Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate 7024305 Shewana3_1497 aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead (RefSeq)
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__ANA3:7024305 Length = 748 Score = 305 bits (782), Expect = 4e-87 Identities = 242/762 (31%), Positives = 356/762 (46%), Gaps = 65/762 (8%) Query: 13 NLSRRRFLASTAVGALVIGFGLPLGAGRVQ---AATSAERGTQVPAFLEIRPDGTVRLLS 69 N+SRR L GA +G GL LGA + A + ++ ++ F+ I D V L Sbjct: 9 NISRRDVLK--LFGA--VGGGLALGASGLSWSPMALAQDQQARLNLFIAIGEDDKVYLTC 64 Query: 70 PFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMSYP 129 E GQG T + QI+ EEL+AD + + Y T GS S+R +Y Sbjct: 65 HRSEMGQGIRTGILQILAEELEADWDKIVPIQGLADKRYASQN-----TDGSRSIRENYD 119 Query: 130 TMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVPD 189 MR +GA+AR ML QA A +W VPV E+ + +V+HA SGR+ +GELA A +P+P Sbjct: 120 RMREMGAMARTMLEQAAAARWKVPVSEVQAKDHQVLHAKSGRAARFGELALDAAGLPLPT 179 Query: 190 PASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGS 249 S+ L+ F+ IG + +D TGKA+Y D++VDNML+A++ P LG V S Sbjct: 180 ADSLRLKAVKDFKQIGASRQIVDMQAMLTGKAVYGYDIQVDNMLYASIMRPPVLGSDVAS 239 Query: 250 LRNQSQVEGMKGVHSVHVLP-----------GAVAVVAERWWHAKRAVEAIQVDWQEAAA 298 L + S + GV V+ LP G VAVVA W A + +A+QV W ++A Sbjct: 240 L-DDSAARKVAGVVDVYRLPTSKGAPAFQALGGVAVVATNTWSALQGRKALQVSWTQSAN 298 Query: 299 DSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQ 358 S S +E + Q P + GD A T ++A Y YL H+ Sbjct: 299 SS-------HDSKTYLQELVDKVQAPGKVVRQVGDEVKAWPKDDT-LKAIYTVPYLIHSS 350 Query: 359 LEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLY 418 +EPP A A G EIW Q P + ++A G+ + ++ LLGG FGR Sbjct: 351 IEPPVATANVTEKG-CEIWASTQTPQSTQQNVAVALGIAEDAVKVNVTLLGGGFGRKSKP 409 Query: 419 DSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEA-- 476 D + +A L+K RP+K+ WSRE+E ++ ++A D P A+ A Sbjct: 410 DFS---VEAALLSKQFKRPVKVSWSREDEIQNGYYHAISAQCYQALFDANNKPTALLART 466 Query: 477 --VSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGN 534 S + E + G ++D G +A+ N R + +G+ RSV N Sbjct: 467 GFPSISSTFAEGVEYPSGGELD----LGFVDVPFALANLRYEAVKASAHSRIGWMRSVCN 522 Query: 535 SLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQA--AGELSGGWKRGPF--- 589 + F SF+DE+A K ++ LL R T Q G R P Sbjct: 523 IQHGFGVGSFVDEMAHKAKLSCPDMWRSLLGQARRETFENQGFKYGNYGEDLTRHPVDVG 582 Query: 590 ---------------TAEDGTRRARGVAMASPFGSHTAAIAEVSI-ENGKVKVHDIWQAI 633 + G + G A+ F S A V + E+ ++KV + AI Sbjct: 583 RYLKVIEAVEQAQAKAPKAGKNQGWGFAVHRSFVSVVAVAMRVEVGEDKQLKVLNAIAAI 642 Query: 634 DPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVR 693 D G++VNP V+AQ GA+ GLS L+ E Y GK N+ YP+L Q+ + V Sbjct: 643 DAGTVVNPDRVKAQTEGAIVFGLSLALMGEISYQQGKVMQSNFHDYPLLRLPQVPEMEVI 702 Query: 694 VVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPLSR 735 +++S G+GEP +P VAP++ NA+ TG R+R LP+++ Sbjct: 703 IIDSDAPPAGVGEPGVPPVAPSLTNAIFAATGLRIRDLPVNK 744 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: 1179 Number of extensions: 71 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 739 Length of database: 748 Length adjustment: 40 Effective length of query: 699 Effective length of database: 708 Effective search space: 494892 Effective search space used: 494892 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