Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate HSERO_RS22390 HSERO_RS22390 alcohol dehydrogenase
Query= BRENDA::C7G3B8 (472 letters) >FitnessBrowser__HerbieS:HSERO_RS22390 Length = 466 Score = 432 bits (1110), Expect = e-125 Identities = 207/404 (51%), Positives = 277/404 (68%), Gaps = 3/404 (0%) Query: 28 NADEDLIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIYSTNITPDPTYGIGTY 87 +A++ I +G Y+AR GDCVACHTS G +AGGL++ +PIG IYSTNITPD +GIG + Sbjct: 61 SAEDQQILRGAYLARAGDCVACHTSKGGAPFAGGLALASPIGAIYSTNITPDKQHGIGDW 120 Query: 88 TFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHGAQPIAQKNHPTDI 147 ++++F +R GV K G T+YPAMPYPS++R+T +DM+ALYAYF P AQ+N DI Sbjct: 121 SYEDFARLMRTGVTKAGYTVYPAMPYPSYSRLTDEDMQALYAYFSKAVPPSAQENRANDI 180 Query: 148 SWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGPGHCGACHTPRGFGMQE 207 WP+SMRWPL++WR VFAP P +TPA G+D E+ARG YLV G GHCG+CH+PR MQE Sbjct: 181 PWPLSMRWPLALWRKVFAPTPAPYTPAAGSDQELARGAYLVEGLGHCGSCHSPRAVTMQE 240 Query: 208 KALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDEDLFLFLKSGRTDHSAAFGGM 267 KAL GG FL GG V+D W PSLRN+ G+ WS DL FL++GR ++A+FG M Sbjct: 241 KALKEDGGRLFLSGGQVVDGWSVPSLRNEHGGGIAGWSQADLVEFLRTGRNQYTASFGAM 300 Query: 268 ADVVGWSTQYFTDADLHAMVKYIKSLPPVPPARGDYSYDASTAQMLDSNNISGNAGAKTY 327 DV+ S QY +DADL+AM +Y+ SLPP A Y YD++TAQ G GA+ Y Sbjct: 301 NDVIEDSMQYMSDADLNAMARYLLSLPPRQQA-APYRYDSATAQAAYDGRPDG-PGARIY 358 Query: 328 VDQCAICHRNDGGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGGVLPPTNWAPSAVAMPD 387 +D+CA CHR++G G + FP LAGNPV+ + + TS I++ GG P T A + + M Sbjct: 359 LDRCAACHRSNGTGYGKAFPALAGNPVLQTSDATSAIRIILQGGRQPSTASATAGLVMAP 418 Query: 388 YKNILSDQQIADVVNFIRSAWGNRAPANTTAADIQKLRLDHTPL 431 Y +L DQQ+A+V ++I++AWGNR TTAA++ K+R P+ Sbjct: 419 YAQLLDDQQVAEVTSYIQTAWGNRG-GTTTAAEVAKVRKTAVPV 461 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: 785 Number of extensions: 46 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 472 Length of database: 466 Length adjustment: 33 Effective length of query: 439 Effective length of database: 433 Effective search space: 190087 Effective search space used: 190087 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