Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate Ac3H11_2239 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2239 Length = 759 Score = 361 bits (926), Expect = e-104 Identities = 268/747 (35%), Positives = 388/747 (51%), Gaps = 50/747 (6%) Query: 9 DAPVNLSRRRFLASTAVGALVIGFGLPLGAGRVQAATSAERGT----QVPAFLEIRPDGT 64 DA ++RR FL TA +G PL A A +A G Q AF+ I DGT Sbjct: 36 DAADGMARRTFLKVTAASGFALG-AFPLAATAQGAGAAAPAGLKPHEQPSAFVRIDADGT 94 Query: 65 VRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSV 124 V + ++ GQG T + I+ EELDAD + AY G+ +TGGS S+ Sbjct: 95 VTVTINRLDFGQGVQTGLPMILAEELDADWSKVRSVHGDANPAYADPAFGMHLTGGSNSI 154 Query: 125 RMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALD 184 + SY R LGA RAML+ A A QWGV L T G VV G+ LGYG LA +A+ Sbjct: 155 KNSYTQYRELGARTRAMLVGAAAAQWGVDASALRTSNGFVV-GPGGKKLGYGALAEAAMK 213 Query: 185 MPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLG 244 PVP+ +TL+DP QFR IGKP RLDA KS+G+ Y ID+++ ML A V P G Sbjct: 214 QPVPE--KVTLKDPKQFRIIGKPTGRLDAKAKSSGQQDYGIDVRLPGMLTAVVARPPVFG 271 Query: 245 MTVGSLRNQSQVEGMKGVHSVHVLP-----GAVAVVAERWWHAKRAVEAIQVDWQEAAAD 299 SL + S + +KGV +V +P VA++A+ +W AK+ +A++V+W +A Sbjct: 272 AKPKSL-DDSAAKAIKGVKAVLRVPTDRGGEGVAIIADGYWPAKQGRDALKVEWDTSA-- 328 Query: 300 SALRVMPADFSS--DKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHA 357 V D ++ ++RE LAA+ G + + D+A L GA ++ A + YL HA Sbjct: 329 ----VAKPDTTALLAQYRE-LAAKPG---NVAMQADMA-PLAGAAHKISAEFVFPYLAHA 379 Query: 358 QLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFL 417 +EP + + + D E+W+ Q P + AK GL P + +++ + GG FGR + Sbjct: 380 PMEPLNCTVKLDAD-KAELWMGTQMPGLDAMAAAKTLGLQPQNVKVNTQMAGGGFGRRAI 438 Query: 418 YDSANPYPQAIALAKA-----VSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPV 472 +++ +A +AKA ++ P++ +WSRE++ RP+ V + D +G + Sbjct: 439 -PTSDYVVEACGVAKAARTVGITAPVRTLWSREDDIKGGYYRPMHVHRAEIGFDAQGKVL 497 Query: 473 A----IEAVSATEG-PTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLG 527 A I S T+G P EA K G ID TA+EG+ + Y +P K P+L Sbjct: 498 AWDHSIVGQSITKGSPFEAFMVKNG--IDATAIEGMK-EPYDLPMKLTVHHPDVNVPVL- 553 Query: 528 YWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLRD-NPRLTTLLQAAGELSGGWKR 586 +WRSVG++ + E+ +DE+A DP R+ L+ D +PR LQ A SG K+ Sbjct: 554 WWRSVGSTHTAYVMETLIDEVARATKQDPVAYRMALMGDKHPRHKAALQLAVAQSGYGKK 613 Query: 587 GPFTAEDGTRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEA 646 + RA GVA+ F S A + E S+++G K+H I + +VNP VEA Sbjct: 614 -----KLAAGRAWGVAVHESFQSVVAYVVEASVKDGTPKLHSITAGVHCNLVVNPKSVEA 668 Query: 647 QVNGAVALGLSQTLLEEAVYV-DGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIG 705 QV G +GLS L A+ + DG N+ + + M +V V +V S E G+G Sbjct: 669 QVQGGALMGLSMCLPGAAITLKDGVVEQSNFGDFAVPRITDMPQVAVHIVPSAEPPTGMG 728 Query: 706 EPPLPAVAPAVANAVAQLTGQRVRSLP 732 EP LP +APA ANAVA+LTG+ R LP Sbjct: 729 EPGLPPLAPAFANAVARLTGKTPRELP 755 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: 1425 Number of extensions: 83 Number of successful extensions: 12 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: 759 Length adjustment: 40 Effective length of query: 699 Effective length of database: 719 Effective search space: 502581 Effective search space used: 502581 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