Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate PP_3948 PP_3948 nicotinate dehydrogenase subunit B
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__Putida:PP_3948 Length = 1187 Score = 231 bits (588), Expect = 1e-64 Identities = 146/376 (38%), Positives = 207/376 (55%), Gaps = 23/376 (6%) Query: 26 ALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPIGVIYSTNITPD-KTGIGDYSFED 84 A++++G +A AGDC CHT GK AGGL M+TP G +YSTNITPD +TGIG +SF Sbjct: 804 AMLERGRQVAAAGDCAVCHTVSGGKANAGGLAMDTPFGTLYSTNITPDPETGIGRWSFAA 863 Query: 85 FDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGVAPVARDNQDSDIPWPL 144 F++A+R G+++ G LYPA P+ S+ ++DADMQALYAY M PV ++ + + +P Sbjct: 864 FERAMREGISRDGRHLYPAFPYTSFRNINDADMQALYAYLM-SQTPVRQEAPANQMRFPF 922 Query: 145 SMRWPLSIWRWMFAPSVE-TPAPAAGSDPVISRGAYLVEGLGHCGACHTPRALTMQEKAL 203 + R ++ W F E P P + +RGAYLV+GLGHC ACH+PR L EK Sbjct: 923 NQRPLMAGWNARFLQRGEYQPDPQRSAQ--WNRGAYLVDGLGHCTACHSPRNLMGAEK-- 978 Query: 204 SASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLKTGRSDRSAVFGGMSDV 263 GGS +L+G ++GW A +L K WSE++L +L TG S++ V G Sbjct: 979 ---GGSSYLAGGM-VDGWEAPALNALGKSST-PWSEDELFNYLSTGFSEKHGVAAGPMGP 1033 Query: 264 VVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDKQVAQALWNGDDSKPGAAVYIDNC 323 VV + + +D+ AIA YL SL + +P A + G V+ C Sbjct: 1034 VVSELATLPKSDVRAIAHYLSSL-----EGEPQALAANAAPQVDTHVSLSNGERVFKGAC 1088 Query: 324 AACHRTDGHG--YTRVFPALAGNPVLQSADATSLIHIVLKGGTLPATHSAPSTFTMPAFA 381 CH +DG G V P++A N + S +L+ +VL G PAT MP F Sbjct: 1089 LGCH-SDGLGPKLFGVSPSMAVNSNVHSDLPDNLLRVVLHGIPTPATRDLG---YMPGFK 1144 Query: 382 WRLSDQEVADVVNFIR 397 LSD++VAD+ ++R Sbjct: 1145 DSLSDRQVADLAAYLR 1160 Lambda K H 0.316 0.131 0.404 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: 1405 Number of extensions: 80 Number of successful extensions: 6 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: 434 Length of database: 1187 Length adjustment: 39 Effective length of query: 395 Effective length of database: 1148 Effective search space: 453460 Effective search space used: 453460 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