Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate GFF2133 PS417_10880 alcohol dehydrogenase
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__WCS417:GFF2133 Length = 447 Score = 372 bits (955), Expect = e-107 Identities = 186/394 (47%), Positives = 244/394 (61%), Gaps = 12/394 (3%) Query: 33 LIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIYSTNITPDPTYGIGTYTFKEF 92 L+ +GEYVARL DCVACH+ +AGGL + TP+G I++TNITPD + GIGTY+ +F Sbjct: 49 LVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADF 108 Query: 93 DEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHGVQPIAQKNHPTDISWPMS 152 D AVRHGV G LYPAMPYPS+ +++ DD+KALYA+FM G++P Q N P+DI WP++ Sbjct: 109 DRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLN 168 Query: 153 MRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGPGHCGACHTPRGFGMQEKALDA 212 MRWP+++W VFAP + P DA RG Y+V GPGHCG+CHTPRG EKALD Sbjct: 169 MRWPIALWNGVFAPT-ATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDE 227 Query: 213 SGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDEDLFLFLKSGRTDHSAAFGGMADVVG 272 +G P FL G ++D W APSLR DP GLGRWS+ + FLK+GR H+ +G M + Sbjct: 228 AGAP-FL-AGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFN 285 Query: 273 WSTQYYTDADLHAMVKYIKSLPPVPPARG-DYSYDASTAQMLDSNNFSGNAGAKTYVEQC 331 STQ+ D DL A+ +Y+KSLP P G + Y A A GA TY +C Sbjct: 286 NSTQFMQDDDLAAIARYLKSLPGDPQRDGAPWQYQAVAA-------VQDAPGAHTYATRC 338 Query: 332 AICHRNDGGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNI 391 A CH DG G PPLAG ++ S +I ++G + P A MP ++ Sbjct: 339 ASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQ 398 Query: 392 LSDQQIADVVNFIRSAWGNRAPANTTAADIQKLR 425 LSD +IA+V++++RS WGN A A + KLR Sbjct: 399 LSDTEIAEVLSYVRSTWGNNGGA-VDANAVGKLR 431 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: 704 Number of extensions: 42 Number of successful extensions: 4 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: 472 Length of database: 447 Length adjustment: 33 Effective length of query: 439 Effective length of database: 414 Effective search space: 181746 Effective search space used: 181746 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: 51 (24.3 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