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 GFF2133 PS417_10880 alcohol dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__WCS417:GFF2133 Length = 447 Score = 382 bits (982), Expect = e-110 Identities = 195/405 (48%), Positives = 253/405 (62%), Gaps = 10/405 (2%) Query: 29 DSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPTYGIGRYTF 88 + ALV +G YVARL DCVACH+ +AGGLE+ +P+G I++TNITPD + GIG Y+ Sbjct: 46 EPALVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSL 105 Query: 89 AEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDKQPDISW 148 A+FD AVRHG+ G LYPAMPYPS+ +++ +D++ALYA+FM G+KP QP+ DI W Sbjct: 106 ADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPW 165 Query: 149 PLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPRGFAMQEKA 208 PL+MRWP+ +W +F+P+ + P D RG Y+V GPGHCG+CHTPRG A EKA Sbjct: 166 PLNMRWPIALWNGVFAPT-ATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKA 224 Query: 209 LDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSGRIDHSAVFGGMGD 268 LD AG P FL+ GA +D W APSLR DP GLGRWSE I FLK+GR H+ V+G M + Sbjct: 225 LDEAGAP-FLA-GALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTE 282 Query: 269 VVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANMLASGNTASVPGADTYVK 328 STQ+ DDDL AIA+YLKSLP P G + A PGA TY Sbjct: 283 AFNNSTQFMQDDDLAAIARYLKSLPGDPQRDG------APWQYQAVAAVQDAPGAHTYAT 336 Query: 329 ECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPSNWAPSAVAMPGYS 388 CA CH DG G PPLAG + + S +N+ +G ++ P A MP + Sbjct: 337 RCASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFR 396 Query: 389 KSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLRDTGAPVSSS 433 + LS +IA+V++++R++WGN G V A V KLR P SSS Sbjct: 397 EQLSDTEIAEVLSYVRSTWGNNG-GAVDANAVGKLRGHTDPASSS 440 Score = 32.0 bits (71), Expect = 4e-05 Identities = 34/136 (25%), Positives = 63/136 (46%), Gaps = 20/136 (14%) Query: 23 AQTPDADSALVQKGAYVAR-LGDCVACHT---------ALH--GQSYAGGLEIKSPIGTI 70 A PD D AL +GAY+ + G C +CHT AL G + G + + Sbjct: 187 AAKPDQD-ALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAG----ALLDGW 241 Query: 71 YSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAM--PYPSFSRMTKEDMQALYA 128 Y+ ++ DP G+GR++ + + ++ G R + +Y +M + + ++ ++D A A Sbjct: 242 YAPSLRQDPNTGLGRWSEPQIVQFLKTG-RNAHAVVYGSMTEAFNNSTQFMQDDDLAAIA 300 Query: 129 YFMHGVKPVAQPDKQP 144 ++ + Q D P Sbjct: 301 RYLKSLPGDPQRDGAP 316 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: 705 Number of extensions: 37 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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