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 H281DRAFT_02833 H281DRAFT_02833 Cytochrome c, mono- and diheme variants
Query= SwissProt::O34215 (441 letters) >FitnessBrowser__Burk376:H281DRAFT_02833 Length = 438 Score = 316 bits (810), Expect = 8e-91 Identities = 182/421 (43%), Positives = 245/421 (58%), Gaps = 28/421 (6%) Query: 17 ALADDQANDALVKRGEYLARAGDCVACHSVKGGQPFAGGLPMATP-IGTIYSTNITPDKT 75 A A D + AL+KRGEYLA AGDC+ACH+ G+PFAGGLP+ P +GTIYS+NITPD Sbjct: 29 AKAVDGNDAALIKRGEYLATAGDCMACHTTAKGKPFAGGLPLKVPMLGTIYSSNITPDPQ 88 Query: 76 TGIGDYSYDDFQKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKALYAYFMHGVAPVAQA 135 TGIG +S +DF +A+R GV+K+G LYPAMPY SYA VSD D+KALYAYF +GV PV QA Sbjct: 89 TGIGTWSLEDFDRALRKGVSKDGHNLYPAMPYVSYAKVSDGDVKALYAYFRYGVVPVQQA 148 Query: 136 NKDSDIPWPLSMRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYLVEGLGHCGACHTPR 195 + SDI WPL+MRWPL +W +F +Q Q+ RG YLV+GL HC CHTPR Sbjct: 149 TRASDIAWPLNMRWPLTVWNWMFLKS-GPYQAKPQQSAEWNRGAYLVQGLAHCSTCHTPR 207 Query: 196 SITMQEKALSNDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSEDDLRQFLRYGRNDH 255 MQE+AL G+ +L GS + W N+ G+G WS L Q+L+ G Sbjct: 208 GFAMQEQALDETGS-GFLGGS--VLADWDGYNITSSPDSGIGGWSHTQLVQYLQTGSVPG 264 Query: 256 TA-AFGGMTDVVEHSLQHLSDDDITAIARYLKSL------GAKDASQTVF-----TQDDQ 303 A A G M + VEHS +SD DI AIA Y++++ GA+ S++ + D Sbjct: 265 LAQAAGPMAEAVEHSFSKMSDADIGAIATYVRTVPPVNDGGAQSGSRSRSAWGKPSTDVA 324 Query: 304 VAKALWKGDDSQTGASVYVDSCAACHKTDGSRLSALLPGAAWQP----GGAGEPDPTSLI 359 + + D + A +Y+ +CA CH+ G P + P G +P +L+ Sbjct: 325 RLRGVAMNDGTLDPARLYLGNCATCHQASGKG----TPDGYYPPLLHNSTVGASNPGNLM 380 Query: 360 HIVLTGGTLPGVQGAPTAITMPAFGWRLNDQQVADVVNFIRGSWGNGAKATVTAKDVASL 419 ++L G + A + MPAF +LND Q+A + N++ +GN A V+ KDVA L Sbjct: 381 QVILHGVQR---KAAGNDVGMPAFAAQLNDAQIAALTNYVTTQFGNPAAQRVSEKDVARL 437 Query: 420 R 420 R Sbjct: 438 R 438 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: 625 Number of extensions: 40 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: 441 Length of database: 438 Length adjustment: 32 Effective length of query: 409 Effective length of database: 406 Effective search space: 166054 Effective search space used: 166054 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