Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate Ac3H11_2872 Putative diheme cytochrome c-553
Query= BRENDA::C7G3B8 (472 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2872 Length = 426 Score = 279 bits (713), Expect = 1e-79 Identities = 154/383 (40%), Positives = 217/383 (56%), Gaps = 19/383 (4%) Query: 33 LIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIYSTNITPDPTYGIGTYTFKEF 92 L+++GEY+AR+G+C+ACHT+ G +AGG I+TP G ++S+N+TPD GIG++T EF Sbjct: 45 LVQRGEYLARVGNCMACHTTQGGAPFAGGRGIETPFGVVHSSNLTPDKAQGIGSWTSAEF 104 Query: 93 DEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHGAQP-IAQKNHPTDISWPM 151 A+ HG KDG LYPA PYP++ ++T++D A++AY +QP +A+ N + +P Sbjct: 105 WRAMHHGRSKDGRLLYPAFPYPNYTQVTREDSDAIFAYLQ--SQPAVAEPNRAHALRFPY 162 Query: 152 SMRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGPGHCGACHTPRGFGMQEKALD 211 + + L +WR++F P P AE RG YLV G GHC ACHTPR AL Sbjct: 163 NTQAALGVWRALFF-TPGAPQPEATQSAEYNRGAYLVNGLGHCTACHTPR------NALG 215 Query: 212 A-SGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDEDLFLFLKSGRTDHSAAFGGMADV 270 A + F GG + NW AP+L G+ W +D+ LK+G + G MA+V Sbjct: 216 ATTDAKAFTGGLIPVQNWYAPALNAAHEAGVKEWKTDDVVALLKTGVAPQGSVLGPMAEV 275 Query: 271 VGWSTQYFTDADLHAMVKYIKSLPPVPPARGDYSYDASTAQMLDSNNISGNAGAKTYVDQ 330 V S Q+ +DAD AM Y+++LP R + A A L GAK Y Sbjct: 276 VFRSAQHLSDADARAMAVYLQALPQ-QEHRALAAGAAPPASAL-------ARGAKVYEQH 327 Query: 331 CAICHRNDGGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKN 390 CA CH + G G FP LAGN V +PT++ +V+ GG LP T P MP ++ Sbjct: 328 CAQCHGDQGQGEPGAFPALAGNRAVTLADPTNLVRVVLQGGYLPATAGNPRPHGMPPFQQ 387 Query: 391 ILSDQQIADVVNFIRSAWGNRAP 413 +LSD+ IA V +R++WGNRAP Sbjct: 388 LLSDEDIAAVTTLVRNSWGNRAP 410 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: 643 Number of extensions: 47 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: 426 Length adjustment: 33 Effective length of query: 439 Effective length of database: 393 Effective search space: 172527 Effective search space used: 172527 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