Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate Dsui_2086 Dsui_2086 cytochrome c
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__PS:Dsui_2086 Length = 696 Score = 370 bits (950), Expect = e-107 Identities = 194/423 (45%), Positives = 254/423 (60%), Gaps = 13/423 (3%) Query: 7 KAALGAVAVGLLAGTSLAHAQNADEDLIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKT 66 ++A + LA L A+ AD I +GEY+ARLGDCVACHT+ G+ AGG + T Sbjct: 21 RSAAATFLLSALAAAGLGRAEAADAGQIARGEYLARLGDCVACHTAEGGKSMAGGRELAT 80 Query: 67 PIGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKA 126 P G ++STNITPD GIG YTF +FD A+R GV DG LYPAMPYPS+A+MT +DM+A Sbjct: 81 PFGVLFSTNITPDKETGIGNYTFAQFDRAMRKGVAADGHNLYPAMPYPSYAKMTGEDMQA 140 Query: 127 LYAYFMHGVQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEY 186 LYAY M G+ P+ Q N PT + WP + RW LS+W F A F P G DA RG Y Sbjct: 141 LYAYLMQGLAPVKQANKPTAMRWPFNQRWGLSLWNWAFLDA-TPFQPDAGKDATWNRGAY 199 Query: 187 LVTGPGHCGACHTPRGFGMQEKALDASG--GPDFLGGGGVIDNWIAPSLRNDPVLGLGRW 244 LV G GHCGACHTPRG QEKA+ +G G FL G +++W A SLR G W Sbjct: 200 LVQGLGHCGACHTPRGIAFQEKAMSDAGSKGKHFL-AGETVESWRALSLR-------GLW 251 Query: 245 SDEDLFLFLKSGRTDHSAAFGGMADVVGWSTQYYTDADLHAMVKYIKSLPPVPPARGDYS 304 + ED LFLK+G+ + A G MA+V+ STQ+ D DL A+ Y+KSLPP S Sbjct: 252 TVEDTALFLKTGQNRFATASGNMAEVIHHSTQHVKDEDLVAIATYLKSLPPGEHELPAPS 311 Query: 305 YDASTAQMLDSNNFSGNAGAKTYVEQCAICHRNDGGGVARMFPPLAGNPVVVSDNPTSVA 364 S N + G YV+ C CHR DG GV+++FPPLAGNP V + +P ++ Sbjct: 312 VPRSEVAGKVPGNLFSSRGGLAYVQFCGDCHRQDGNGVSKIFPPLAGNPAVTAKDPATLL 371 Query: 365 HIVVDGGVLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTAADIQKL 424 HI + G T P MP + L+DQ++A+++ F+RS+WGN A TA+ ++K+ Sbjct: 372 HITLTGWKTASTAAHPRVFTMPGFAR-LNDQELAELITFVRSSWGNGGEA-VTASQVKKM 429 Query: 425 RLD 427 R + Sbjct: 430 RAE 432 Score = 38.9 bits (89), Expect = 6e-07 Identities = 29/83 (34%), Positives = 38/83 (45%), Gaps = 18/83 (21%) Query: 281 ADLHAMVKYIKSLPPVP------PARGDYSYDASTAQMLDSNNFSGNAGAKTYVEQCAIC 334 AD+ AMV Y + P RG D S DS+N G K Y EQCA+C Sbjct: 545 ADMKAMVAYFDWMKGATKPEDKVPGRGIGKIDRSLKP--DSDN-----GKKIYAEQCAVC 597 Query: 335 HRNDGGGV-----ARMFPPLAGN 352 H +G G+ ++PPL G+ Sbjct: 598 HGENGEGLKSADGKMVYPPLWGD 620 Lambda K H 0.318 0.135 0.430 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: 1015 Number of extensions: 56 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: 472 Length of database: 696 Length adjustment: 36 Effective length of query: 436 Effective length of database: 660 Effective search space: 287760 Effective search space used: 287760 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 (21.7 bits) S2: 53 (25.0 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