Align Choline dehydrogenase; Alcohol dehydrogenase; EC 1.1.1.- (characterized)
to candidate CA265_RS24860 CA265_RS24860 alcohol dehydrogenase
Query= SwissProt::P71017 (402 letters) >FitnessBrowser__Pedo557:CA265_RS24860 Length = 382 Score = 202 bits (513), Expect = 2e-56 Identities = 119/382 (31%), Positives = 199/382 (52%), Gaps = 10/382 (2%) Query: 12 KFHTFEIPTVIKHGIGAIKHTGEEVAALGVSKALLVTDPGIYKAGVADPVIESLKEAGIE 71 K H F PT I+ G GA+K ++ + L+VTDP I + + E LK GI Sbjct: 5 KIHQFNFPTTIRFGAGAVKELPAYLSEHNLKAPLIVTDPTIAQLPFFKRIAEDLKAKGIA 64 Query: 72 VVLFNKVEPNPPVRLVNEGSELYKKENCNGLVAVGGGSSMDTAKAIGVEATHEGSVLDYE 131 V +F+ + NP V +G+E++ N + ++ +GGG+++D A+AI + H + Y+ Sbjct: 65 VEVFSDIHKNPVKSDVYKGTEVWDATNRDSIIGIGGGAALDVARAIVLRVNHREDLFKYD 124 Query: 132 -AADGKKPLENRIPPLTTIPTTAGTGSEVTQWAVITDEEREFKFNTGGPLIAAHLTIIDP 190 G + N +P TIPTT+GTGSEV + A+I D+E K P + A + DP Sbjct: 125 DLIGGDIYVTNDVPHFITIPTTSGTGSEVGRSAIIADDETHQKKILFSPKLMAQIVFADP 184 Query: 191 ELHVSMPPHVTAMTGIDALAHAIECYTMKFAQPITDAVALMAIEYAAHYIKRAFADGEDL 250 EL + +PP +TA TG+DAL H +E Y K P+ D +AL I ++RA + DL Sbjct: 185 ELTMDLPPFITAATGMDALTHNMEAYLAKNFHPMCDGIALEGISLIKDALERA-TNNPDL 243 Query: 251 EARYGMAQAAMLAGLSYGSESAGAAHAMSQTLGGIIPVAHGQCVAAMMGPVMEYNWKGYP 310 E+R M A+M+ +++ + G H+++ L ++ HG A + M++N G+ Sbjct: 244 ESRSKMLMASMMGAIAF-QKGLGVVHSLAHPLSSLLDTHHGLANAVNIPYGMQFNIAGFE 302 Query: 311 EKFARIAKAFGIDTSKMTTEEAAKASVNWMYDLVEDLEVP-TLEEQGVSPDMIERLSKEA 369 ++F +IA+ + +E +A V +++DL + +P L + GV + IE L+ A Sbjct: 303 DRFKKIARTLDL------KDENGEAVVKYLFDLNTKVNIPHKLSDIGVKNEHIETLADLA 356 Query: 370 MKDPQTFGNPRDLNEKAYNWIY 391 D NP+ ++ + +Y Sbjct: 357 FADFAHPNNPKPVSRADFKQLY 378 Lambda K H 0.315 0.132 0.384 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: 379 Number of extensions: 13 Number of successful extensions: 3 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: 402 Length of database: 382 Length adjustment: 31 Effective length of query: 371 Effective length of database: 351 Effective search space: 130221 Effective search space used: 130221 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: 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