Align Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized)
to candidate Pf6N2E2_4408 2-Keto-D-gluconate dehydrogenase (EC 1.1.99.4), membrane-bound, cytochrome c
Query= SwissProt::O34215 (441 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4408 Length = 474 Score = 262 bits (669), Expect = 2e-74 Identities = 169/443 (38%), Positives = 228/443 (51%), Gaps = 51/443 (11%) Query: 2 MKSILALVLGTLSFAALADDQANDALVKRGEYLARAGDCVACHSVKGGQPFAGGLPMATP 61 M+++LA L ++ + + D G+ LA A DCVACHS GG+PFAGG P+ +P Sbjct: 19 MRNMLAGGLALMTISLATHGETLDTSASPGKRLAVAADCVACHSTVGGKPFAGGYPLNSP 78 Query: 62 IGTIYSTNITPDKTTGIGDYSYDDFQKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKAL 121 +GTIYSTNITP ++ GIG Y+ DF +AVR GV +G LYPAMPY SYA ++D D+ AL Sbjct: 79 MGTIYSTNITPSRSAGIGQYTQADFARAVRDGVTPDGTHLYPAMPYTSYAKMTDSDVAAL 138 Query: 122 YAYFMHGVAPVAQANKDSDIPWPLSMRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYL 181 Y YFM V PV + +++ +P ++R + W +F K F+ + + RG YL Sbjct: 139 YQYFMDEVEPVDTPSPKTELDFPFNIRASMLGWNALFHRQ-KRFEADPGKSAQVNRGDYL 197 Query: 182 VEGLGHCGACHTPRSITMQEKALSNDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSE 241 V L HC CHTPR++ M A N A LSG S + W A N+ D G+G WS Sbjct: 198 VNALAHCDTCHTPRNVLM---AADNAKA---LSGGS--LGAWYAPNITSDKTSGIGAWSS 249 Query: 242 DDLRQFLRYGRNDHTA-AFGGMTDVVEHSLQHLSDDDITAIARYLK-----SLGAKDASQ 295 D+L +LR G + A A G M + VEHSLQ+L ++D+ AIA YL + G + A Sbjct: 250 DELVAYLRSGHVEGKAQAAGPMAEAVEHSLQYLGEEDLKAIAAYLLQTQPIATGERQARH 309 Query: 296 TVFTQDDQVAKALWKGDDSQTGASVYVDSCAACHKTDGSRLSALLPGAAWQPGGAGEPDP 355 T + G ++ +CA CH Q G G + Sbjct: 310 TFGQASNDELNLRGGKPQDNPGWHIFSGTCANCH----------------QANGEGTREY 353 Query: 356 TSLIHIVLTG-----------GTLPGVQGAPTAITMPAFG------WRLNDQQVADVVNF 398 SL H T G V G AI MPAFG RL+DQQ+ADV N+ Sbjct: 354 PSLFHNTATSRRDNLIATIVYGVHREVDG--VAIDMPAFGPGALFTDRLDDQQIADVSNY 411 Query: 399 IRGSWGNGAKATVTAKDVASLRK 421 + +GN A VTA DVA +R+ Sbjct: 412 VLSRYGN-AGLNVTAADVAQVRE 433 Lambda K H 0.317 0.133 0.409 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: 612 Number of extensions: 44 Number of successful extensions: 7 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: 441 Length of database: 474 Length adjustment: 33 Effective length of query: 408 Effective length of database: 441 Effective search space: 179928 Effective search space used: 179928 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 (21.6 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