Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate PP_4232 PP_4232 Cytochrome c family protein
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__Putida:PP_4232 Length = 403 Score = 249 bits (635), Expect = 2e-70 Identities = 157/419 (37%), Positives = 224/419 (53%), Gaps = 27/419 (6%) Query: 12 AVAVGLLAGTSLAHAQNADEDLIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTI 71 A+A+GL A +S A A AD+ +K+GEY+AR DC+ACHT+ G YAGGL I +P GTI Sbjct: 9 ALALGL-AVSSFALA--ADDAQVKRGEYLARAADCMACHTAEGGAPYAGGLPIHSPFGTI 65 Query: 72 YSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYF 131 Y +NITPD YGIG Y+ EF AV G RKDGA LYPAMPY S+ + ++D A+ AY Sbjct: 66 YGSNITPDKQYGIGNYSADEFFAAVTEGKRKDGANLYPAMPYTSYHLIKREDSDAILAYL 125 Query: 132 MHGVQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGP 191 M + PI + T + +P ++R LS W ++ + + P G RG+Y+V Sbjct: 126 M-TIPPINRPAPQTALRFPFNVRMGLSGWNMLYGKSVQ-LQPTEGKSPAWQRGQYMVEVL 183 Query: 192 GHCGACHTPR---GFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDED 248 GHCG CHTPR G Q++ L GG++ ++APSL + G W+ D Sbjct: 184 GHCGECHTPRNPIGALQQDQRL----------SGGLLGGYLAPSLLAQDLAERG-WTQPD 232 Query: 249 LFLFLKSGRTDHSAAFGGMADVVGWSTQYYTDADLHAMVKYIKSLPPVPPARGDYSYDAS 308 L FLK G + + F M VV STQ+ DADL AM Y+ P PPA+ A Sbjct: 233 LTTFLKHGISAQGSMFNEMFPVVHHSTQHLEDADLAAMATYLLGDQP-PPAK------AI 285 Query: 309 TAQMLDSNNFSGNAGAKTYVEQCAICHRNDGGGVARMFPPLAGNPVVVSDNPTSVAHIVV 368 + L+ + S G + Y+ CA CH DG G + + GN V+ + ++ +V+ Sbjct: 286 ESVALEQMSDSAKRGHQQYLNVCAGCHGVDGEGKPHIAVAMRGNTVLRQADSRNLVKVVL 345 Query: 369 DGGVLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTAADIQKLRLD 427 +G MP + + L DQQ+ D+VN++R AWG P + + +L+ + Sbjct: 346 EGIREQQFTGFERMQPMPGFADKLDDQQVIDMVNYLRQAWGG-LPGDLNVQQLAELKAE 403 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: 603 Number of extensions: 30 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: 403 Length adjustment: 32 Effective length of query: 440 Effective length of database: 371 Effective search space: 163240 Effective search space used: 163240 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