Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate PP_3623 PP_3623 Alcohol dehydrogenase cytochrome c subunit
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__Putida:PP_3623 Length = 447 Score = 384 bits (987), Expect = e-111 Identities = 201/404 (49%), Positives = 257/404 (63%), Gaps = 12/404 (2%) Query: 24 AHAQNADEDLIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIYSTNITPDPTYG 83 A A AD L+ +GEYVARL DCVACH+ G+ +AGGL + TP+G I++TNITPD G Sbjct: 38 AQATAADPALVSRGEYVARLSDCVACHSLPGGKPFAGGLEMATPLGAIHATNITPDRDSG 97 Query: 84 IGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHGVQPIAQKNH 143 IG YT +FD AVR GV G LYPAMPYPS+A+++ DD+KALYA+FMHGVQP Q N Sbjct: 98 IGNYTLADFDRAVRQGVAPGGRRLYPAMPYPSYAKLSDDDVKALYAFFMHGVQPARQANL 157 Query: 144 PTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGPGHCGACHTPRGF 203 +DI WP+++RWP+++W +FA A +T G DA+ RG Y+V GPGHCG+CHTPRG Sbjct: 158 GSDIPWPLNLRWPIALWNGLFA-ATTPYTDKAGQDAQWNRGAYIVQGPGHCGSCHTPRGL 216 Query: 204 GMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDEDLFLFLKSGRTDHSAA 263 EKALD SG P FL G ++D W APSLR D GLGRWS+ ++ FLK+GR H+ Sbjct: 217 AFNEKALDDSGKP-FL-SGALLDGWYAPSLRADHNTGLGRWSEAEIAQFLKTGRNRHAVV 274 Query: 264 FGGMADVVGWSTQYYTDADLHAMVKYIKSLPPVPPARG-DYSYDA-STAQMLDSNNFSGN 321 +G M + STQ+ D DL A+ Y+KSLP P G + Y A S A LDS Sbjct: 275 YGSMTEAFNNSTQFMHDDDLAAIAHYLKSLPGDPQRDGAPWHYQAESLATRLDS------ 328 Query: 322 AGAKTYVEQCAICHRNDGGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGGVLPPTNWAPS 381 GA+TYV +CA CH DG G A PPLAG ++ S +I ++G P Sbjct: 329 PGARTYVTRCASCHGLDGKGQAEWMPPLAGATSALAKESASAINITLNGSQRVVAAGVPD 388 Query: 382 AVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTAADIQKLR 425 A MP + LSDQ+IADV++F+R+AWGN+ A A + KLR Sbjct: 389 AYRMPALREQLSDQEIADVLSFVRTAWGNQGGA-VDAQAVGKLR 431 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: 694 Number of extensions: 33 Number of successful extensions: 4 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: 447 Length adjustment: 33 Effective length of query: 439 Effective length of database: 414 Effective search space: 181746 Effective search space used: 181746 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