Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate HSERO_RS06965 HSERO_RS06965 alcohol dehydrogenase
Query= BRENDA::C7G3B8 (472 letters) >FitnessBrowser__HerbieS:HSERO_RS06965 Length = 422 Score = 272 bits (696), Expect = 1e-77 Identities = 150/393 (38%), Positives = 222/393 (56%), Gaps = 15/393 (3%) Query: 34 IKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIYSTNITPDPTYGIGTYTFKEFD 93 + +G+Y+AR G+C+ACHT+ G YAGG +I +P GT+Y++NITPD T GIG ++ +F Sbjct: 39 LAQGQYLARAGNCMACHTARGGAPYAGGRAIASPFGTLYTSNITPDKTTGIGQWSADDFW 98 Query: 94 EAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHGAQPIAQKNHPTDISWPMSM 153 A+ HG K+G LYPA PY S+ R+++ D AL+AY + P+A+ N + +P Sbjct: 99 RALHHGRGKEGQFLYPAFPYTSYTRLSRADSDALFAY-LQSLPPVARANQAHTLRFPYDQ 157 Query: 154 RWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGPGHCGACHTPRGFGMQEKALDAS 213 R L +WR+++ P+ + P P DA+ RG YLV G GHC ACH+ R L AS Sbjct: 158 RMLLGLWRALYF-TPQSYQPDPRQDAQWNRGAYLVQGAGHCSACHSAR------NRLGAS 210 Query: 214 GGPDFLGGGGV-IDNWIAPSLRNDPVLGLGRWSDEDLFLFLKSGRTDHSAAFGGMADVVG 272 P L GG + W AP L GL WS D+ LK+G + H+ G M+++VG Sbjct: 211 IEPLALAGGVIPALQWYAPPLHGG-ADGLQDWSTADIAALLKTGVSPHAVTLGPMSEIVG 269 Query: 273 WSTQYFTDADLHAMVKYIKSLPPVPPARGDYSYDASTAQMLDSNNISGNAGAKTYVDQCA 332 S QY DAD+ AM Y+KSL P + D + ++ + ++ I G + Y C Sbjct: 270 RSLQYLNDADVSAMAVYLKSL---PASAADDAARPASVEPAEAERIM-KQGKQLYGTLCV 325 Query: 333 ICHRNDGGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNIL 392 CH G G A +PPLAGN + +P + V++GG P T P MP + L Sbjct: 326 DCHGGKGQGSAPDYPPLAGNRAIAGPHPANAVRAVLNGGFPPSTAGNPYPFGMPPFGPQL 385 Query: 393 SDQQIADVVNFIRSAWGNRAPANTTAADIQKLR 425 SDQ++A VV+++R++WGN+ +AA++ + R Sbjct: 386 SDQEVAAVVSYVRNSWGNQG-GLVSAAEVNRYR 417 Score = 55.1 bits (131), Expect = 5e-12 Identities = 38/131 (29%), Positives = 58/131 (44%), Gaps = 18/131 (13%) Query: 172 TPAPGTDAEIARGEYLVTGPGHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNW--- 228 TPAP ++A+G+YL G+C ACHT R GG + GG + + Sbjct: 30 TPAPDPTRQLAQGQYLARA-GNCMACHTAR------------GGAPYAGGRAIASPFGTL 76 Query: 229 IAPSLRNDPVLGLGRWSDEDLFLFLKSGRTDHSAAFGGMADVVGWSTQYFTDADLHAMVK 288 ++ D G+G+WS +D + L GR ++ + AD A+ Sbjct: 77 YTSNITPDKTTGIGQWSADDFWRALHHGRGKEGQFLYPAFPYTSYTR--LSRADSDALFA 134 Query: 289 YIKSLPPVPPA 299 Y++SLPPV A Sbjct: 135 YLQSLPPVARA 145 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: 759 Number of extensions: 59 Number of successful extensions: 8 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: 422 Length adjustment: 33 Effective length of query: 439 Effective length of database: 389 Effective search space: 170771 Effective search space used: 170771 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