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 GFF2557 PS417_13035 aldehyde dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__WCS417:GFF2557 Length = 1175 Score = 221 bits (563), Expect = 1e-61 Identities = 139/388 (35%), Positives = 205/388 (52%), Gaps = 32/388 (8%) Query: 31 ALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPTYGIGRYTFAE 90 A +++G +A +GDC CHTA G + AGGL +++P GT+YS+NITPD GIG +++ Sbjct: 795 ATLERGRLLAAVGDCAVCHTAPGGATNAGGLAMQTPFGTLYSSNITPDVKTGIGAWSYPA 854 Query: 91 FDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDKQPDISWPL 150 F+ A+R GI +DG LYPA PY +F + + DMQALYAY M V PV+Q + +P Sbjct: 855 FERAMRDGIGRDGRNLYPAFPYTAFRNINEADMQALYAYLMSQV-PVSQAPTPNAMRFPF 913 Query: 151 SMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPRGFAMQEKALD 210 ++R + W + + + +P P + RG+YLV G GHC ACH+PR EK Sbjct: 914 NIRPLMAGWNAL-NLRRGEISPQPERSEQWNRGNYLVNGLGHCAACHSPRNLMGAEK--- 969 Query: 211 AAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGR----WSEDDIYTFLKSGRID-HSAVFGG 265 GG FL+GG +D W AP+L GL + W+ED ++T+L +G D H G Sbjct: 970 --GGKSFLAGGT-VDGWEAPALN-----GLSKASTPWTEDQLFTYLSTGYSDAHGVAAGP 1021 Query: 266 MGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANMLASGNTASVPGADT 325 MG VV+ D+ A+A YL SL +G+ + A + + N + G Sbjct: 1022 MGPVVS-ELSKLPKADIRAMAVYLASL------KGDAA---AEAPAVTAANVPNPDGRRV 1071 Query: 326 YVKECAICHRND-GGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPSNWAPSAVAM 384 + C CH + G + + P A N V ++ P +L+ VI G P + M Sbjct: 1072 FEGACKACHADGLGPKLFGVSPSFATNTNVHSDQPDNLIKVILQGISKPATQ---DLGYM 1128 Query: 385 PGYSKSLSAQQIADVVNFIRTSWGNKAP 412 PG+ SLS Q+AD+ ++R + AP Sbjct: 1129 PGFKDSLSNSQVADLAAYLRAQFAPNAP 1156 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: 1569 Number of extensions: 91 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: 468 Length of database: 1175 Length adjustment: 40 Effective length of query: 428 Effective length of database: 1135 Effective search space: 485780 Effective search space used: 485780 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