Align Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate PP_3948 PP_3948 nicotinate dehydrogenase subunit B
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__Putida:PP_3948 Length = 1187 Score = 224 bits (572), Expect = 9e-63 Identities = 145/390 (37%), Positives = 202/390 (51%), Gaps = 31/390 (7%) Query: 30 SALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPTYGIGRYTFA 89 +A++++G VA GDC CHT G++ AGGL + +P GT+YSTNITPDP GIGR++FA Sbjct: 803 AAMLERGRQVAAAGDCAVCHTVSGGKANAGGLAMDTPFGTLYSTNITPDPETGIGRWSFA 862 Query: 90 EFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDKQPDISWP 149 F+ A+R GI +DG LYPA PY SF + DMQALYAY M PV Q + +P Sbjct: 863 AFERAMREGISRDGRHLYPAFPYTSFRNINDADMQALYAYLM-SQTPVRQEAPANQMRFP 921 Query: 150 LSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPRGFAMQEKAL 209 + R + W F ++ P P + RG YLV G GHC ACH+PR EK Sbjct: 922 FNQRPLMAGWNARFL-QRGEYQPDPQRSAQWNRGAYLVDGLGHCTACHSPRNLMGAEK-- 978 Query: 210 DAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGR----WSEDDIYTFLKSGRID-HSAVFG 264 GG +L+GG +D W AP+L LG+ WSED+++ +L +G + H G Sbjct: 979 ---GGSSYLAGGM-VDGWEAPALN-----ALGKSSTPWSEDELFNYLSTGFSEKHGVAAG 1029 Query: 265 GMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANMLASGNTASVPGAD 324 MG VV+ D+ AIA YL SL P + ++ S GA Sbjct: 1030 PMGPVVS-ELATLPKSDVRAIAHYLSSLEGEPQALAANAAPQVDTHVSLSNGERVFKGA- 1087 Query: 325 TYVKECAICHRNDGGG--VARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPSNWAPSAV 382 C CH +DG G + + P +A N V ++ P +L+ V+ HG P + Sbjct: 1088 -----CLGCH-SDGLGPKLFGVSPSMAVNSNVHSDLPDNLLRVVLHGIPTPATR---DLG 1138 Query: 383 AMPGYSKSLSAQQIADVVNFIRTSWGNKAP 412 MPG+ SLS +Q+AD+ ++R + P Sbjct: 1139 YMPGFKDSLSDRQVADLAAYLRHRFAADKP 1168 Lambda K H 0.317 0.134 0.425 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: 1527 Number of extensions: 84 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: 468 Length of database: 1187 Length adjustment: 40 Effective length of query: 428 Effective length of database: 1147 Effective search space: 490916 Effective search space used: 490916 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