Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate H281DRAFT_03306 H281DRAFT_03306 Cytochrome c, mono- and diheme variants
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__Burk376:H281DRAFT_03306 Length = 434 Score = 364 bits (935), Expect = e-105 Identities = 192/423 (45%), Positives = 258/423 (60%), Gaps = 12/423 (2%) Query: 8 AALGAVAVGLLAGTSLAHAQNADEDLIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTP 67 A LGA + + A L+ +GEY+A+ DC CHT++ GQ Y GGL + +P Sbjct: 14 AMLGAFTTPCVTAEPAGASDPALAALVARGEYLAKASDCAGCHTAVGGQAYGGGLGLTSP 73 Query: 68 IGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKAL 127 GTI S+NITPD YGIG Y++++F +VR GV LYPAMPY SF++M+ DDM+AL Sbjct: 74 FGTIMSSNITPDRRYGIGAYSYEDFARSVREGVSPGNKRLYPAMPYASFSKMSDDDMRAL 133 Query: 128 YAYFMHGVQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYL 187 YAYFMHGV+P + PT +++P + RW L W+ FAP + + P G DA+ RG +L Sbjct: 134 YAYFMHGVKPAPEPAPPTKLAFPFNQRWVLYFWQLAFAPT-EPYRPKAGRDAQWNRGAFL 192 Query: 188 VTGPGHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDE 247 V GPGHCGACHTPRG G QE+ D S P +L GGV DNW P+L DP GLGR ++ Sbjct: 193 VQGPGHCGACHTPRGPGFQERGYDES-SPMYL-TGGVNDNWFGPNLTGDPGSGLGRIGEK 250 Query: 248 DLFLFLKSGRTDHSAAFGGMADVVGWSTQYYTDADLHAMVKYIKSLPPVPPARGDYSYDA 307 DL FLK+G AFG M + V STQY TD D AM Y+KSLP P+ SY+ Sbjct: 251 DLAAFLKTGHGAGLVAFGSMVEQVEDSTQYLTDEDALAMAHYVKSLPAQKPSG---SYEP 307 Query: 308 STAQMLDSNNFS-----GNAGAKTYVEQCAICHRNDGGGVARMFPPLAGNPVVVSDNPTS 362 L + N + + GA+ Y+ CA CH G G+ +FP LAGNP V++++ TS Sbjct: 308 HAQPDLPTRNGNRVDAPQSVGARVYISFCARCHGVQGAGMPNVFPRLAGNPSVITEDTTS 367 Query: 363 VAHIVVDGGVLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTAADIQ 422 + ++V+GG P T P AMP + L++ Q+A+V+++IR++WGN A TA DIQ Sbjct: 368 LIRLMVEGGNSPATISGPPRQAMPGFAQTLTNAQMANVLSWIRTSWGNDA-RPVTANDIQ 426 Query: 423 KLR 425 LR Sbjct: 427 SLR 429 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: 700 Number of extensions: 43 Number of successful extensions: 5 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: 434 Length adjustment: 33 Effective length of query: 439 Effective length of database: 401 Effective search space: 176039 Effective search space used: 176039 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