Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate HSERO_RS08845 HSERO_RS08845 NADH dehydrogenase
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__HerbieS:HSERO_RS08845 Length = 431 Score = 333 bits (853), Expect = 1e-95 Identities = 173/415 (41%), Positives = 253/415 (60%), Gaps = 4/415 (0%) Query: 139 ILSENLRLDSKSMDDYLAIGGYSALSKVLFQ-MTPEDVMGEIKKSNLRGRGGGGFPAWRK 197 ++ +L ++ ++DY+ GGY +L ++L + +TPE V+ ++K S LRGRGG GFP K Sbjct: 12 LILADLNGENWHLEDYVKRGGYESLKRILNEKITPEQVIADLKASGLRGRGGAGFPTGLK 71 Query: 198 WEESRNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVR 257 W KY++ N DEG+PG F DR +I NPH+++EG+IIG YA+G G+ Y+ Sbjct: 72 WSFMPRQFPGQKYLVCNTDEGEPGTFKDRDIIRYNPHALIEGMIIGGYAMGITVGYNYIH 131 Query: 258 QEYPLAVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGR 317 E A E A+ +A GF+G +ILG+GF F + H G GA++CGE +AL+ +LEG+ Sbjct: 132 GEIFSAYERFEEALEEARAAGFLGDNILGTGFSFQLHAHHGYGAYICGEETALLESLEGK 191 Query: 318 AGEPRPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLV 377 G+PR K A G++ P+ +NN ET+A V I G + G + GTKIFS+ Sbjct: 192 KGQPRFKPPFPASFGLYGKPTTINNTETFAAVPFIFKVGPQAYAEMGKPNNGGTKIFSIS 251 Query: 378 GKITNTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIP-EAMLDLPVDFD 436 G + G E+P+G ++ ++ GG+ GGKK KAV GG S I + M+D +D+D Sbjct: 252 GDVERPGNYEIPLGTPFSTLL-ELAGGMRGGKKIKAVIPGGSSAPVIRGDVMMDTTMDYD 310 Query: 437 ELTKAGSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRIT 496 + KAGSM+GSG +IVMDE CMV F +ESCG+CTPCREG M ++ RI Sbjct: 311 AIAKAGSMLGSGAVIVMDETRCMVKSLLRLSYFYYEESCGQCTPCREGTGWMYRMVERIE 370 Query: 497 VGKGKEGDIELLEELAES-TGAALCALGKSAPNPVLSTIRYFRDEYEAHIREKKC 550 G GK D+++L +A++ G +CALG +A PV + ++ FR+E+E HI K C Sbjct: 371 NGHGKMEDLDVLNSVADNIQGRTICALGDAAAMPVRAFVKNFREEFEYHIEHKHC 425 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: 749 Number of extensions: 33 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: 431 Length adjustment: 35 Effective length of query: 600 Effective length of database: 396 Effective search space: 237600 Effective search space used: 237600 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