Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate AO353_27065 AO353_27065 cytochrome C oxidase Cbb3
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__pseudo3_N2E3:AO353_27065 Length = 415 Score = 233 bits (594), Expect = 9e-66 Identities = 134/399 (33%), Positives = 207/399 (51%), Gaps = 21/399 (5%) Query: 20 AAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVACHSLAGKAPFAGGLE 79 A GL + + A +Q+Q + RGEY+AR +DC+ACH+ G AP+AGGL Sbjct: 11 AVGLAVSLMAIQQAQAADQQQ---------IKRGEYLARAADCMACHTAPGGAPYAGGLP 61 Query: 80 MATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDD 139 + +P G I+ TNITPDK GIG YS +F A+ G G LYPAMPY SY + +D Sbjct: 62 IVSPFGTIYGTNITPDKDHGIGQYSDDEFFAALTEGKRRDGANLYPAMPYTSYHLMPRED 121 Query: 140 IKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTATYAAKPDQDALWNRG 199 A++A ++Q + P N+ + + +P N+R + WN ++ + W RG Sbjct: 122 SDAIHA-YLQTVAPINRAAPVTRLSFPFNVRLGLMGWNMLYGKDVKLTPAEGKSEDWKRG 180 Query: 200 AYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAPSLRQDPNTGLGRWSE 259 Y+V GHCG CHTPRGL D+ L G LL+G+ APSL + G W+ Sbjct: 181 QYLVDVLGHCGECHTPRGLP-GAMQQDKR----LTGGLLNGYLAPSLLANDLAARG-WTH 234 Query: 260 PQIVQFLKTGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSLPGDPQRDGAPWQY 319 + FLK G +A ++ M F+NSTQ + + DLA++A +L GDP Sbjct: 235 QDLSSFLKHGMSAQGTMFNEMFPVFHNSTQNLNEPDLASMATFLL---GDPPPQARVLSE 291 Query: 320 QAVAAVQDAP--GAHTYATRCASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNG 377 + + ++ G Y CA CHG++G+G+P + G T+ ++ + + + +G Sbjct: 292 VPLDKMTESARRGRQDYLNVCAGCHGVNGEGKPHIAVAMQGNTTLRLEDPRNLLRVIEDG 351 Query: 378 SQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRSTWG 416 +G MP F ++LS+ ++ +++SY+R WG Sbjct: 352 IGEQKFAGFERMQPMPGFADKLSNQQMTDLISYLRQAWG 390 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: 528 Number of extensions: 30 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: 415 Length adjustment: 32 Effective length of query: 415 Effective length of database: 383 Effective search space: 158945 Effective search space used: 158945 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