Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate H281DRAFT_01475 H281DRAFT_01475 isoquinoline 1-oxidoreductase, beta subunit
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__Burk376:H281DRAFT_01475 Length = 740 Score = 403 bits (1036), Expect = e-116 Identities = 276/748 (36%), Positives = 412/748 (55%), Gaps = 41/748 (5%) Query: 5 NELLDAPVNLSRRRFL-ASTAVGALVIGFGLPLG---AG---RVQAATSAERGTQVPAFL 57 ++L DA V SRR FL A+ AV A+ GL +G AG R AAT + AFL Sbjct: 5 SDLTDA-VRPSRRTFLKAAGAVAAVGANIGLTIGFEWAGMGRRALAATMPDATFAPNAFL 63 Query: 58 EIRPDGTVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPP-GEAYVVMENG-L 115 + PD +V +++ +E GQG +T +A IV EELDA+ VE+AP + Y + G + Sbjct: 64 RVAPDNSVTVIAKHVEMGQGAYTGIATIVAEELDANWQDVRVESAPADAKRYANLAFGTM 123 Query: 116 RITGGSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGY 175 + TGGS ++ S+ +R GA ARAML+ A A QW VP EL T+ G V HAA+ RS Y Sbjct: 124 QGTGGSSAMANSWMQLREAGAKARAMLVSAAAAQWQVPATELVTRDGSVHHAATNRSATY 183 Query: 176 GELASSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHA 235 G LAS+A +PVP + L+ P FR IG + R+D K+ G A +++D+ ML A Sbjct: 184 GSLASAAARLPVPQ--KVALKSPKDFRLIGHQLPRVDVPPKTDGTAQFTLDVTFPGMLVA 241 Query: 236 AVQHAPRLGMTVGSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQE 295 +Q P G TV S + S + + GV SV +PG VAVVA+ +W AK+ +A++V+W + Sbjct: 242 LLQRPPLFGATVKSF-DASAAKAVPGVVSVVQVPGGVAVVAKGFWAAKQGRDALKVEWDD 300 Query: 296 AAADSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLN 355 + A+ +D ++R LA Q G T +G+ AL GA ++ A+Y YL Sbjct: 301 SKAEKR----SSDAIMAEYRR-LAEQPGATA--RKDGNAEQALSGAAKKISASYSFPYLA 353 Query: 356 HAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRH 415 HA +EP A+ + + + EIW +Q + +A+ A+ GLDP Q+ +++ GG FGR Sbjct: 354 HAPMEPLDAVVKLTAN-SCEIWAGDQFQTVDQANAARTAGLDPQQVKIYTLYAGGSFGRR 412 Query: 416 FLYDSANPY-PQAIALAKAVSR---PIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLP 471 ++ + Y +A+++A+A+ P+KL W+RE++ + RP+ K A L G Sbjct: 413 A--NTRSDYIVEAVSIARALGANGTPVKLQWTREDDIHGGLYRPMYFHKLDAGLTADGKL 470 Query: 472 VA-----IEAVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVK-GAPM 525 V + + P ++ K G ID T+VEG + +YAIPN + + G P+ Sbjct: 471 VGWRHRIVGQSILGDTPFASVMVKNG--IDATSVEGAANLAYAIPNISVELTTTQTGVPV 528 Query: 526 LGYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWK 585 L +WR VG+S F E+F+DE A G DP+ R LL PR+ +L+ A + +G Sbjct: 529 L-WWRVVGSSHTAFAVEAFIDEAAHAAGKDPFAFRRDLLAHEPRMRAVLELAAQKAGWDP 587 Query: 586 RGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSIE-NGKVKVHDIWQAIDPGSIVNPAIV 644 P R RG+A+A F + A +AEVS++ +G VKV + A+D G+ +NP ++ Sbjct: 588 AKPLPKG----RGRGIAVAEAFKTFVAQVAEVSVDQDGNVKVERVVCAVDCGTPINPDVI 643 Query: 645 EAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGI 704 AQ+ G + GL L DGK N+D Y +L A+M +V V +V+SGE G+ Sbjct: 644 AAQMEGGIGFGLGAALHSAITLKDGKVEQNNFDSYQVLRIAEMPKVEVHIVQSGEAPTGV 703 Query: 705 GEPPLPAVAPAVANAVAQLTGQRVRSLP 732 GEP + V PAVANA+ TG+R+ LP Sbjct: 704 GEPGVAPVGPAVANAIFAATGKRLYDLP 731 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: 1281 Number of extensions: 65 Number of successful extensions: 10 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: 740 Length adjustment: 40 Effective length of query: 699 Effective length of database: 700 Effective search space: 489300 Effective search space used: 489300 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