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 N515DRAFT_2297 N515DRAFT_2297 Cytochrome c, mono- and diheme variants
Query= SwissProt::O34215 (441 letters) >FitnessBrowser__Dyella79:N515DRAFT_2297 Length = 441 Score = 247 bits (630), Expect = 6e-70 Identities = 152/407 (37%), Positives = 216/407 (53%), Gaps = 34/407 (8%) Query: 28 VKRGEYLARAGDCVACHSVKGGQPFAGGLPMATPIGTIYSTNITPDKTTGIGDYSYDDFQ 87 V RGEYL RA DC ACH+V GGQP+ GG+ P GTIYSTNIT DK TGIGD+S D+F Sbjct: 53 VARGEYLTRAADCAACHTVPGGQPYTGGVAFKMPFGTIYSTNITADKETGIGDWSDDEFV 112 Query: 88 KAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKALYAYFMHGVAPVAQANKDSDIPWPLSM 147 +A+ GV K+G LYPA PY SY +S +D+ A+ AY + + P + +++ +P Sbjct: 113 RALHAGVRKDGKPLYPAFPYTSYTALSRDDVLAIKAY-LFSLPPKHAPARPNELSFPFDQ 171 Query: 148 RWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYLVEGLGHCGACHTPRSITMQEKALSND 207 RW L++W +F + ++P + RG YL LGHC CHTPR+ K Sbjct: 172 RWGLSVWNALFLKK-QRYEPVQGKSQAWNRGAYLATALGHCDECHTPRNAMYALK----- 225 Query: 208 GAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSEDDLRQFLRYGR-NDHTAAFGGMTDVV 266 D LSG + GW A N+ D G+G WSE L +L G + A G M +VV Sbjct: 226 -RGDALSGE--VLQGWKAYNITSDKTYGIGNWSEQQLADYLSKGHASGRGTASGPMGEVV 282 Query: 267 EHSLQHLSDDDITAIARYLKSLGAKDASQTVFTQDDQVAKALWKGDDSQ---------TG 317 ++SLQ+L+ +DI A+ YL+ + + S +D+ A AL + G Sbjct: 283 QYSLQYLTPEDIGALVTYLREVKPQQGS-AGSEVNDRPALALASSASAPGAEELAQGGLG 341 Query: 318 ASVYVDSCAACHKTDG----SRLSALLPGAAWQPGGAGEPDPTSLIHIVLTGGTLPGVQG 373 ++ +C++CH +G S +ALL A A +P +L ++L G TL G Sbjct: 342 QHLFQGACSSCHLWNGQGRQSEAAALLGTQA-----ANDPQAHNLTQVILQGSTLRTAHG 396 Query: 374 APTAITMPAFGWRLNDQQVADVVNFIRGSWGNGAKATVTAKDVASLR 420 +MP+FG D +VA + NF+ +G G AT+TA +VA R Sbjct: 397 ---ETSMPSFGQAYTDAEVAALGNFVLTHFG-GKPATLTADEVAKRR 439 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: 607 Number of extensions: 43 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 441 Length of database: 441 Length adjustment: 32 Effective length of query: 409 Effective length of database: 409 Effective search space: 167281 Effective search space used: 167281 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