Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate H281DRAFT_02833 H281DRAFT_02833 Cytochrome c, mono- and diheme variants
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Burk376:H281DRAFT_02833 Length = 438 Score = 338 bits (868), Expect = 2e-97 Identities = 187/434 (43%), Positives = 249/434 (57%), Gaps = 29/434 (6%) Query: 21 AGLLAWYVTREPATPFEQE-QAGATFEPALVSRGEYVARLSDCVACHSLAGKAPFAGGLE 79 +G AW + P F Q+ +A + AL+ RGEY+A DC+ACH+ A PFAGGL Sbjct: 11 SGAFAWS-SALPVCAFAQDAKAVDGNDAALIKRGEYLATAGDCMACHTTAKGKPFAGGLP 69 Query: 80 MATP-LGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDD 138 + P LG I+++NITPD TGIGT+SL DFDRA+R GV+ G LYPAMPY SY K+SD Sbjct: 70 LKVPMLGTIYSSNITPDPQTGIGTWSLEDFDRALRKGVSKDGHNLYPAMPYVSYAKVSDG 129 Query: 139 DIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTATYAAKPDQDALWNR 198 D+KALYA+F G+ P Q SDI WPLNMRWP+ +WN +F + Y AKP Q A WNR Sbjct: 130 DVKALYAYFRYGVVPVQQATRASDIAWPLNMRWPLTVWNWMFLKSGPYQAKPQQSAEWNR 189 Query: 199 GAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAPSLRQDPNTGLGRWS 258 GAY+VQG HC +CHTPRG A E+ALDE G+ FL G++L W ++ P++G+G WS Sbjct: 190 GAYLVQGLAHCSTCHTPRGFAMQEQALDETGSGFLGGSVLADWDGYNITSSPDSGIGGWS 249 Query: 259 EPQIVQFLKTGR-NAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSLPGDPQRDGAPW 317 Q+VQ+L+TG A G M EA +S M D D+ AIA Y++++P P DG Sbjct: 250 HTQLVQYLQTGSVPGLAQAAGPMAEAVEHSFSKMSDADIGAIATYVRTVP--PVNDGGAQ 307 Query: 318 QYQAVAAVQDAPG------------------AHTYATRCASCHGLDGKGQPE-WMPPLAG 358 + P A Y CA+CH GKG P+ + PPL Sbjct: 308 SGSRSRSAWGKPSTDVARLRGVAMNDGTLDPARLYLGNCATCHQASGKGTPDGYYPPLLH 367 Query: 359 ATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRSTWGNN 418 ++ A + + + L+G QR A + MPAF QL+D +IA + +YV + +GN Sbjct: 368 NSTVGASNPGNLMQVILHGVQRKAAG---NDVGMPAFAAQLNDAQIAALTNYVTTQFGNP 424 Query: 419 GG-AVDANAVGKLR 431 V V +LR Sbjct: 425 AAQRVSEKDVARLR 438 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: 666 Number of extensions: 47 Number of successful extensions: 9 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: 438 Length adjustment: 32 Effective length of query: 415 Effective length of database: 406 Effective search space: 168490 Effective search space used: 168490 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