Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate CCNA_01892 CCNA_01892 short chain dehydrogenase
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__Caulo:CCNA_01892 Length = 546 Score = 120 bits (301), Expect = 6e-32 Identities = 88/245 (35%), Positives = 119/245 (48%), Gaps = 10/245 (4%) Query: 15 VLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKY-PGTVATRADVSDAAQIE 73 VL++GGA GIG + AG QV V D + D P A DVS AQI Sbjct: 35 VLVTGGADGIGWAACQRFARAGDQVLVADRNVERARERADSLGPDHHAIAMDVSSEAQIR 94 Query: 74 AVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATIN-INLTAQYRFAHHAVPML 132 F+ G LDVLVNNAG+ P AE A + IN+T + A A ++ Sbjct: 95 EGFEQLHREFGRLDVLVNNAGVTDPQPTATLDQTAEEVARLQAINVTGAFLAAREAGRLM 154 Query: 133 KESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGIVE 192 E HG ++++AS AG + A RT Y+A+K A++ L ++LA E +RVNA+LPG Sbjct: 155 IEQGHGAIINLASGAGLVALAKRTSYSASKAAVISLTRTLACEWAAKGVRVNAVLPGYTR 214 Query: 193 GPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVTGQA 252 + I A + L++I L RM E++A A FL S AA V G Sbjct: 215 TQMVQDQIDAGLLDPSI--------VLSRIPLGRMGEPEEMAEGAFFLASDAASYVVGAT 266 Query: 253 ISVDG 257 + VDG Sbjct: 267 LVVDG 271 Score = 93.2 bits (230), Expect = 1e-23 Identities = 72/252 (28%), Positives = 118/252 (46%), Gaps = 12/252 (4%) Query: 7 LQPYPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDV-SESALAVFRDKYPGTVATRAD 65 L P P + I+GG GIG + + AG ++ V + +E A A+ + +AD Sbjct: 291 LAPSPRVSA-ITGGGRGIGRCVVDLFHAAGDRLLVIERDAEGAKALAEALGDEHIVVQAD 349 Query: 66 VSDAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFA 125 ++D A +EA F + G LDVL+NNAG A + ++ + ++N + A Sbjct: 350 ITDVAAVEAAFAQAQARWGRLDVLINNAGAADVFKPSLEQTAQDFTSVYDLNFSGPLATA 409 Query: 126 HHAVPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNA 185 A ++ + G ++++ S+AG R Y A K A+ + +SLA E + IRVN Sbjct: 410 KAAARLMSQG--GVIVNLGSIAGLGALPQRNAYCAAKAAVTMMSRSLACEWASAGIRVNT 467 Query: 186 LLPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAA 245 + PG +E P + + A Q + + + R+ +VA FL SPAA Sbjct: 468 VAPGYIETPAVLALKSAGRAQF--------DKIRRRAPIGRLGDPMEVARTIAFLASPAA 519 Query: 246 RNVTGQAISVDG 257 V G ++VDG Sbjct: 520 SYVAGATLTVDG 531 Lambda K H 0.318 0.133 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: 351 Number of extensions: 17 Number of successful extensions: 6 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: 262 Length of database: 546 Length adjustment: 30 Effective length of query: 232 Effective length of database: 516 Effective search space: 119712 Effective search space used: 119712 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: 50 (23.9 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