Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate HSERO_RS22810 HSERO_RS22810 alcohol dehydrogenase
Query= BRENDA::C7G3B8 (472 letters) >FitnessBrowser__HerbieS:HSERO_RS22810 Length = 423 Score = 339 bits (869), Expect = 1e-97 Identities = 179/427 (41%), Positives = 259/427 (60%), Gaps = 15/427 (3%) Query: 3 INRLKAALGAVAVGLLAGTSLAHAQNADEDLIKKGEYVARLGDCVACHTSLNGQKYAGGL 62 + +L + A+A L A +L AQ AD+DL+ +G+Y+AR GDC+ACH++ Y+GGL Sbjct: 1 MKKLTSLFAALAWSLGALGTLTTAQAADQDLVARGQYLARAGDCMACHSAAGKPAYSGGL 60 Query: 63 SIKTPIGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQD 122 +I + G IYSTNITPD +GIG Y+ +F AVRHGVR DG LYPAMPYPS+A+++ + Sbjct: 61 AIDSGHGIIYSTNITPDKEHGIGNYSEAQFSAAVRHGVRADGTQLYPAMPYPSYAKVSDE 120 Query: 123 DMKALYAYFMHGAQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEIA 182 D+ ALY YFM G QP+A + +S+P ++RW + +W +VF K F G AEI Sbjct: 121 DIHALYTYFMQGVQPVASTPPASSMSFPFNIRWGMKLW-NVFFANDKPFREQDGWSAEIK 179 Query: 183 RGEYLVTGPGHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGLG 242 RG YLV G GHCG+CHTPRG M EKA D+S FL GG ++ W PSLR G+ Sbjct: 180 RGAYLVEGLGHCGSCHTPRGVAMNEKASDSSQA-QFLSGGD-LNGWAVPSLR-----GMP 232 Query: 243 RWSDEDLFLFLKSGRTDHSAAFGGMADVVGWSTQYFTDADLHAMVKYIKSLPPVPPARG- 301 WS +D+ +L++GR ++ G M+ VV ST + DL AM Y+K+L PV + Sbjct: 233 HWSAQDIVDYLQTGRNKTASVAGEMSLVVEHSTSHLKREDLQAMAAYLKTLSPVASSGSG 292 Query: 302 ---DYSYDASTAQMLDSNNISGNAGAKTYVDQCAICHRNDGGGVARMFPPLAGNPVVVSD 358 DA+ +++ + +++ G + Y+D CA CH G G +FP L G VV ++ Sbjct: 293 RVIPQGVDATVSKLTAAKDLT--LGERLYLDNCAACHFVTGRGAPGIFPVLDGATVVNAE 350 Query: 359 NPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTA 418 NP+++ H+++ G P T APS + MP + + LSD++ A + F+R WGN A + Sbjct: 351 NPSALLHVILAGARTPSTEKAPSILVMPGFAHRLSDEEAAALATFVRQGWGNHA-GKVSE 409 Query: 419 ADIQKLR 425 ++ KLR Sbjct: 410 REVGKLR 416 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: 647 Number of extensions: 36 Number of successful extensions: 6 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: 423 Length adjustment: 33 Effective length of query: 439 Effective length of database: 390 Effective search space: 171210 Effective search space used: 171210 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