDPMEVARTIAFLASPAASYVAGATLTVD 530 Query: 250 GGYTVW 255 GG+T + Sbjct: 531 GGWTAF 536 Lambda K H 0.319 0.134 0.408 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: 433 Number of extensions: 26 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 255 Length of database: 546 Length adjustment: 30 Effective length of query: 225 Effective length of database: 516 Effective search space: 116100 Effective search space used: 116100 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 (21.8 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