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 H281DRAFT_05401 H281DRAFT_05401 Cytochrome c, mono- and diheme variants
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__Burk376:H281DRAFT_05401 Length = 431 Score = 387 bits (994), Expect = e-112 Identities = 216/434 (49%), Positives = 270/434 (62%), Gaps = 20/434 (4%) Query: 1 MINRLKVTFSAA---AFSLLAGT--ALAQTPDADSALVQKGAYVARLGDCVACHTALHGQ 55 M N LK F AA A LA T A A AD ALVQ+GAY+A+ GDC ACHTA G+ Sbjct: 1 MKNTLK-GFGAALCVALPFLAQTSPASAAASAADQALVQRGAYLAKAGDCAACHTAPKGK 59 Query: 56 SYAGGLEIKSPIGTIYSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSF 115 +AGGL + +P+G IY+TNITPD GIG YT +F A+R G+ KDG LYPAMPYPS+ Sbjct: 60 PFAGGLPMNTPMGQIYTTNITPDAQTGIGSYTEQDFARAMREGVAKDGHNLYPAMPYPSY 119 Query: 116 SRMTKEDMQALYAYFMHGVKPVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPG 175 +++ EDM+ALYA+FM GV PV Q +++ DI WP++MRWPL +W M+F + PG Sbjct: 120 AKVNDEDMKALYAFFMSGVAPVQQANRESDIKWPMNMRWPLKLWNMVFLEKGV-YQNKPG 178 Query: 176 TDPEIARGDYLVTGPGHCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRND 235 D RG YL+ G GHCG+CHTPRG A QEKALD G FL+GG +DNW A +L + Sbjct: 179 KDVAWNRGAYLIQGLGHCGSCHTPRGIAFQEKALDETGSA-FLTGGL-LDNWYATNLTGE 236 Query: 236 PVVGLGRWSEDDIYTFLKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPV 295 VGLGRWS+ D+ FLK+G H++ FG M V+ STQ D D+ A+ YLKSLP V Sbjct: 237 HNVGLGRWSDQDLQAFLKTGANRHASAFGSMTSVINNSTQNLNDGDIAAMTTYLKSLPAV 296 Query: 296 -----PPSQGNYTYDPSTANMLASGNTASVPGADTYVKECAICHRNDGGGVARMFPPLAG 350 PP Y YDP T ++ A+ GA Y C CH DG G A M PLAG Sbjct: 297 GGNGAPP----YKYDPQTTK-VSLNRPANDAGARVYTAYCMHCHGVDGRGFAPMLAPLAG 351 Query: 351 NPVVVTENPTSLVNVIAHGGVLPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNK 410 NP V+ ++ +SL+NV +G P+ MP Y+ L+ QQIADV+ F+R W N Sbjct: 352 NPNVLEKDASSLINVTLNGTEDLVIGGIPAPYPMPKYAPVLNDQQIADVLTFVRAGWNNG 411 Query: 411 APGTVTAADVTKLR 424 AP VTAADVTKLR Sbjct: 412 AP-AVTAADVTKLR 424 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: 683 Number of extensions: 31 Number of successful extensions: 9 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: 431 Length adjustment: 33 Effective length of query: 435 Effective length of database: 398 Effective search space: 173130 Effective search space used: 173130 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