Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate WP_028990044.1 G579_RS0109820 xanthine dehydrogenase family protein molybdopterin-binding subunit
Query= metacyc::MONOMER-20833 (739 letters) >NCBI__GCF_000423825.1:WP_028990044.1 Length = 723 Score = 425 bits (1093), Expect = e-123 Identities = 280/739 (37%), Positives = 394/739 (53%), Gaps = 36/739 (4%) Query: 8 LDAPVNLSRRRFLASTAV--GALVIGFGLP------LGAGRVQAATSAERGTQVPAFLEI 59 + A + RR FL +A+ G L +G LP R +A A + A++ I Sbjct: 1 MSARFDAGRRHFLKVSALVGGGLAVGVYLPGCDRRPSEPPRPKAGAPAAQRFAPNAWVRI 60 Query: 60 RPDGTVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITG 119 PD V ++ E GQG T+M +V EELDAD + AP AY + G++ TG Sbjct: 61 TPDDMVTIVVDKSEMGQGVMTSMPMLVAEELDADWQRVKLVQAPADPAYRNPKIGIQATG 120 Query: 120 GSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELA 179 GS SV S+ +R+ GA ARAML+ A A++W V T+ G+V+H SGR YGELA Sbjct: 121 GSTSVSSSWEPLRQAGATARAMLVAAAAREWQVTPESCRTEKGKVLHPDSGRQARYGELA 180 Query: 180 SSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQH 239 S A P+P + L+ P F+ IGKP+ RLD K G A++ ID+KV +ML A V H Sbjct: 181 SLAARQPLPQ--DVPLKSPKDFQLIGKPLARLDTPAKVDGSAVFGIDVKVPDMLIATVAH 238 Query: 240 APRLGMTVGSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQ---EA 296 P G + + +Q + + GV +V + +AVVA +W A++ ++A+QV W A Sbjct: 239 CPVFGGKLAGY-DATQAKAIPGVRAVLPVESGIAVVARDYWTARKGLQAVQVQWDLGPNA 297 Query: 297 AADSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNH 356 DSA DK A Q P+ ++G+ AL A VEA Y + H Sbjct: 298 KLDSA--------GIDKLLTQAAGQ--PSAVAHDQGNAEQALGDAAKTVEAVYQLPFAAH 347 Query: 357 AQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHF 416 A +EP + A D E+W+P Q+ + AK TGL Q+ +H+ LLGG FGR F Sbjct: 348 ATMEPMNCTAHVRGD-ACEVWVPTQSQTGVQMTAAKITGLPQEQVIVHTTLLGGGFGRRF 406 Query: 417 LYDSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVA-IE 475 D +A+ L++AV P+KLIW REE+ D RP + RA LD G+PVA Sbjct: 407 EQDFV---AEAVQLSQAVGAPVKLIWPREEDMQHDFYRPAMYNQLRAGLDRDGMPVAWTH 463 Query: 476 AVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNS 535 ++ + + + D IDP++VEG + YAIPN + + +G+WRSVGNS Sbjct: 464 RLAGPSIMSRVMPQRVKDGIDPSSVEGAAELPYAIPNIHVDYVMKDTGVPVGFWRSVGNS 523 Query: 536 LNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGT 595 F ESFLDELA GG DP LR LL D R +L+ A + GW G A G Sbjct: 524 HTAFVKESFLDELAAAGGKDPLALRRALLSDAAREREVLELAAD-KAGW-GGKLPAGHG- 580 Query: 596 RRARGVAMASPFGSHTAAIAEVSI-ENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVAL 654 RG+A+ FGS+ A +AEVS+ ++G ++VH I A+D G++VNP V AQV A+ Sbjct: 581 ---RGLAVHKSFGSYAAQVAEVSVAKDGTLRVHRIVCALDCGTVVNPDTVRAQVESAIIY 637 Query: 655 GLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAP 714 GL+ TL G+ + N++ YP+L + + V ++ S E G+GEP +P VAP Sbjct: 638 GLTATLKGPITLAGGRVQQSNFNDYPLLRLDETPLIEVHLLPSREPPSGVGEPAVPPVAP 697 Query: 715 AVANAVAQLTGQRVRSLPL 733 AVANAV TG+R+R LP+ Sbjct: 698 AVANAVFAATGKRIRHLPI 716 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: 1355 Number of extensions: 85 Number of successful extensions: 9 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: 723 Length adjustment: 40 Effective length of query: 699 Effective length of database: 683 Effective search space: 477417 Effective search space used: 477417 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 Apr 09 2024. 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