Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate WP_061533487.1 CAter10_RS11315 xanthine dehydrogenase family protein molybdopterin-binding subunit
Query= metacyc::MONOMER-20833 (739 letters) >NCBI__GCF_001584165.1:WP_061533487.1 Length = 709 Score = 395 bits (1016), Expect = e-114 Identities = 255/726 (35%), Positives = 384/726 (52%), Gaps = 33/726 (4%) Query: 15 SRRRFLASTAV--GALVIGFGLPLGAGRVQAATSAERGTQVPAFLEIRPDGTVRLLSPFM 72 +RR FL S+A+ G L +G LP G + A +A A++ I D T+ L+S Sbjct: 4 TRRDFLKSSALAGGGLTLGIMLP---GFMDEALAAGTIYTPNAWVHIADDNTITLISARS 60 Query: 73 EGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMSYPTMR 132 E GQG +TA+ ++ EEL D V APP Y G +ITGGS S+R + +R Sbjct: 61 EMGQGVYTALPMLIAEELGVDVHKVKVAIAPPNAVYTNALLGAQITGGSTSIRDGWEKLR 120 Query: 133 RLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVPDPAS 192 GA AR ML+ A A +W V L + G +V+ +G+ +G LA +A +PVP Sbjct: 121 IGGAQARIMLVSAAASKWHVDPAALRVENG-MVYGPNGKKASFGALAEAASKLPVPK--D 177 Query: 193 ITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGSLRN 252 + L+DP F+ +GK KRLD K G A+Y ID+K+ M++A+++ P +G V S + Sbjct: 178 VQLKDPKDFKIVGKATKRLDTPSKVNGSAVYGIDVKLPGMVYASLEQCPVIGGKVLSF-D 236 Query: 253 QSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQE---AAADSALRVMPADF 309 S+ M GV V + VAV A +W AK+A E ++V W E A D+A +M Sbjct: 237 ASKARAMPGVIDVVQIDDGVAVAANSYWRAKKAREQLKVQWDEGPVAKIDNAT-MMDGIR 295 Query: 310 SSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALARFN 369 +++K+ + + ++ GD A A++GA ++ Y +Q L HA LEP + A F Sbjct: 296 AAEKNAKIINIKK--------TGDAAKAMQGAAKVLKVEYQSQLLAHATLEPQNFTADFK 347 Query: 370 PDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIA 429 DG + Q + ++AK G+ P + + + LGG FGR D QA Sbjct: 348 -DGKCRVIGSTQFQQGAQGNVAKALGIKPEDVDVQTTFLGGGFGRRLEVDFI---VQAAQ 403 Query: 430 LAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEALAG 489 ++KAV +P+KL+W+RE++ D RP+A+ + LD G PVA+ ++ T+ G Sbjct: 404 ISKAVGKPVKLVWTREDDTTHDFYRPMALHRMAGGLDADGKPVALTFQLTSQSVTQRAFG 463 Query: 490 KQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLDELA 549 D +DP E S Y IPN + GYWRSV ++LN F ESF+DE+A Sbjct: 464 LPKDTLDPFMAEA-SVVGYGIPNMTQDLVIHDTGLRAGYWRSVSHALNAFANESFIDEMA 522 Query: 550 DKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGS 609 G DPY RL LL PR +L+ A + +G P + RG+A+ + + Sbjct: 523 AAAGKDPYAFRLSLLDQQPRFANVLKQAAQKAGWGTPLP------SGHFRGIALMEGYDT 576 Query: 610 HTAAIAEVSI-ENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVD 668 + A +AE+S+ ++ ++KVH + D G +VNP VEAQ+ ++A GLS L + Sbjct: 577 YMAQVAEISMHDDNEIKVHRVVVVADLGHMVNPDTVEAQLQSSIAFGLSAALGGQITLEK 636 Query: 669 GKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRV 728 G+ + N+ YP++ +M ++ V +V S EK GGIGEP + PAVANAV TG+RV Sbjct: 637 GRVQQSNFGDYPVVRMNEMPKIDVTLVASTEKPGGIGEPATALIGPAVANAVFAATGKRV 696 Query: 729 RSLPLS 734 R +PL+ Sbjct: 697 RKMPLT 702 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: 1217 Number of extensions: 63 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: 709 Length adjustment: 40 Effective length of query: 699 Effective length of database: 669 Effective search space: 467631 Effective search space used: 467631 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