Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate BWI76_RS20170 BWI76_RS20170 NADH-quinone oxidoreductase subunit F
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Koxy:BWI76_RS20170 Length = 445 Score = 336 bits (862), Expect = 1e-96 Identities = 167/405 (41%), Positives = 251/405 (61%), Gaps = 11/405 (2%) Query: 151 MDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKW-----EESRNAP 205 +D+Y + GY+ K L M P++++ +K + L+GRGG GF KW +ES N Sbjct: 26 LDEYQSKNGYAGARKALSGMAPDEIVTAVKDAGLKGRGGAGFSTGLKWSLMPKDESMN-- 83 Query: 206 DPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVE 265 I+Y++ NADE +PG + DR L+E PH ++EG++I A+A+ A+ G+I++R EY A + Sbjct: 84 --IRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAQ 141 Query: 266 NINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKY 325 ++ AI +A+E G +GK+ILG+GFDF + VH GAG ++CGE +AL+ +LEGR PR K Sbjct: 142 HLRRAIAEATEAGLLGKNILGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSKP 201 Query: 326 IHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGL 385 A GVW P+ +NNVET NV I+ G +W+ + T+ GTK+ G++ N G+ Sbjct: 202 PFPASSGVWGKPTCVNNVETLCNVPAILANGVEWYQNISTSKDAGTKLMGFSGRVKNPGV 261 Query: 386 VEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMM 445 E+P G T R+I+ GG+ G KFKA Q GG + EA LDLP++F+ + KAGS + Sbjct: 262 WELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFLTEAHLDLPMEFESIGKAGSRL 321 Query: 446 GSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDI 505 G+ + +D + MV + R +F ESCG CTPCR+G+ + +L + G+G+ GDI Sbjct: 322 GTALAMAVDHEIGMVPLVRNLEEFFARESCGWCTPCRDGLPWSVKILRALERGEGQPGDI 381 Query: 506 ELLEELAE--STGAALCALGKSAPNPVLSTIRYFRDEYEAHIREK 548 E LE+L G CA A P+ S I+YFR+E+EA I+++ Sbjct: 382 ETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFEAGIKQQ 426 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: 722 Number of extensions: 37 Number of successful extensions: 3 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: 445 Length adjustment: 35 Effective length of query: 600 Effective length of database: 410 Effective search space: 246000 Effective search space used: 246000 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