Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate N515DRAFT_2810 N515DRAFT_2810 NADH dehydrogenase subunit F (EC 1.6.5.3)
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Dyella79:N515DRAFT_2810 Length = 436 Score = 297 bits (761), Expect = 6e-85 Identities = 164/416 (39%), Positives = 241/416 (57%), Gaps = 7/416 (1%) Query: 135 QQRNILSENLRLDSK-SMDDYLAIGGYSALSKVLFQMT-PEDVMGEIKKSNLRGRGGGGF 192 Q+ ++ L D +MD Y +GGY A K+L + P ++ EIKKSNLRGRGG GF Sbjct: 8 QEHQVVYTTLHFDKPWAMDSYTQVGGYEAWKKILAEKPDPNALIEEIKKSNLRGRGGAGF 67 Query: 193 PAWRKWEESRNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEG 252 P KW + KY++ N+DE +PG DR ++ NPH+++EG+ I Y G+ Sbjct: 68 PTGLKWSFMPKG-NMQKYILCNSDESEPGTCKDRDILRFNPHAVIEGMAIACYCTGSTAA 126 Query: 253 FIYVRQEYPLA-VENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALM 311 + Y+R E+ E+ A+++A G +GK+I G+G D + +GAGA++CGE +ALM Sbjct: 127 YNYLRGEFHHEPYEHFEEALKEAYAAGLLGKNIQGTGIDVDIYGALGAGAYICGEETALM 186 Query: 312 TALEGRAGEPRPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGT 371 +LEG+ G+PR K A G++ PS +NN ET+A+V I+ KGADWF + + G Sbjct: 187 ESLEGKKGQPRFKPPFPANFGLYGKPSTINNTETYASVPAILRKGADWFLAQSKTKNGGP 246 Query: 372 KIFSLVGKITNTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIP-EAMLD 430 KIFS+ G + G EVP+G T +++ ++ GG+ G+K K GG S + E + Sbjct: 247 KIFSVSGCVQKGGNFEVPLGTTFDELL-EMAGGLRPGRKLKGAIPGGVSMPVLKAEQLKG 305 Query: 431 LPVDFDELTKAGSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLA 490 LP D+D L + +GSG ++V+D+ C V R F ESCG+CTPCREG M Sbjct: 306 LPFDYDTLRDLKTGLGSGAIVVLDDTVCTVRFTRRISQFFHKESCGQCTPCREGTGWMHR 365 Query: 491 VLTRITVGKGKEGDIELLEELA-ESTGAALCALGKSAPNPVLSTIRYFRDEYEAHI 545 VL RI GKG D+ L+ +A + G +CA G++A PV +R F DE+E +I Sbjct: 366 VLDRIVEGKGTMEDLHRLKAIAGQIEGHTICAFGEAAAWPVQGFLRQFWDEFEYYI 421 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: 797 Number of extensions: 51 Number of successful extensions: 6 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: 436 Length adjustment: 35 Effective length of query: 600 Effective length of database: 401 Effective search space: 240600 Effective search space used: 240600 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: 52 (24.6 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