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 Ac3H11_3427 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)
Query= SwissProt::O34215 (441 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3427 Length = 1243 Score = 239 bits (610), Expect = 4e-67 Identities = 153/394 (38%), Positives = 215/394 (54%), Gaps = 24/394 (6%) Query: 24 NDALVKRGEYLARAGDCVACHSVKGGQPFAGGLPMATPIGTIYSTNITPDKTTGIGDYSY 83 N A ++RG LA AGDC CH+ GG P GG M TP G IY+TN+TPD TGIG +S+ Sbjct: 848 NAATIERGRLLAAAGDCAVCHTAPGGTPNTGGRAMETPFGKIYTTNLTPDAETGIGQWSF 907 Query: 84 DDFQKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKALYAYFMHGVAPVAQANKDSDIPW 143 FQ+A+R G+++ G LYPA PY S+A +SD+D+ ALYAY M A A+ K +++ + Sbjct: 908 SAFQRAMREGISQGGKHLYPAFPYTSFAKMSDDDLTALYAYLMAQPAVRAEVPK-TELTF 966 Query: 144 PLSMRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYLVEGLGHCGACHTPRSITMQEKA 203 P S+R +A W +F D F+P P RG YLV+G+GHCGACHTPR+ E Sbjct: 967 PFSVRPLMAGWNALF-HDATPFKPDPTRPPEWNRGAYLVQGVGHCGACHTPRNALGAEL- 1024 Query: 204 LSNDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSEDDLRQFLRYGRN-DHTAAFGGM 262 G +LSG A IDGW A L G ++ + W+ D L +LR+G + H +A G M Sbjct: 1025 ----GGAAFLSG--AMIDGWEAPALTGLSKAPV-PWTADALYGYLRHGHSPQHGSASGPM 1077 Query: 263 TDVVEHSLQHLSDDDITAIARYLKSLGAKDASQTVFTQDDQ-----VAKALWKGDDSQTG 317 VV L HL DDDI A+A YL S A +A+ + Q VA+A Sbjct: 1078 APVV-RELAHLPDDDIRAMASYLASFTAAEAATQPVSDPQQRAQTAVAQAAALAPQPGQA 1136 Query: 318 ASVYVDSCAACHKT-DGSRLSAL-LPGAAWQPGGAGEPDPTSLIHIVLTGGTLPGVQGAP 375 ++ +CAACH DG +L + +P A + PD +L+ +++ G P + Sbjct: 1137 QRLFDGACAACHHDGDGPKLLGVNVPLALNSNLHSDRPD--NLLQVIVHGIREPAARDIG 1194 Query: 376 TAITMPAFGWRLNDQQVADVVNFIRGSWGNGAKA 409 MP FG L+D Q+ ++ ++R + G A Sbjct: 1195 ---FMPGFGHALSDAQITELAGYMRQRYAPGRPA 1225 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: 1466 Number of extensions: 85 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: 1243 Length adjustment: 40 Effective length of query: 401 Effective length of database: 1203 Effective search space: 482403 Effective search space used: 482403 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: 55 (25.8 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