Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate Pf6N2E2_5939 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5939 Length = 771 Score = 354 bits (909), Expect = e-102 Identities = 258/771 (33%), Positives = 392/771 (50%), Gaps = 73/771 (9%) Query: 13 NLSRRRFL-ASTAVGALVIG--FGLP--LGAGRVQAATSAERGT--QVPAFLEIRPDGTV 65 NLSRR FL ++A G LV+ +GLP + A G ++ I DG+V Sbjct: 12 NLSRRGFLKGASATGVLVLAATWGLPDAFAEEKKFGAEGMPHGAVDDPKVYVSIATDGSV 71 Query: 66 RLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVR 125 ++ E GQG T+++ +V +EL+AD A V+ AP EA G + T GS S+R Sbjct: 72 TVICNRSEMGQGVRTSLSMVVADELEADWARVKVQQAPADEARF----GNQDTDGSRSMR 127 Query: 126 MSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDM 185 Y MRR GA AR ML A A QW VPVGE Q +V+H SGR LGYGELA++A + Sbjct: 128 HWYEPMRRCGAAARTMLELAAAAQWKVPVGECHAQLHKVLHQPSGRELGYGELAAAASAL 187 Query: 186 PVPDPASITLRDPSQFRWIGKPVKR-LDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLG 244 VP S+ L+ PS+FR+IGK R +D D G+A++ D+ D ML+A + P G Sbjct: 188 AVPSRGSLRLKQPSEFRYIGKEASRAIDGADIVNGRAVFGADVHFDGMLYAVIARPPVYG 247 Query: 245 MTVGSLRNQS--QVEGMKGVHSVHVLP--------GAVAVVAERWWHAKRAVEAIQVDWQ 294 V S+ + + +V G+ V + P G VAVVA+ W A + EA+++ W Sbjct: 248 GKVKSVDSSAALKVPGVVKVVQIEGRPLPSEFQPLGGVAVVAKNTWAAIKGREALKIQWD 307 Query: 295 EAAADSALRVMPADFSSDKHR-EFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQY 353 + A + S +R E AA P + + GD+ AL A + +EA+Y+ + Sbjct: 308 DGP--------NAGYDSIAYRKELEAAALKPGKVVRSSGDLDDALAKADSTLEASYYLPH 359 Query: 354 LNHAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFG 413 L+ + +EP A+ARF DG E W P+QAP + R +A+R G+ ++T++ LLGG FG Sbjct: 360 LSQSPMEPMVAVARFK-DGQCEAWAPSQAPQVTRERVAERLGIPFEKVTVNITLLGGGFG 418 Query: 414 RHFLYDSANPYPQAIALAKAV-SRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPV 472 R D +A LAK + I++ W+RE++ ++ +A L+ G+P Sbjct: 419 RKSKPDFV---VEAAVLAKEFPGQAIRVQWTREDDIHHSYFHTVSAEYLKAGLNQDGMPS 475 Query: 473 AIEAVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSV 532 + T A + G++ +YAIPN R+ +G++RSV Sbjct: 476 GWLHRTVAPSITALFAPGMTHEAPFEIGMGVTNMAYAIPNLRLENPEAVAHARVGWYRSV 535 Query: 533 GNSLNDFFYESFLDELADKGGHDPYELRLHLLR-------------------------DN 567 N + F +SF+DELA K G DP + ++ LL D Sbjct: 536 SNIPHGFAIQSFIDELAHKAGQDPLKYQVKLLGPDRKIDPRSLSEEWNYGESPERYPIDT 595 Query: 568 PRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSI-ENGKVKV 626 R+ T+L+ A + + GW R E R G+A+ F ++ AA+ EV + ++G V V Sbjct: 596 ARIRTVLETAAK-AAGWGR-----ELPKGRGLGLAVHYSFVTYVAAVIEVEVKDDGTVIV 649 Query: 627 HDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPI----L 682 H A+D G +NP + +Q GA +GL ++ E + DGK + N+ +Y + L Sbjct: 650 HKADIAVDCGPQINPERIRSQFEGACVMGLGNAMVGEISFKDGKVQQDNFHMYEVARMSL 709 Query: 683 APAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPL 733 AP ++A VH+ +GG+GEP +P +APA+ NA+ TG+R+RSLP+ Sbjct: 710 APKEVA-VHLVTPPGEVPLGGVGEPGVPPIAPALCNAIFAATGKRIRSLPV 759 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: 1400 Number of extensions: 74 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 739 Length of database: 771 Length adjustment: 40 Effective length of query: 699 Effective length of database: 731 Effective search space: 510969 Effective search space used: 510969 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