Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate PP_3382 PP_3382 gluconate 2-dehydrogenase cytochrome c subunit
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Putida:PP_3382 Length = 417 Score = 387 bits (994), Expect = e-112 Identities = 200/394 (50%), Positives = 252/394 (63%), Gaps = 9/394 (2%) Query: 46 EPALVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSL 105 + A V GEY+AR DCVACH+ G PFAGGL M TP+G +++TNITP S GIG YS Sbjct: 25 DDAQVRLGEYLARAGDCVACHTAKGGKPFAGGLPMETPIGTVYSTNITPAAS-GIGQYSF 83 Query: 106 ADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPW 165 DFD+AVR G+ G LYPAMPYPSY ++S+ D++ALYA+FM+G+ P Q N SDIPW Sbjct: 84 EDFDQAVRRGIGKDGSTLYPAMPYPSYARVSEQDMQALYAYFMKGVAPVEQANKASDIPW 143 Query: 166 PLNMRWPIALWNGVFAPTA-TYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKA 224 PL+MRWP+A+W GVFAP A + A D + NRGAY+V+G GHCG+CHTPR L EKA Sbjct: 144 PLSMRWPLAIWRGVFAPEAKPWQASATADPVVNRGAYLVEGLGHCGACHTPRALTMQEKA 203 Query: 225 LDEA-GAPFLAG-ALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTE 282 L A G FLAG A L+GW A +LR D GLG WSE Q+VQFLKTGR+ + V+G M++ Sbjct: 204 LSAADGEQFLAGSAPLEGWIAKNLRGDHKDGLGSWSEAQLVQFLKTGRSDRSAVFGGMSD 263 Query: 283 AFNNSTQFMQDDDLAAIARYLKSL-PGDPQRDGAPWQYQAVAAV----QDAPGAHTYATR 337 +S Q M D DL AIARYLK+L P +P + Q A+ PGA Y Sbjct: 264 VVEHSMQHMSDADLTAIARYLKTLPPSNPDDQLHVYDKQVADALWKGDDSKPGAAVYIDN 323 Query: 338 CASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFRE 397 CA+CH DG+G P LAG ++ S I++ L G P + MPAF Sbjct: 324 CAACHRTDGQGYTRVFPALAGNPVVQTADATSLIHVVLAGGTVPATHSAPSNFTMPAFGW 383 Query: 398 QLSDTEIAEVLSYVRSTWGNNGGAVDANAVGKLR 431 +LSD E+AEV++++RS+WGN G AV A V LR Sbjct: 384 RLSDQEVAEVVNFIRSSWGNQGSAVTAGDVKSLR 417 Lambda K H 0.318 0.133 0.423 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: 600 Number of extensions: 36 Number of successful extensions: 7 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: 447 Length of database: 417 Length adjustment: 32 Effective length of query: 415 Effective length of database: 385 Effective search space: 159775 Effective search space used: 159775 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