Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate AO356_24165 AO356_24165 formate dehydrogenase
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24165 Length = 519 Score = 332 bits (851), Expect = 2e-95 Identities = 195/511 (38%), Positives = 289/511 (56%), Gaps = 21/511 (4%) Query: 38 ASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEGIC--YLKVKPEDV 95 A GA +V A E E L V T G P+V + G+ + V P DV Sbjct: 14 AVGADKVADALVREAERRQLPLTVLR--TSSRGLYWLEPLVELDSAGVRLGFGPVTPADV 71 Query: 96 PEIVSHTIKEKKVVDRLLYEDPATGTRALRE-SDIPFYKNQQRNILSENLRLDSKSMDDY 154 P ++ L DP + AL +IP+ K+QQR + + S+DDY Sbjct: 72 PGLLD-----------ALAGDPGSHPLALGPVEEIPYLKSQQRLLFARAGITQPLSLDDY 120 Query: 155 LAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIKYVIVN 214 A GG+ L++ + QM DV+ + S LRGRGG FPA KW R+A P KYV+ N Sbjct: 121 RARGGFLGLARSI-QMDGADVVASVLDSGLRGRGGAAFPAGIKWRTVRDAQGPQKYVVCN 179 Query: 215 ADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQA 274 ADEGD G F DR L+EG+P ++EG+II AVGA G+IYVR EYP AV +N A+ A Sbjct: 180 ADEGDSGTFADRMLMEGDPFLLIEGMIIAGIAVGATMGYIYVRSEYPDAVSTLNDALHIA 239 Query: 275 SERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVW 334 E G++G ++ GSG F ++V +GAGA++CGE +AL+ +LEG+ G R K A++G++ Sbjct: 240 REAGYLGANVDGSGRVFELEVRVGAGAYICGEETALLESLEGKRGTVRAKPPLPALQGLF 299 Query: 335 DHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTL 394 P++++NV T +V I+ KGA ++ +G S GT F L G + + GLVE G++L Sbjct: 300 GLPTLVHNVLTLTSVPIILEKGAQFYRDFGMGRSLGTMPFQLAGNVRHGGLVERAFGLSL 359 Query: 395 RDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGMIVMD 454 R+++ GGG G+ KA Q GGP G +P + D P+D++ G+M+G GG++V D Sbjct: 360 RELVEGYGGGTASGRPLKAAQVGGPLGAWVPPSQFDTPLDYEAFAAMGAMLGHGGVVVAD 419 Query: 455 EDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRI---TVGKGKEGDIELLEEL 511 + M +AR+ + F +ESCGKCTPCR G + + V+ R+ T ++ LL++L Sbjct: 420 DSLDMAQMARFALQFCAEESCGKCTPCRIGSTRGVEVVDRLIASTEAGARQEQALLLQDL 479 Query: 512 AESTG-AALCALGKSAPNPVLSTIRYFRDEY 541 ++ +LCALG PV S +++F ++ Sbjct: 480 CDTLQYGSLCALGGMTSYPVASALKHFPADF 510 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: 43 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: 519 Length adjustment: 36 Effective length of query: 599 Effective length of database: 483 Effective search space: 289317 Effective search space used: 289317 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 Apr 09 2024. 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