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_3623 PP_3623 Alcohol dehydrogenase cytochrome c subunit
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__Putida:PP_3623 Length = 447 Score = 389 bits (1000), Expect = e-113 Identities = 207/413 (50%), Positives = 262/413 (63%), Gaps = 12/413 (2%) Query: 23 AQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPTYG 82 AQ AD ALV +G YVARL DCVACH+ G+ +AGGLE+ +P+G I++TNITPD G Sbjct: 38 AQATAADPALVSRGEYVARLSDCVACHSLPGGKPFAGGLEMATPLGAIHATNITPDRDSG 97 Query: 83 IGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDK 142 IG YT A+FD AVR G+ G LYPAMPYPS+++++ +D++ALYA+FMHGV+P Q + Sbjct: 98 IGNYTLADFDRAVRQGVAPGGRRLYPAMPYPSYAKLSDDDVKALYAFFMHGVQPARQANL 157 Query: 143 QPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPRGF 202 DI WPL++RWP+ +W +F+ + +T G D + RG Y+V GPGHCG+CHTPRG Sbjct: 158 GSDIPWPLNLRWPIALWNGLFA-ATTPYTDKAGQDAQWNRGAYIVQGPGHCGSCHTPRGL 216 Query: 203 AMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSGRIDHSAV 262 A EKALD +G P FLS GA +D W APSLR D GLGRWSE +I FLK+GR H+ V Sbjct: 217 AFNEKALDDSGKP-FLS-GALLDGWYAPSLRADHNTGLGRWSEAEIAQFLKTGRNRHAVV 274 Query: 263 FGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGN--YTYDPSTANMLASGNTASV 320 +G M + STQ+ DDDL AIA YLKSLP P G + S A L S Sbjct: 275 YGSMTEAFNNSTQFMHDDDLAAIAHYLKSLPGDPQRDGAPWHYQAESLATRLDS------ 328 Query: 321 PGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPSNWAPS 380 PGA TYV CA CH DG G A PPLAG + + S +N+ +G + P Sbjct: 329 PGARTYVTRCASCHGLDGKGQAEWMPPLAGATSALAKESASAINITLNGSQRVVAAGVPD 388 Query: 381 AVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLRDTGAPVSSS 433 A MP + LS Q+IADV++F+RT+WGN+ G V A V KLR P SSS Sbjct: 389 AYRMPALREQLSDQEIADVLSFVRTAWGNQG-GAVDAQAVGKLRGHTDPASSS 440 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: 687 Number of extensions: 30 Number of successful extensions: 4 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: 447 Length adjustment: 33 Effective length of query: 435 Effective length of database: 414 Effective search space: 180090 Effective search space used: 180090 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