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 PP_4232 PP_4232 Cytochrome c family protein
Query= SwissProt::Q47945 (478 letters) >FitnessBrowser__Putida:PP_4232 Length = 403 Score = 257 bits (656), Expect = 6e-73 Identities = 159/416 (38%), Positives = 223/416 (53%), Gaps = 25/416 (6%) Query: 21 AAAIGLMAVSFGAAHAQDADEALIKRGEYVARLSDCIACHTALHGQPYAGGLEIKSPIGT 80 A A+GL SF A AD+A +KRGEY+AR +DC+ACHTA G PYAGGL I SP GT Sbjct: 9 ALALGLAVSSFALA----ADDAQVKRGEYLARAADCMACHTAEGGAPYAGGLPIHSPFGT 64 Query: 81 IYSTNITPDPEHGIGNYTLEDFTKALRKGIRKDGATVYPAMPYPEFARLSDDDIRAMYAF 140 IY +NITPD ++GIGNY+ ++F A+ +G RKDGA +YPAMPY + + +D A+ A+ Sbjct: 65 IYGSNITPDKQYGIGNYSADEFFAAVTEGKRKDGANLYPAMPYTSYHLIKREDSDAILAY 124 Query: 141 FMHGVKPVALQNKAPDISWPLSMRWPLGMWRAMFVPS--MTPGVDKSISDPEVARGEYLV 198 M + P+ + +P ++R L W ++ S + P KS P RG+Y+V Sbjct: 125 LM-TIPPINRPAPQTALRFPFNVRMGLSGWNMLYGKSVQLQPTEGKS---PAWQRGQYMV 180 Query: 199 NGPGHCGECHTPRGFGMQVKAYGTAGGNAYLAGGAPIDNWIAPSLRSNSDTGLGRWSEDD 258 GHCGECHTPR G + L+GG + ++APSL + D W++ D Sbjct: 181 EVLGHCGECHTPR------NPIGALQQDQRLSGGL-LGGYLAPSLLA-QDLAERGWTQPD 232 Query: 259 IVTFLKSGRIDHSAVFGGMADVVAYSTQHWSDDDLRATAKYLKSMPAVPEGKNLGQDDGQ 318 + TFLK G ++F M VV +STQH D DL A A YL P K + + Sbjct: 233 LTTFLKHGISAQGSMFNEMFPVVHHSTQHLEDADLAAMATYLLG-DQPPPAKAI-----E 286 Query: 319 TTALLNKGGQGNAGAEVYLHNCAICHMNDGTGVNRMFPPLAGNPVVITDDPTSLANVVAF 378 + AL G + YL+ CA CH DG G + + GN V+ D +L VV Sbjct: 287 SVALEQMSDSAKRGHQQYLNVCAGCHGVDGEGKPHIAVAMRGNTVLRQADSRNLVKVVLE 346 Query: 379 GGILPPTNSAPSAVAMPGFKNHLSDQEMADVVNFMRKGWGNNAPGTVSASDIQKLR 434 G MPGF + L DQ++ D+VN++R+ WG PG ++ + +L+ Sbjct: 347 GIREQQFTGFERMQPMPGFADKLDDQQVIDMVNYLRQAWG-GLPGDLNVQQLAELK 401 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: 592 Number of extensions: 26 Number of successful extensions: 5 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: 403 Length adjustment: 32 Effective length of query: 446 Effective length of database: 371 Effective search space: 165466 Effective search space used: 165466 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