Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate GFF4233 HP15_4173 NADH dehydrogenase (quinone)
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Marino:GFF4233 Length = 512 Score = 329 bits (843), Expect = 2e-94 Identities = 193/512 (37%), Positives = 287/512 (56%), Gaps = 18/512 (3%) Query: 37 LASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEG--ICYLKVKPED 94 L+ GA +V + GL E+ G G P+V + + I + V+ D Sbjct: 14 LSMGADKVAKLIERHANARGL--EIELVRNGSRGLFWLEPLVEVETDSGRIGFGPVEAHD 71 Query: 95 VPEIVSHTIKEKKVVDRLLYEDPATGTRAL-RESDIPFYKNQQRNILSENLRLDSKSMDD 153 V +V D L+E + L DI + K QQR S D S+ D Sbjct: 72 VDALV----------DAGLFEGKSDHPLCLGMVEDISYLKLQQRLTFSRIGITDPLSIAD 121 Query: 154 YLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAP-DPIKYVI 212 Y + GG+ L + + ++P+ ++ E+K S LRGRGG FP KW+ + P KY++ Sbjct: 122 YRSHGGFVGLEQAV-SLSPQAIVDEVKASGLRGRGGAAFPTGIKWQTVHDEPWQQQKYIV 180 Query: 213 VNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIR 272 NADEGD G F DR +E +P+ ++EG+ I AVGA +GFIY+R EYP+A +N AI Sbjct: 181 CNADEGDSGTFADRLAMECDPYMLIEGMTIAGLAVGATQGFIYLRSEYPVAHRILNEAIS 240 Query: 273 QASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKG 332 +A G++G+D+ GSG F ++V + AGA++CGE ++L+ +LEG+ G R K A+KG Sbjct: 241 RAEAEGYLGRDVRGSGRAFNLEVRLAAGAYICGEETSLLESLEGKRGLVRAKPPLPAIKG 300 Query: 333 VWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGV 392 ++ P+V+NNV ++A V I+ KG + YG S GT L G I GL+E+ GV Sbjct: 301 LFGQPTVVNNVLSFAAVPFILAKGGQTYAHYGMGKSRGTLPIQLAGNIRRGGLIELAFGV 360 Query: 393 TLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGMIV 452 +LR+I+ GGG G+ KAVQ GGP +P+ D P+D++ + G+ +G GG++V Sbjct: 361 SLREILEDFGGGTFTGRPMKAVQVGGPLMAYMPQNQWDTPMDYEAFAQLGAGIGHGGVVV 420 Query: 453 MDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELLEELA 512 D+ M + AR+ ++F ESCGKCTPCR G + L V+ RI G+ E ++ LLEEL Sbjct: 421 FDDTVDMGEQARFAMEFCTVESCGKCTPCRIGSVRGLEVIDRIRAGESPEANLVLLEELC 480 Query: 513 ES-TGAALCALGKSAPNPVLSTIRYFRDEYEA 543 E+ +LCA+G P PV S ++YF D+ A Sbjct: 481 ETMVDGSLCAMGGMTPFPVQSVMKYFPDDLTA 512 Lambda K H 0.319 0.138 0.420 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: 823 Number of extensions: 33 Number of successful extensions: 4 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: 635 Length of database: 512 Length adjustment: 36 Effective length of query: 599 Effective length of database: 476 Effective search space: 285124 Effective search space used: 285124 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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