Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate Pf6N2E2_1903 Putative diheme cytochrome c-553
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1903 Length = 444 Score = 625 bits (1612), Expect = 0.0 Identities = 297/442 (67%), Positives = 347/442 (78%), Gaps = 2/442 (0%) Query: 8 RTAGWLALPCLVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVACHS 67 +T +L +V A L W+V R P +PF E + + + LV RGEYVARLSDCVACHS Sbjct: 3 KTIKYLLPAGIVVAAGLGWFVNRTPFSPFANEASAPSADAQLVQRGEYVARLSDCVACHS 62 Query: 68 LAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYPAM 127 APFAGGLEMATP+G+I+ATNITPDK TGIG YSLADFDRAVR GVA G RLYPAM Sbjct: 63 TPKGAPFAGGLEMATPMGSIYATNITPDKQTGIGNYSLADFDRAVRSGVAADGHRLYPAM 122 Query: 128 PYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTATYA 187 PYPSY KLSDDD++ALYAFFM G+KPA Q N S IPWPLNMRWP+ALWN F Y Sbjct: 123 PYPSYAKLSDDDVRALYAFFMAGVKPAQQQNQQSHIPWPLNMRWPLALWNTAFVDDGAYQ 182 Query: 188 AKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAPSLR 247 AKP +DALWNRGAYIVQG GHCGSCHTPR L NEK+LDE+ A FL+G+LLDGWYAPSLR Sbjct: 183 AKPSEDALWNRGAYIVQGAGHCGSCHTPRSLTMNEKSLDESSATFLSGSLLDGWYAPSLR 242 Query: 248 QDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSLP 307 QDPNTGLGRWSE +IV +LKTGRNAH+VV G+M E FNNSTQ+M D DL AIA YL SLP Sbjct: 243 QDPNTGLGRWSEQEIVDYLKTGRNAHSVVVGTMAEVFNNSTQYMSDPDLKAIAHYLVSLP 302 Query: 308 GDPQRDGAPWQYQAVAAVQ--DAPGAHTYATRCASCHGLDGKGQPEWMPPLAGATSALAK 365 GDP+RDG PW+ A A Q PGA Y +C+SCHG DG GQ W+PPLAGA+S++ K Sbjct: 303 GDPKRDGPPWKPAAKLAEQPLSTPGAANYMAKCSSCHGSDGSGQAPWIPPLAGASSSMVK 362 Query: 366 ESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRSTWGNNGGAVDAN 425 E A++IN TLNGS+RVVA+G+PD+YRMP +R QLSD E+A+VL++VR++WGN GGAV A+ Sbjct: 363 EGATSINATLNGSERVVANGIPDSYRMPPYRNQLSDQEVADVLTFVRTSWGNQGGAVKAD 422 Query: 426 AVGKLRGHTDPASSSPIILHMR 447 V +LR T+PASS+PIIL MR Sbjct: 423 EVKELRERTNPASSNPIILQMR 444 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: 772 Number of extensions: 31 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: 444 Length adjustment: 32 Effective length of query: 415 Effective length of database: 412 Effective search space: 170980 Effective search space used: 170980 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