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 PP_2479 PP_2479 Cytochrome c family protein
Query= SwissProt::O34215 (441 letters) >FitnessBrowser__Putida:PP_2479 Length = 407 Score = 244 bits (624), Expect = 3e-69 Identities = 155/418 (37%), Positives = 239/418 (57%), Gaps = 27/418 (6%) Query: 2 MKSILALVLGTLSFAALADDQ-ANDALVKRGEYLARAGDCVACHSVKGGQPFAGGLPMAT 60 M +++ VL S A LA A + L+ +GEYL RA +CVACH+V GGQPFAGG+ Sbjct: 1 MMKLISNVLTLASAALLAQAAYAQEDLLAKGEYLTRAANCVACHTVPGGQPFAGGVEFKL 60 Query: 61 PIGTIYSTNITPDKTTGIGDYSYDDFQKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKA 120 P G+++S NITPD TGIG ++ D+F A++ G+ ++G YPA PY SY+ +S +D+ A Sbjct: 61 PFGSLFSPNITPDPQTGIGAWTDDEFVSALQTGIGRDGKHYYPAFPYTSYSKMSRDDILA 120 Query: 121 LYAYFMHGVAPVAQANKDSDIPWPLSMRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRY 180 + Y + + PV QA +++ I +P + RW + W +F D + FQ +Q RG+Y Sbjct: 121 IKGY-LDSLQPVEQAPRENHIGFPFNQRWGMVFWNLLFLND-EPFQADSQRSAEWNRGKY 178 Query: 181 LVEGLGHCGACHTPRSITMQEKALSNDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWS 240 LVEG GHCG CH+PR++ +A+S++ + L+G+ I GW A N+ D G+G W Sbjct: 179 LVEGPGHCGECHSPRNLF---QAVSSERS---LAGNL--IQGWNAYNISADPVHGIGAWP 230 Query: 241 EDDLRQFLRYGRNDHTA-AFGGMTDVVEHSLQHLSDDDITAIARYLKSLGAKDASQTVFT 299 D L +L+ G + G M +VVE+SL+HL+D D AIA +LK + Sbjct: 231 TDVLAGYLKDGAAPGLGLSSGPMAEVVENSLRHLTDADRQAIAVFLKDSPPRSEG---VP 287 Query: 300 QDDQVAKALWKGDDSQTGASVYVDSCAACHKTDGS---RLSALLPGAAWQPGGAGEPDPT 356 + QV A G S G ++ ++CA+CH+ DG+ +A+L G +P + Sbjct: 288 RPQQVTLA-EPGSGSALGNKLFAEACASCHRWDGTGNQSQTAMLLGLK----TVNDPAAS 342 Query: 357 SLIHIVLTGGTLPGVQGAPTAITMPAFGWRLNDQQVADVVNFIRGSWG-NGAKATVTA 413 +L+ I+L+G G AP MP+FG DQ++A + +F+ +G +GA+ +V A Sbjct: 343 NLLGILLSG---HGAADAPVNRRMPSFGNIYTDQELAALSSFMLQRFGESGAQVSVPA 397 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: 527 Number of extensions: 45 Number of successful extensions: 8 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: 407 Length adjustment: 32 Effective length of query: 409 Effective length of database: 375 Effective search space: 153375 Effective search space used: 153375 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