Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate CCNA_01892 CCNA_01892 short chain dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__Caulo:CCNA_01892 Length = 546 Score = 137 bits (346), Expect = 4e-37 Identities = 95/257 (36%), Positives = 136/257 (52%), Gaps = 16/257 (6%) Query: 18 RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77 + +++VVL+TG A GIG A FA +++++D E+ A G D HA+ Sbjct: 29 KAQSRVVLVTGGADGIGWAACQRFARAGDQVLVADRNVERARERAD---SLGPDHHAIAM 85 Query: 78 DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDP-----LEMTEEDWRRCFAIDLDG 132 DVS++ + GR+DVLVN AGV DP L+ T E+ R AI++ G Sbjct: 86 DVSSEAQIREGFEQLHREFGRLDVLVNNAGVT---DPQPTATLDQTAEEVARLQAINVTG 142 Query: 133 AWYGCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKG 192 A+ + MIEQG G+IIN+AS + Y +K ++ LTR L E+A KG Sbjct: 143 AFLAAREAGRLMIEQGHGAIINLASGAGLVALAKRTSYSASKAAVISLTRTLACEWAAKG 202 Query: 193 VRVNAIAPGYIETQLNVDYWN-GFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDE 251 VRVNA+ PGY TQ+ D + G DP R P R+G+P E+A A FLASD Sbjct: 203 VRVNAVLPGYTRTQMVQDQIDAGLLDPSIVLSRI----PLGRMGEPEEMAEGAFFLASDA 258 Query: 252 APFINASCITIDGGRSV 268 A ++ + + +DGG +V Sbjct: 259 ASYVVGATLVVDGGYTV 275 Score = 122 bits (307), Expect = 1e-32 Identities = 90/265 (33%), Positives = 136/265 (51%), Gaps = 16/265 (6%) Query: 4 PLSLPPVPEPPKGERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAA 63 P S P P P +V +TG +GIG +V F + RL++ + AE + +A Sbjct: 281 PASTTPAPSPLAPSP---RVSAITGGGRGIGRCVVDLFHAAGDRLLVIERDAEGAKALA- 336 Query: 64 HWRERGADVH-ALKADVSNQQDLHAMARHAVERHGRIDVLVNCAGV-NVFRDPLEMTEED 121 E D H ++AD+++ + A A R GR+DVL+N AG +VF+ LE T +D Sbjct: 337 ---EALGDEHIVVQADITDVAAVEAAFAQAQARWGRLDVLINNAGAADVFKPSLEQTAQD 393 Query: 122 WRRCFAIDLDGAWYGCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLT 181 + + ++ G KA M + GV I+N+ S +P Y AK + ++ Sbjct: 394 FTSVYDLNFSGPLATAKAAARLMSQGGV--IVNLGSIAGLGALPQRNAYCAAKAAVTMMS 451 Query: 182 RALGIEYAPKGVRVNAIAPGYIETQLNVDYWN-GFADPYAERQRALDLHPPRRIGQPIEV 240 R+L E+A G+RVN +APGYIET + + G A R+RA P R+G P+EV Sbjct: 452 RSLACEWASAGIRVNTVAPGYIETPAVLALKSAGRAQFDKIRRRA----PIGRLGDPMEV 507 Query: 241 AMTAVFLASDEAPFINASCITIDGG 265 A T FLAS A ++ + +T+DGG Sbjct: 508 ARTIAFLASPAASYVAGATLTVDGG 532 Lambda K H 0.321 0.137 0.419 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: 348 Number of extensions: 19 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: 272 Length of database: 546 Length adjustment: 30 Effective length of query: 242 Effective length of database: 516 Effective search space: 124872 Effective search space used: 124872 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: 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