Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate GFF2535 PGA1_c25750 NADH-quinone oxidoreductase subunits E/F (fused)
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Phaeo:GFF2535 Length = 576 Score = 273 bits (698), Expect = 2e-77 Identities = 177/531 (33%), Positives = 271/531 (51%), Gaps = 62/531 (11%) Query: 13 ARKDIVSRIDPTKPCIS--VCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPG 70 A D+V + P ++ VC C +GA + A + L+ ++V C G Sbjct: 104 AHFDVVREGETPPPALTIRVCDSLSCELAGAEALQKALEDGLD----ASQVRVLRAPCMG 159 Query: 71 FCERGPIVMIYPEGICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIP 130 C+ P++ I I + PE V ++ A T A IP Sbjct: 160 RCDTAPVLEIGHNHIDH--ATPEKVQAAIA-----------------ADDTHA----HIP 196 Query: 131 FYKNQQRNILSENLRLDSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGG 190 Y+ + Y A GGY+ L + E V ++K++ LRG GG Sbjct: 197 AYE----------------TFAAYEADGGYATLKDLRANGDWEAVQAKVKEAGLRGLGGA 240 Query: 191 GFPAWRKWEESRNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAH 250 GFP+ KW R P +Y+ VN DEG+PG F DR +E PH LEG++I A+AV A Sbjct: 241 GFPSGTKWGFVRANEGP-RYLAVNGDEGEPGTFKDRYYLERTPHVFLEGMLIAAWAVEAE 299 Query: 251 EGFIYVRQEYPLAVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSAL 310 + FIY+R EYP +E + I E G I+ +G+ + + GAGA++CGE SA+ Sbjct: 300 KAFIYMRDEYPAVLEILRREITALEEAG-----IVEAGY---IDLRRGAGAYICGEESAM 351 Query: 311 MTALEGRAGEPRPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTG 370 + ++EG+ GEPR + A G++ P++++NVET V ++ +G + S G G Sbjct: 352 IESIEGKRGEPRHRPPFVAQVGIFGRPTLVHNVETLYWVCKVNREGPECLNSVEKNGRKG 411 Query: 371 TKIFSLVGKITNTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLD 430 + +S+ G++ N G+ +P G T+ DII GG + G FKA Q GGPS G +P +M D Sbjct: 412 LRSYSVSGRVKNPGVHLLPAGSTITDIIEACGGMLDG-HAFKAYQPGGPSSGLLPASMHD 470 Query: 431 LPVDFDELTKAGSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLA 490 +P+DFD L G+ +GS ++V+ + D A + F +DESCG+CTPCR G + + Sbjct: 471 IPLDFDTLQPHGTFIGSAAVVVLSDKDSARDAALNMLRFFEDESCGQCTPCRVGCEKAVK 530 Query: 491 VLTRITVGKGKEGDIELLEEL-AESTGAALCALGKSAPNPVLSTIRYFRDE 540 ++ K+ D LLEEL A ++C LG++APNP+ TI++F +E Sbjct: 531 LMGE------KKWDQGLLEELSAAMVDTSICGLGQAAPNPIRLTIKHFPEE 575 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: 915 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: 576 Length adjustment: 37 Effective length of query: 598 Effective length of database: 539 Effective search space: 322322 Effective search space used: 322322 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