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 Echvi_1808 Echvi_1808 Cytochrome c.
Query= SwissProt::Q47945 (478 letters) >FitnessBrowser__Cola:Echvi_1808 Length = 330 Score = 85.9 bits (211), Expect = 2e-21 Identities = 71/235 (30%), Positives = 109/235 (46%), Gaps = 30/235 (12%) Query: 44 IKRGEYVAR-LSDCIACHT-----ALHGQPYAGGLEIKSPI--------GTIYSTNITPD 89 I RGEY+A + C+ CH+ G P+ G + G S NITP+ Sbjct: 48 IARGEYLANHVMLCMDCHSDRNYSLFSGPPHPGTKGLGGDRFDRSMGLPGVFVSPNITPE 107 Query: 90 PEHGIGNYTLEDFTKALRKGIRKDGATVYPAMPYPEFARLSDDDIRAMYAFFMHGVKPVA 149 GIGN+T + + + G++K+G ++P MPY + +L +DI+A+ A ++ + P Sbjct: 108 ---GIGNWTDGELYRLITTGVKKNGEPIFPVMPYQSYGKLDPEDIKAVIA-YIRTLAPQK 163 Query: 150 LQNKAPDISWPLSMRWPLGMWRAMFVPSMTPGVDKSISDPEVARGEYLVNGPGHCGECHT 209 +I +P++ + R M PS + + +A GEYLV CGECHT Sbjct: 164 SNIPPREIDFPVNF-----IIRTM--PSKATPTTRPNKEDVIAYGEYLVTAAA-CGECHT 215 Query: 210 PRGFGMQVKAYGTAGGNAYLAGGAPIDNWIAPSLRSNSDTGLGRWSEDDIVTFLK 264 G V Y GG A+ +P N + S + TGLG S++D V K Sbjct: 216 KFEKGKFVGPY-LGGGRAF---PSPNGNIVRSSNLTFHSTGLGNKSKEDFVRQFK 266 Score = 39.3 bits (90), Expect = 2e-07 Identities = 28/120 (23%), Positives = 50/120 (41%), Gaps = 13/120 (10%) Query: 41 EALIKRGEYVARLSDCIACHTALH-----GQPYAGGLEIKSPIGTIYSTNITPDPEHGIG 95 E +I GEY+ + C CHT G GG SP G I ++ G+G Sbjct: 195 EDVIAYGEYLVTAAACGECHTKFEKGKFVGPYLGGGRAFPSPNGNIVRSSNLTFHSTGLG 254 Query: 96 NYTLEDFTKALRK-------GIRKDGATVYPAMPYPEFARLSDDDIRAMYAFFMHGVKPV 148 N + EDF + ++ + MP+ +A + D+ ++Y ++ ++P+ Sbjct: 255 NKSKEDFVRQFKQYSPELYTPTKVGEGEFQTIMPWTMYAGMDTTDLASIYE-YLRSLEPI 313 Score = 38.1 bits (87), Expect = 4e-07 Identities = 30/133 (22%), Positives = 64/133 (48%), Gaps = 17/133 (12%) Query: 187 SDPEVARGEYLVNGPGHCGECHTPRGFGM-----QVKAYGTAGGNAYLAGGAPIDNWIAP 241 S ++ARGEYL N C +CH+ R + + G G + G P +++P Sbjct: 44 STEQIARGEYLANHVMLCMDCHSDRNYSLFSGPPHPGTKGLGGDRFDRSMGLP-GVFVSP 102 Query: 242 SLRSNSDTGLGRWSEDDIVTFLKSG-RIDHSAVFGGMADVVAYSTQHWSD-DDLRATAKY 299 ++ + G+G W++ ++ + +G + + +F V+ Y + D +D++A Y Sbjct: 103 NI---TPEGIGNWTDGELYRLITTGVKKNGEPIF----PVMPYQSYGKLDPEDIKAVIAY 155 Query: 300 LKSMPAVPEGKNL 312 ++++ P+ N+ Sbjct: 156 IRTL--APQKSNI 166 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: 504 Number of extensions: 42 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 478 Length of database: 330 Length adjustment: 31 Effective length of query: 447 Effective length of database: 299 Effective search space: 133653 Effective search space used: 133653 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: 50 (23.9 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