Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate 3607873 Dshi_1281 Respiratory-chain NADH dehydrogenase domain 51 kDa subunit (RefSeq)
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Dino:3607873 Length = 565 Score = 265 bits (678), Expect = 3e-75 Identities = 145/395 (36%), Positives = 225/395 (56%), Gaps = 17/395 (4%) Query: 147 DSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPD 206 D +++ Y A GGY L + E V ++K+S LRG GG GFP+ KW R P Sbjct: 186 DYETLAAYRAEGGYGVLRDLRASGDWEVVQAQVKQSGLRGLGGAGFPSGTKWGFVRANPG 245 Query: 207 PIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVEN 266 P +Y+ VN DEG+PG F DR +E PH LEG++I A+AV A +IY+R EYP +E Sbjct: 246 P-RYLAVNGDEGEPGTFKDRHYLERVPHLFLEGMLIAAWAVEAERCYIYMRDEYPAVLEI 304 Query: 267 INLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYI 326 + I E G +++ GAGA++CGE SA++ ++EG+ G PR + Sbjct: 305 LRREIAALEEAGIAEPG--------HIELRRGAGAYICGEESAMIESIEGKRGMPRHRPP 356 Query: 327 HTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLV 386 + A G++ P++++NVET + +I +G + ++ G + +S+ G++ G+ Sbjct: 357 YVAQVGLFGRPTLVHNVETLHWIARICREGPEVLSATTHNDRVGLRSYSVSGRVARPGVY 416 Query: 387 EVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMG 446 +P G T+ DII GG+ G FKA Q GGPS G +P + D+P+DFD L G+ +G Sbjct: 417 LLPAGSTILDIID-AAGGMAEGHVFKAFQPGGPSSGLLPASAADVPLDFDTLQPLGTFIG 475 Query: 447 SGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIE 506 S ++V+ + D A + F +DESCG+CTPCR G + + ++ + + D Sbjct: 476 SAAVVVLSDQDRARDAALNMLRFFEDESCGQCTPCRVGCEKAVKLM------QAERWDAG 529 Query: 507 LLEELAES-TGAALCALGKSAPNPVLSTIRYFRDE 540 LL EL + A++C LG++APNP+LSTI++F +E Sbjct: 530 LLSELCTAMADASICGLGQAAPNPILSTIKHFPEE 564 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: 871 Number of extensions: 53 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: 635 Length of database: 565 Length adjustment: 37 Effective length of query: 598 Effective length of database: 528 Effective search space: 315744 Effective search space used: 315744 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