Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate Dsui_2086 Dsui_2086 cytochrome c
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__PS:Dsui_2086 Length = 696 Score = 367 bits (943), Expect = e-106 Identities = 185/391 (47%), Positives = 246/391 (62%), Gaps = 17/391 (4%) Query: 50 VSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFD 109 ++RGEY+ARL DCVACH+ G AGG E+ATP G + +TNITPDK TGIG Y+ A FD Sbjct: 48 IARGEYLARLGDCVACHTAEGGKSMAGGRELATPFGVLFSTNITPDKETGIGNYTFAQFD 107 Query: 110 RAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNM 169 RA+R GVA G LYPAMPYPSY K++ +D++ALYA+ MQG+ P Q N P+ + WP N Sbjct: 108 RAMRKGVAADGHNLYPAMPYPSYAKMTGEDMQALYAYLMQGLAPVKQANKPTAMRWPFNQ 167 Query: 170 RWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAG 229 RW ++LWN F + +DA WNRGAY+VQG GHCG+CHTPRG+AF EKA+ +AG Sbjct: 168 RWGLSLWNWAFLDATPFQPDAGKDATWNRGAYLVQGLGHCGACHTPRGIAFQEKAMSDAG 227 Query: 230 AP---FLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNN 286 + FLAG ++ W A SLR G W+ FLKTG+N A G+M E ++ Sbjct: 228 SKGKHFLAGETVESWRALSLR-------GLWTVEDTALFLKTGQNRFATASGNMAEVIHH 280 Query: 287 STQFMQDDDLAAIARYLKSLPGDPQRDGAPWQYQAVAA------VQDAPGAHTYATRCAS 340 STQ ++D+DL AIA YLKSLP AP ++ A + + G Y C Sbjct: 281 STQHVKDEDLVAIATYLKSLPPGEHELPAPSVPRSEVAGKVPGNLFSSRGGLAYVQFCGD 340 Query: 341 CHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLS 400 CH DG G + PPLAG + AK+ A+ ++ITL G + + P + MP F +L+ Sbjct: 341 CHRQDGNGVSKIFPPLAGNPAVTAKDPATLLHITLTGWKTASTAAHPRVFTMPGF-ARLN 399 Query: 401 DTEIAEVLSYVRSTWGNNGGAVDANAVGKLR 431 D E+AE++++VRS+WGN G AV A+ V K+R Sbjct: 400 DQELAELITFVRSSWGNGGEAVTASQVKKMR 430 Score = 27.3 bits (59), Expect = 0.002 Identities = 10/19 (52%), Positives = 13/19 (68%) Query: 330 GAHTYATRCASCHGLDGKG 348 G YA +CA CHG +G+G Sbjct: 586 GKKIYAEQCAVCHGENGEG 604 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: 984 Number of extensions: 48 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 447 Length of database: 696 Length adjustment: 36 Effective length of query: 411 Effective length of database: 660 Effective search space: 271260 Effective search space used: 271260 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: 53 (25.0 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