Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate Pf6N2E2_1204 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1204 Length = 745 Score = 358 bits (920), Expect = e-103 Identities = 268/740 (36%), Positives = 379/740 (51%), Gaps = 38/740 (5%) Query: 9 DAPVNLSRRRFLASTAVGALVIGF--GLPLGAGRVQAATSAERGTQVPAFLEIRPDGTVR 66 D+P L RR FL +G L +G L L AA + Q AF++I P G V Sbjct: 24 DSPATLPRRSFLKIVGIGGLALGAFPHLALAQETNGAAVPLKPSQQPSAFVQIAPSGEVT 83 Query: 67 LLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRM 126 + +E GQG T + I+ EELDAD + AY+ G+ +TGGS S++ Sbjct: 84 VTINRLEFGQGVQTGLPMILAEELDADWSLVRSRNGNSDAAYMDPNFGIHLTGGSNSIKN 143 Query: 127 SYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMP 186 SY R LGA ARAMLL A A +W V V L+TQ G V+ A GR YGELA +A+ MP Sbjct: 144 SYTQYRELGARARAMLLSAAAARWNVDVASLSTQAGMVLGPA-GRKASYGELAEAAMAMP 202 Query: 187 VPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMT 246 VP+ ITL+DP FR IG+ R+DA KS+G+ + ID+ + L A V P G Sbjct: 203 VPE--QITLKDPKDFRIIGQATTRIDAKAKSSGQQDFGIDMHLPGQLTAVVARPPVFGAR 260 Query: 247 VGSLRNQSQVEGMKGVHSVHVLP---GA--VAVVAERWWHAKRAVEAIQVDWQEAAADSA 301 + SL + S KGV +V +P GA VAVVA+ +W AK A +A++V+W SA Sbjct: 261 IASL-DDSAARATKGVKAVLRVPLDGGAEGVAVVADSYWQAKLARDALKVEWDA----SA 315 Query: 302 LRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEP 361 + + ++ ++RE LA Q GP D + +A A Q++A + YL HA +EP Sbjct: 316 VEKVDSEKQLAQYRE-LANQPGPLHFDADMTPLA----SAPHQLDAEFVFPYLAHAPMEP 370 Query: 362 PSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSA 421 + + DG ++W+ Q P A AK GL P QI ++ GG FGR + + Sbjct: 371 LNCTVQLAGDGA-QLWVGTQFPGGDGAAAAKVLGLKPEQIQVNVQTAGGGFGRRGV-PTN 428 Query: 422 NPYPQAIALAKA-----VSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIE- 475 + A +AKA V+ PI+ +WSRE++ RP+ + + R DD G +A + Sbjct: 429 DFVVLACEVAKAARTAGVNAPIRTLWSREDDIKGGYYRPMHLHRARIGFDDSGKVLAWDH 488 Query: 476 -AVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGN 534 V + G+ + IDPTA EGL Y +P + P+L +WRSVG+ Sbjct: 489 ALVGQSIITGTVFGGRVKNGIDPTATEGLR-NPYPLPMRLTVHHPKLNVPVL-WWRSVGS 546 Query: 535 SLNDFFYESFLDELADKGGHDPYELRLHLLRD-NPRLTTLLQAAGELSGGWKRGPFTAED 593 + F E+ +DE+A DP R+ L D +PR LQ A + S KR + Sbjct: 547 THTAFVMETLIDEIARTTKQDPVAYRMKLFGDQSPRHREALQLAVDKSEYGKR-----QL 601 Query: 594 GTRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVA 653 A GVA+ F S A + E S+++G+ +H++ + VNP VEAQV GA Sbjct: 602 PAGHAWGVAVHESFSSVVAYVVEASVQDGRPVLHNVTAGVHCNLAVNPRSVEAQVQGAAL 661 Query: 654 LGLSQTLLEEAVYV-DGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAV 712 +GLS L A+ + DG + N+ + + M V +V S E G+GEP LPA+ Sbjct: 662 MGLSMCLPGGAITLKDGVVQQSNFADFSVPRITDMPTFAVHIVPSAEPPTGMGEPGLPAL 721 Query: 713 APAVANAVAQLTGQRVRSLP 732 APA ANAVA LTG+ +R LP Sbjct: 722 APAFANAVASLTGKPLRELP 741 Lambda K H 0.317 0.134 0.394 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: 1390 Number of extensions: 84 Number of successful extensions: 13 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: 739 Length of database: 745 Length adjustment: 40 Effective length of query: 699 Effective length of database: 705 Effective search space: 492795 Effective search space used: 492795 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 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