Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate 349653 BT0125 NADH:ubiquinone oxidoreductase subunit (NCBI ptt file)
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Btheta:349653 Length = 635 Score = 609 bits (1571), Expect = e-178 Identities = 295/582 (50%), Positives = 392/582 (67%), Gaps = 1/582 (0%) Query: 28 ISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEGICY 87 I +C G GC AS + + + +E +G+T +V+ GC GFCE+GPIV I P+ Y Sbjct: 46 ILICGGTGCKASSSQGITENLQKAIERNGITDKVDVITVGCFGFCEKGPIVKIIPDNTFY 105 Query: 88 LKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSENLRLD 147 +V PED EI+S I + ++RLLY DP T + FY+ Q R L +D Sbjct: 106 TQVTPEDAEEIISEHIIGGRRIERLLYIDPKTEQTVSDSKHMDFYRKQLRIALRNCGFID 165 Query: 148 SKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDP 207 S+++++Y+A GY AL+ L P DV+ IK+S LRGRGGGGFP KWE + Sbjct: 166 SENIEEYIAREGYFALADCLLNKQPADVIDIIKRSGLRGRGGGGFPTGLKWEFASKQVSN 225 Query: 208 IKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENI 267 +KYV+ NADEGDPGAFMDR+++EG+PHSI+E + I Y++G+ +G +Y+R EYPLA+ + Sbjct: 226 VKYVVCNADEGDPGAFMDRSIMEGDPHSIVEAMCICGYSIGSSKGLVYIRAEYPLAINRL 285 Query: 268 NLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIH 327 AI QA E G +G ILG+ F F +++ GAGAFVCGE +AL+ ++EG+ GEP K Sbjct: 286 KKAIEQAREYGLLGDHILGTDFSFDIEIRYGAGAFVCGEETALIHSMEGKRGEPTLKPPF 345 Query: 328 TAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVE 387 A G P+ +NNVET AN+ I+TKGA+WF S GT S GTK+F+L GKI N GL+E Sbjct: 346 PAESGYLGKPTNVNNVETLANIPIILTKGAEWFASIGTERSKGTKVFALAGKINNVGLIE 405 Query: 388 VPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGS 447 VPMG TLR++I ++GGGI GGKKFKAVQTGGPSGGC+ E LD P+DFD L AGSMMGS Sbjct: 406 VPMGTTLREVIYEIGGGIKGGKKFKAVQTGGPSGGCLTEKHLDTPIDFDNLLAAGSMMGS 465 Query: 448 GGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIEL 507 GGMIVMDED CMV +AR+++DF +ESCGKCTPCR G +++L +L +IT G+G E D++ Sbjct: 466 GGMIVMDEDDCMVSVARFYLDFTVEESCGKCTPCRIGNKRLLELLNKITEGRGTEKDLDT 525 Query: 508 LEELAE-STGAALCALGKSAPNPVLSTIRYFRDEYEAHIREKKCPALSCKEMIAFHIDPE 566 L L ALC LG+++PNPVLST+ FRDEY H+R+K C A CK ++ + I+PE Sbjct: 526 LATLGRVIKDTALCGLGQTSPNPVLSTLDNFRDEYLEHVRDKTCRAKQCKSLLTYTINPE 585 Query: 567 KCKACGSCFRQCPAEAIQGGKKLIHIIDQEKCTKCGTCLDVC 608 C C C + CPA+AI G + H+I EKC KCG C+ C Sbjct: 586 LCIGCHLCAKNCPADAISGLVRKPHVIHPEKCIKCGMCMARC 627 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: 1240 Number of extensions: 65 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 635 Length of database: 635 Length adjustment: 38 Effective length of query: 597 Effective length of database: 597 Effective search space: 356409 Effective search space used: 356409 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: 54 (25.4 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