Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate PP_3623 PP_3623 Alcohol dehydrogenase cytochrome c subunit
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Putida:PP_3623 Length = 447 Score = 780 bits (2014), Expect = 0.0 Identities = 377/445 (84%), Positives = 398/445 (89%), Gaps = 3/445 (0%) Query: 5 RFARTAGWLALPCLVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVA 64 RFARTAGWLALPCLVAAGLLAWYVTREPA+PF QA A +PALVSRGEYVARLSDCVA Sbjct: 4 RFARTAGWLALPCLVAAGLLAWYVTREPASPFADAQATAA-DPALVSRGEYVARLSDCVA 62 Query: 65 CHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLY 124 CHSL G PFAGGLEMATPLGAIHATNITPD+ +GIG Y+LADFDRAVR GVAPGGRRLY Sbjct: 63 CHSLPGGKPFAGGLEMATPLGAIHATNITPDRDSGIGNYTLADFDRAVRQGVAPGGRRLY 122 Query: 125 PAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTA 184 PAMPYPSY KLSDDD+KALYAFFM G++PA Q N+ SDIPWPLN+RWPIALWNG+FA T Sbjct: 123 PAMPYPSYAKLSDDDVKALYAFFMHGVQPARQANLGSDIPWPLNLRWPIALWNGLFAATT 182 Query: 185 TYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAP 244 Y K QDA WNRGAYIVQGPGHCGSCHTPRGLAFNEKALD++G PFL+GALLDGWYAP Sbjct: 183 PYTDKAGQDAQWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDDSGKPFLSGALLDGWYAP 242 Query: 245 SLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYLK 304 SLR D NTGLGRWSE +I QFLKTGRN HAVVYGSMTEAFNNSTQFM DDDLAAIA YLK Sbjct: 243 SLRADHNTGLGRWSEAEIAQFLKTGRNRHAVVYGSMTEAFNNSTQFMHDDDLAAIAHYLK 302 Query: 305 SLPGDPQRDGAPWQYQA--VAAVQDAPGAHTYATRCASCHGLDGKGQPEWMPPLAGATSA 362 SLPGDPQRDGAPW YQA +A D+PGA TY TRCASCHGLDGKGQ EWMPPLAGATSA Sbjct: 303 SLPGDPQRDGAPWHYQAESLATRLDSPGARTYVTRCASCHGLDGKGQAEWMPPLAGATSA 362 Query: 363 LAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRSTWGNNGGAV 422 LAKESASAINITLNGSQRVVA+GVPDAYRMPA REQLSD EIA+VLS+VR+ WGN GGAV Sbjct: 363 LAKESASAINITLNGSQRVVAAGVPDAYRMPALREQLSDQEIADVLSFVRTAWGNQGGAV 422 Query: 423 DANAVGKLRGHTDPASSSPIILHMR 447 DA AVGKLRGHTDPASSSPIILHMR Sbjct: 423 DAQAVGKLRGHTDPASSSPIILHMR 447 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: 877 Number of extensions: 33 Number of successful extensions: 3 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: 447 Length adjustment: 33 Effective length of query: 414 Effective length of database: 414 Effective search space: 171396 Effective search space used: 171396 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