Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate Pf1N1B4_4869 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4869 Length = 746 Score = 347 bits (889), Expect = 2e-99 Identities = 261/747 (34%), Positives = 379/747 (50%), Gaps = 39/747 (5%) Query: 3 LINELLDAPVNLSRRRFLASTAVGALVIGFGLPLGAGRVQAATSA---ERGTQVPAFLEI 59 L + +D P L RR FL VG L +G L + A + Q AF++I Sbjct: 18 LERDQIDGPTTLPRRSFLKILGVGGLALGAFPHLALAQQPGDNRAMPLKPSQQPSAFVQI 77 Query: 60 RPDGTVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITG 119 P+G V + +E GQG T + I+ EELDAD + AY G+ +TG Sbjct: 78 APNGEVTVTINRLEFGQGVQTGLPMILAEELDADWSLVRSRNGTSDIAYQDPLFGMHLTG 137 Query: 120 GSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELA 179 GS S++ SY R LGA ARAMLL A A +W V + L+TQ G V+ A GR YGELA Sbjct: 138 GSNSIKNSYTQYRELGARARAMLLAAAAARWNVDMASLSTQSGMVLGPA-GRKASYGELA 196 Query: 180 SSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQH 239 +A+ +PVP+ +ITL+DP FR IG R+DA KS+G+ + ID+K+ L A V Sbjct: 197 EAAMALPVPE--TITLKDPKDFRIIGHATTRIDAKAKSSGQQDFGIDMKLPGQLTAVVAR 254 Query: 240 APRLGMTVGSLRNQSQVEGMKGVHSVHVLP---GA--VAVVAERWWHAKRAVEAIQVDWQ 294 P G + SL + S +KGV +V +P GA VAVVA+ +W AK+ +A+++ W Sbjct: 255 PPVFGAKIASL-DDSAARAIKGVKAVLRVPLDGGAEGVAVVADGYWQAKQGRDALKLQWD 313 Query: 295 EAAADSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYL 354 + + +D +RE LA + GP E D+A L+ A +++A + YL Sbjct: 314 TTTVEK----VDSDKQLADYRE-LAGRPGPRL---FEADMA-PLETAPHRLDAEFVFPYL 364 Query: 355 NHAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGR 414 HA +EP + + + + E+W+ Q A A+ L P QI ++ GG FGR Sbjct: 365 AHAPMEPLNCTVKLSEE-RCELWVGTQFAGADSAAAARVLNLKPEQIQINVQTAGGGFGR 423 Query: 415 HFLYDSANPYPQAIALAKA-----VSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKG 469 + S + A +AKA ++ P++ +WSRE++ RP+ + + R DD G Sbjct: 424 RGIATS-DIVVLACEVAKAARMAGLNVPVRTLWSREDDIKGGYYRPMHLHRARLGFDDTG 482 Query: 470 LPVAIEAVSATEGPTEA--LAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLG 527 +A + V + G+ + IDPTA EG+ Y +P + P+L Sbjct: 483 KVLAWDHVVVGQSIISGTMFGGRVKNGIDPTATEGMR-DPYPLPMRLTVHHPKLNVPVL- 540 Query: 528 YWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLRD-NPRLTTLLQAAGELSGGWKR 586 +WRSVG++ F E+ +DE+A DP R+ L D +PR LQ A + S KR Sbjct: 541 WWRSVGSTHTAFVMETVIDEIARTTKQDPVAYRMKLFADQSPRHRAALQLAVDKSEYGKR 600 Query: 587 GPFTAEDGTRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEA 646 E RA GVA+ F S A + E S++NG+ +H + + +VNP VEA Sbjct: 601 -----ELPAGRAWGVAVHESFSSVVAYVVEASVQNGRPVLHHVTAGVHCNLVVNPRSVEA 655 Query: 647 QVNGAVALGLSQTLLEEAVYV-DGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIG 705 QV GA +GLS L A+ + DG + N+ + + M + VV S E G+G Sbjct: 656 QVQGAALMGLSMCLPGGAITLKDGVVQQSNFADFSVPRITDMPEFSIHVVPSAEPPTGMG 715 Query: 706 EPPLPAVAPAVANAVAQLTGQRVRSLP 732 EP LP +APA ANAVA+LTG+ VR LP Sbjct: 716 EPGLPPLAPAFANAVARLTGKPVRELP 742 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: 1408 Number of extensions: 75 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: 746 Length adjustment: 40 Effective length of query: 699 Effective length of database: 706 Effective search space: 493494 Effective search space used: 493494 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