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 Pf6N2E2_4408 2-Keto-D-gluconate dehydrogenase (EC 1.1.99.4), membrane-bound, cytochrome c
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4408 Length = 474 Score = 259 bits (661), Expect = 2e-73 Identities = 158/406 (38%), Positives = 224/406 (55%), Gaps = 22/406 (5%) Query: 36 GAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPTYGIGRYTFAEFDEAV 95 G +A DCVACH+ + G+ +AGG + SP+GTIYSTNITP + GIG+YT A+F AV Sbjct: 48 GKRLAVAADCVACHSTVGGKPFAGGYPLNSPMGTIYSTNITPSRSAGIGQYTQADFARAV 107 Query: 96 RHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDKQPDISWPLSMRWP 155 R G+ DG+ LYPAMPY S+++MT D+ ALY YFM V+PV P + ++ +P ++R Sbjct: 108 RDGVTPDGTHLYPAMPYTSYAKMTDSDVAALYQYFMDEVEPVDTPSPKTELDFPFNIRAS 167 Query: 156 LGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPRGFAMQEKALDAAGGP 215 + W +F K F PG ++ RGDYLV HC CHTPR M AA Sbjct: 168 MLGWNALFH-RQKRFEADPGKSAQVNRGDYLVNALAHCDTCHTPRNVLM------AADNA 220 Query: 216 DFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSGRIDHSA-VFGGMGDVVAWST 274 LSGG+ + W AP++ +D G+G WS D++ +L+SG ++ A G M + V S Sbjct: 221 KALSGGS-LGAWYAPNITSDKTSGIGAWSSDELVAYLRSGHVEGKAQAAGPMAEAVEHSL 279 Query: 275 QYFTDDDLHAIAKYLKSLPPVPPS--QGNYTYDPSTAN--MLASGNTASVPGADTYVKEC 330 QY ++DL AIA YL P+ Q +T+ ++ + L G PG + C Sbjct: 280 QYLGEEDLKAIAAYLLQTQPIATGERQARHTFGQASNDELNLRGGKPQDNPGWHIFSGTC 339 Query: 331 AICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPSNWAPSAVAM-PG--Y 387 A CH+ +G G R +P L N T +L+ I +G A A PG + Sbjct: 340 ANCHQANGEG-TREYPSLFHN--TATSRRDNLIATIVYGVHREVDGVAIDMPAFGPGALF 396 Query: 388 SKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLRDTG--APVS 431 + L QQIADV N++ + +GN A VTAADV ++R+ G AP++ Sbjct: 397 TDRLDDQQIADVSNYVLSRYGN-AGLNVTAADVAQVREGGPKAPIA 441 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: 671 Number of extensions: 33 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: 474 Length adjustment: 33 Effective length of query: 435 Effective length of database: 441 Effective search space: 191835 Effective search space used: 191835 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