Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate WP_061531860.1 CAter10_RS00515 xanthine dehydrogenase family protein molybdopterin-binding subunit
Query= metacyc::MONOMER-20833 (739 letters) >NCBI__GCF_001584165.1:WP_061531860.1 Length = 726 Score = 335 bits (860), Expect = 4e-96 Identities = 241/736 (32%), Positives = 370/736 (50%), Gaps = 35/736 (4%) Query: 11 PVNLSRRRFLASTAVGA--LVIGFGLPLGAGRVQAATSAERGTQVPAFLEIRPDGTVRLL 68 P SRR FL ++AV LV+GF +P G A T+ ++ AFL + PD V + Sbjct: 6 PSKNSRRTFLKASAVSGVGLVLGFYIPSLTGIASAQTATKKSYPPNAFLRVGPDNKVVIQ 65 Query: 69 SPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMSY 128 ++ GQGT TA+ ++ EELD D E A + + G+++ GGS SV +Y Sbjct: 66 VSKVDIGQGTLTALPMLLAEELDCDWNNVHAELAKGEDVFRDTAFGMQMVGGSTSVAHTY 125 Query: 129 PTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVP 188 R +GA AR+ML+ A AKQW V T G V+ +G+ YG +A++A+ +P P Sbjct: 126 QQYREIGARARSMLVAAAAKQWKVDPAACKTAAG-VITGPTGQHTTYGAVANAAMQLPAP 184 Query: 189 DPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVG 248 + ++ L++P+QF IGK RLD KSTG+ + ID+ + M A + A G +G Sbjct: 185 E--TVQLKNPAQFTIIGKATPRLDGAAKSTGQQKFGIDVDLPGMKVALLARAVPWGAKIG 242 Query: 249 SLRNQSQVEGMKGVHSVHVLPG-----AVAVVAERWWHAKRAVEAIQVDWQEAAADSALR 303 L + S + + GV + +PG +V +VA+ +W AK+A +A++++W + Sbjct: 243 KL-DDSAAKAIPGVRKIFTIPGIRGGQSVVIVADGYWIAKKARDALKIEWDA----KGIE 297 Query: 304 VMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPS 363 + +D +RE P + DV+ +L A ++EA + YL H +EP + Sbjct: 298 RVSSDSLFAAYREAAMKPGTPAA----KADVS-SLATAPKKIEAVFEFPYLAHTPMEPLN 352 Query: 364 ALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANP 423 F D +W +Q M R IAK G+ ++ ++ + GG FGR L +S N Sbjct: 353 MTLHFTGD-ACTVWTGSQFQSMDRQAIAKVLGIAITKVDFNTMMAGGAFGRRALPESENA 411 Query: 424 YPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSA---- 479 A P+K+++SRE++ RP+ V + R D G A + V A Sbjct: 412 VEAAYIAKVMRGTPVKVMYSREDDLHGGYYRPMHVHRVRIGYDASGKIAAWDHVIAGQSI 471 Query: 480 -TEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLND 538 T P E+ K G +D T EG+ YAIPN ++ ++ + + RSVG+S N Sbjct: 472 LTGSPFESFLVKDG--VDGTMTEGVLESHYAIPNLALSVHNMQANVPVLWHRSVGHSHNG 529 Query: 539 FFYESFLDELADKGGHDPYELRLHLL-RDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRR 597 + E+ +DE+A G DP E R L + R + L A SG KR E G Sbjct: 530 YVMETLIDEIARSVGRDPVEYRKALFAQPGGRSSQALDLAVTRSGYGKR---KLEAG--H 584 Query: 598 ARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLS 657 A GVA+ F + A +AEVS+++G+ +VH + + +NP +EAQ+ G + GLS Sbjct: 585 AWGVAVHHAFDTSVAYVAEVSLKDGRPQVHRVTAGVHCNMAINPRTIEAQIQGGLVFGLS 644 Query: 658 QTLL-EEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAV 716 E DG + N+ Y + Q V V +V S + G+GEPP+P +APA+ Sbjct: 645 SIQPGYEITLKDGVVQQSNFPDYMPVLMGQCPTVEVYLVPSADTPTGVGEPPVPPIAPAI 704 Query: 717 ANAVAQLTGQRVRSLP 732 ANAVA LTG+R+R LP Sbjct: 705 ANAVAALTGKRLRKLP 720 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: 1229 Number of extensions: 57 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: 726 Length adjustment: 40 Effective length of query: 699 Effective length of database: 686 Effective search space: 479514 Effective search space used: 479514 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 24 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