Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate PfGW456L13_3925 Putative diheme cytochrome c-553
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3925 Length = 412 Score = 228 bits (580), Expect = 4e-64 Identities = 133/401 (33%), Positives = 201/401 (50%), Gaps = 28/401 (6%) Query: 46 EPALVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSL 105 + A V +GEY+AR +DC+ACH+ G AP+AGGL + +P G I+ TNITP K GIG Y+ Sbjct: 24 DDAQVKQGEYLARAADCMACHTAPGGAPYAGGLPIVSPFGTIYGTNITPSKEHGIGLYND 83 Query: 106 ADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPW 165 +F A+ G G LYPAMPY SY + D A++A +++ ++P + + + + Sbjct: 84 DEFFAALTEGKRRDGANLYPAMPYTSYHLIPRADSDAIHA-YLKTVEPIERAAPVTSLSF 142 Query: 166 PLNMRWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKAL 225 P N+R + WN ++ + W RG Y+V GHCG CHTPRGL + Sbjct: 143 PFNVRLGLMGWNMMYGKDVKLEPAEGKSEAWKRGQYMVDVLGHCGECHTPRGLP-GAMQM 201 Query: 226 DEAGAPFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFN 285 D+ + G +L+G+ APSL G W+ + FLK G +A ++ M F+ Sbjct: 202 DKR----MTGGILNGYLAPSLLATDLAARG-WNHQDLSSFLKHGMSAQGTMFNEMFPVFH 256 Query: 286 NSTQFMQDDDLAAIARYLKSLPGDPQRDGAPWQYQAVAAVQDAP----------GAHTYA 335 NSTQ + D DLAA+A +L GD Q A + + P G Y Sbjct: 257 NSTQGLSDPDLAAMATFLL---GD--------QPPAAKVLVEVPLDKLSPSVQRGRQEYL 305 Query: 336 TRCASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAF 395 CA CH G+G+P + G T+ ++ + + + +G SG MP F Sbjct: 306 NVCAGCHAPGGEGKPHIAVAMRGNTTLRLEDPRNLVRVIDDGIGEQKFSGFEHMQPMPGF 365 Query: 396 REQLSDTEIAEVLSYVRSTWGNNGGAVDANAVGKLRGHTDP 436 ++L+D ++ ++L+Y+R WG + N V KLR P Sbjct: 366 VDKLNDEQLTDLLNYLRQGWGGQPNDLAVNDVQKLRADAPP 406 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: 559 Number of extensions: 32 Number of successful extensions: 5 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: 412 Length adjustment: 32 Effective length of query: 415 Effective length of database: 380 Effective search space: 157700 Effective search space used: 157700 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