Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate SMa1525 SMa1525 NuoF2 NADH I chain F
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Smeli:SMa1525 Length = 421 Score = 387 bits (993), Expect = e-112 Identities = 188/406 (46%), Positives = 266/406 (65%), Gaps = 1/406 (0%) Query: 147 DSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPD 206 D + Y A GGY AL K L + TP++++ +K+SNLRGRGG GFP KW A Sbjct: 14 DGHLLSTYEAGGGYRALRKALGEYTPDEIVELVKESNLRGRGGAGFPTGMKWSFVPKAAG 73 Query: 207 PIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVEN 266 KY+ NADEG+PG F DR ++E +PH ++EGL + AYA+GA ++Y+R EY A+ Sbjct: 74 KPKYLCCNADEGEPGTFKDRIIMERDPHQLIEGLAVSAYAIGAETAYVYIRGEYVTAIRR 133 Query: 267 INLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYI 326 + AI +A E G++G ILGSGF+F V +H GAGA++CGE +A++ +LEG+ +PR K Sbjct: 134 MEQAIAEAHENGYLGIGILGSGFNFMVHIHRGAGAYICGEETAMLESLEGKRAQPRLKPP 193 Query: 327 HTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLV 386 AV G++ P+V+NNVET A V I+ +G+ WF G S G K++ L G++ GL Sbjct: 194 FPAVAGLYASPTVINNVETLACVPHIVMRGSAWFRGIGPDRSPGPKLYCLSGQVRKPGLY 253 Query: 387 EVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMG 446 E+PMG++LR+++ + GG G+K KAV GG S IPE L++ +DFD LT AGSM+G Sbjct: 254 ELPMGISLRELVEEHAGGPLPGRKVKAVIPGGVSAPVIPEGELEVGMDFDSLTAAGSMLG 313 Query: 447 SGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIE 506 S G++V+D+ TCMV +A I+F ESCGKCTPCREG+ + VL RI G+G+ GD+E Sbjct: 314 SAGVVVIDDSTCMVKLATRIIEFFHHESCGKCTPCREGLDWTVKVLRRIEAGEGETGDLE 373 Query: 507 LLEELAEST-GAALCALGKSAPNPVLSTIRYFRDEYEAHIREKKCP 551 LE L + G CALG A + + +++FR E+ AHI E++CP Sbjct: 374 QLEMLCKGIFGNTFCALGDGAAMGLRAALKHFRAEFVAHIEERRCP 419 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: 768 Number of extensions: 42 Number of successful extensions: 2 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: 421 Length adjustment: 35 Effective length of query: 600 Effective length of database: 386 Effective search space: 231600 Effective search space used: 231600 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