Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate Pf6N2E2_4408 2-Keto-D-gluconate dehydrogenase (EC 1.1.99.4), membrane-bound, cytochrome c
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4408 Length = 474 Score = 263 bits (671), Expect = 1e-74 Identities = 157/400 (39%), Positives = 221/400 (55%), Gaps = 32/400 (8%) Query: 51 SRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDR 110 S G+ +A +DCVACHS G PFAGG + +P+G I++TNITP +S GIG Y+ ADF R Sbjct: 46 SPGKRLAVAADCVACHSTVGGKPFAGGYPLNSPMGTIYSTNITPSRSAGIGQYTQADFAR 105 Query: 111 AVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMR 170 AVR GV P G LYPAMPY SY K++D D+ ALY +FM ++P + P+ +++ +P N+R Sbjct: 106 AVRDGVTPDGTHLYPAMPYTSYAKMTDSDVAALYQYFMDEVEPVDTPSPKTELDFPFNIR 165 Query: 171 WPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGA 230 + WN +F + A P + A NRG Y+V HC +CHTPR + A D A A Sbjct: 166 ASMLGWNALFHRQKRFEADPGKSAQVNRGDYLVNALAHCDTCHTPRNVLM---AADNAKA 222 Query: 231 PFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGR-NAHAVVYGSMTEAFNNSTQ 289 L+G L WYAP++ D +G+G WS ++V +L++G A G M EA +S Q Sbjct: 223 --LSGGSLGAWYAPNITSDKTSGIGAWSSDELVAYLRSGHVEGKAQAAGPMAEAVEHSLQ 280 Query: 290 FMQDDDLAAIARYLKSLPGDPQRDGAPWQYQAVAAV------------QDAPGAHTYATR 337 ++ ++DL AIA YL L P G QD PG H ++ Sbjct: 281 YLGEEDLKAIAAYL--LQTQPIATGERQARHTFGQASNDELNLRGGKPQDNPGWHIFSGT 338 Query: 338 CASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPA--- 394 CA+CH +G+G E+ P L T+ ++ + I + G R V GV A MPA Sbjct: 339 CANCHQANGEGTREY-PSLFHNTATSRRD--NLIATIVYGVHREV-DGV--AIDMPAFGP 392 Query: 395 ---FREQLSDTEIAEVLSYVRSTWGNNGGAVDANAVGKLR 431 F ++L D +IA+V +YV S +GN G V A V ++R Sbjct: 393 GALFTDRLDDQQIADVSNYVLSRYGNAGLNVTAADVAQVR 432 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: 618 Number of extensions: 38 Number of successful extensions: 6 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: 474 Length adjustment: 33 Effective length of query: 414 Effective length of database: 441 Effective search space: 182574 Effective search space used: 182574 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