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 AO353_27065 AO353_27065 cytochrome C oxidase Cbb3
Query= SwissProt::Q47945 (478 letters) >FitnessBrowser__pseudo3_N2E3:AO353_27065 Length = 415 Score = 250 bits (639), Expect = 6e-71 Identities = 156/423 (36%), Positives = 226/423 (53%), Gaps = 22/423 (5%) Query: 20 LAAAIGLMAVSFGAAHAQDADEALIKRGEYVARLSDCIACHTALHGQPYAGGLEIKSPIG 79 L A+GL AQ AD+ IKRGEY+AR +DC+ACHTA G PYAGGL I SP G Sbjct: 8 LGTAVGLAVSLMAIQQAQAADQQQIKRGEYLARAADCMACHTAPGGAPYAGGLPIVSPFG 67 Query: 80 TIYSTNITPDPEHGIGNYTLEDFTKALRKGIRKDGATVYPAMPYPEFARLSDDDIRAMYA 139 TIY TNITPD +HGIG Y+ ++F AL +G R+DGA +YPAMPY + + +D A++A Sbjct: 68 TIYGTNITPDKDHGIGQYSDDEFFAALTEGKRRDGANLYPAMPYTSYHLMPREDSDAIHA 127 Query: 140 FFMHGVKPVALQNKAPDISWPLSMRWPLGMWRAMFVP--SMTPGVDKSISDPEVARGEYL 197 ++ V P+ +S+P ++R L W ++ +TP KS + RG+YL Sbjct: 128 -YLQTVAPINRAAPVTRLSFPFNVRLGLMGWNMLYGKDVKLTPAEGKS---EDWKRGQYL 183 Query: 198 VNGPGHCGECHTPRGFGMQVKAYGTAGGNAYLAGGAPIDNWIAPSLRSNSDTGLGRWSED 257 V+ GHCGECHTPRG G + L GG ++ ++APSL +N D W+ Sbjct: 184 VDVLGHCGECHTPRGLP------GAMQQDKRLTGGL-LNGYLAPSLLAN-DLAARGWTHQ 235 Query: 258 DIVTFLKSGRIDHSAVFGGMADVVAYSTQHWSDDDLRATAKYLKSMPAVPEGKNLGQDDG 317 D+ +FLK G +F M V STQ+ ++ DL + A +L P P+ + L + Sbjct: 236 DLSSFLKHGMSAQGTMFNEMFPVFHNSTQNLNEPDLASMATFLLGDPP-PQARVLSE--- 291 Query: 318 QTTALLNKGGQGNAGAEVYLHNCAICHMNDGTGVNRMFPPLAGNPVVITDDPTSLANVVA 377 L G + YL+ CA CH +G G + + GN + +DP +L V+ Sbjct: 292 --VPLDKMTESARRGRQDYLNVCAGCHGVNGEGKPHIAVAMQGNTTLRLEDPRNLLRVIE 349 Query: 378 FGGILPPTNSAPSAVAMPGFKNHLSDQEMADVVNFMRKGWGNNAPGTVSASDIQKLRTTG 437 G MPGF + LS+Q+M D+++++R+ WG P + I++L+ Sbjct: 350 DGIGEQKFAGFERMQPMPGFADKLSNQQMTDLISYLRQAWGGQ-PADLLIGQIEQLK-AD 407 Query: 438 APV 440 APV Sbjct: 408 APV 410 Lambda K H 0.317 0.134 0.421 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: 656 Number of extensions: 45 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: 478 Length of database: 415 Length adjustment: 32 Effective length of query: 446 Effective length of database: 383 Effective search space: 170818 Effective search space used: 170818 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