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 N515DRAFT_0703 N515DRAFT_0703 Cytochrome c
Query= SwissProt::Q47945 (478 letters) >FitnessBrowser__Dyella79:N515DRAFT_0703 Length = 429 Score = 280 bits (717), Expect = 5e-80 Identities = 157/398 (39%), Positives = 218/398 (54%), Gaps = 17/398 (4%) Query: 40 DEALIKRGEYVARLSDCIACHTALHGQPYAGGLEIKSPIGTIYSTNITPDPEHGIGNYTL 99 D ALI +GEY+ + DC +CHT G +AGG + +P G I + N+TPD E G+G ++ Sbjct: 45 DPALIAKGEYLTLVGDCASCHTGQGGARFAGGRVVGTPFGDIPAPNLTPDRETGLGEWSF 104 Query: 100 EDFTKALRKGIRKDGATVYPAMPYPEFARLSDDDIRAMYAFFMHGVKPVALQNKAPDISW 159 E F +AL G+ + G +YPA PY + ++S DD A++A ++ + P+ K P + + Sbjct: 105 EAFRQALHSGVDRHGQFLYPAFPYTSYTKVSRDDALAIFA-YLQSLPPLKQAAKQPGLGF 163 Query: 160 PLSMRWPLGMWRAMFVPSMTPGVDKSISDPEVARGEYLVNGPGHCGECHTPRGFGMQVKA 219 P ++R L WRA++ D S PE RG YLV G GHC ECH R + Sbjct: 164 PYNVRNTLKAWRALYFREGEYVAD-STKSPEWNRGAYLVQGLGHCNECHVER------DS 216 Query: 220 YGTAGGNAYLAGG-APIDNWIAPSLRSNSDTGLGRWSEDDIVTFLKSGRIDHSAVFGGMA 278 +G + L+GG P+ NW AP L + ++ GL WSE DI LK+G+ A FG MA Sbjct: 217 FGGMRSDQSLSGGQIPVQNWYAPDLSTQANGGLAGWSERDIADLLKTGQSAKGAAFGPMA 276 Query: 279 DVVAYSTQHWSDDDLRATAKYLKSMPAVPEGKNLGQDDGQTTALLNKGGQGNAGAEVYLH 338 +VVA STQH +D DL A A YL+S+PA P +LL+ + GA+VY Sbjct: 277 EVVARSTQHLNDADLHAIATYLQSLPARPR-------VSYEPSLLDTKPMLDQGAKVYAE 329 Query: 339 NCAICHMNDGTGVNRMFPPLAGNPVVITDDPTSLANVVAFGGILPPTNSAPSAVAMPGFK 398 CA CH DG GV ++PPL+GN V + VV GG P T P +MP F Sbjct: 330 RCADCHGRDGQGVAGVYPPLSGNSSVNEPTGINAIRVVLLGGFAPSTQGNPRPYSMPPFA 389 Query: 399 NHLSDQEMADVVNFMRKGWGNNAPGTVSASDIQKLRTT 436 L+D ++A VV ++R+ WGN AP V D+ K R T Sbjct: 390 QQLNDADVAAVVTYIRQSWGNQAP-LVQERDVIKYRHT 426 Score = 53.9 bits (128), Expect = 1e-11 Identities = 66/246 (26%), Positives = 97/246 (39%), Gaps = 43/246 (17%) Query: 167 LGMWRAMFVPSMTPGVDKSIS--------DPE-VARGEYLVNGPGHCGECHTPRGFGMQV 217 LG+ +F+ P V +S S DP +A+GEYL G C CHT +G Sbjct: 16 LGLAGWLFLRGGQPSVPRSASRVDAAALKDPALIAKGEYLTL-VGDCASCHTGQG----- 69 Query: 218 KAYGTAGGNAYLAGGAPIDNWIAPSLRSNSDTGLGRWSEDDIVTFLKSGRIDHSAVFGGM 277 AGG G P + AP+L + +TGLG WS + L SG H Sbjct: 70 -GARFAGGRVV---GTPFGDIPAPNLTPDRETGLGEWSFEAFRQALHSGVDRHGQFLYPA 125 Query: 278 ADVVAYSTQHWSDDDLRATAKYLKSMPAVPEG-------------------KNLGQDDGQ 318 +Y+ S DD A YL+S+P + + + L +G+ Sbjct: 126 FPYTSYTKV--SRDDALAIFAYLQSLPPLKQAAKQPGLGFPYNVRNTLKAWRALYFREGE 183 Query: 319 TTALLNKGGQGNAGAEVY--LHNCAICHM-NDGTGVNRMFPPLAGNPVVITDDPTSLANV 375 A K + N GA + L +C CH+ D G R L+G + + + + Sbjct: 184 YVADSTKSPEWNRGAYLVQGLGHCNECHVERDSFGGMRSDQSLSGGQIPVQNWYAPDLST 243 Query: 376 VAFGGI 381 A GG+ Sbjct: 244 QANGGL 249 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: 697 Number of extensions: 39 Number of successful extensions: 7 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: 478 Length of database: 429 Length adjustment: 33 Effective length of query: 445 Effective length of database: 396 Effective search space: 176220 Effective search space used: 176220 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