Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate 202167 SO3048 isoquinoline 1-oxidoreductase, beta subunit, putative (NCBI ptt file)
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__MR1:202167 Length = 748 Score = 307 bits (787), Expect = 1e-87 Identities = 239/758 (31%), Positives = 357/758 (47%), Gaps = 57/758 (7%) 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 SGRS +GELA A +P+P Sbjct: 120 RMREMGAMARTMLEQAAAARWKVPVTEVQAKDHKVMHAKSGRSARFGELALDAAALPLPA 179 Query: 190 PASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGS 249 S+ L+ F+ IG + +D TGKA+Y D++VDNML+A++ P LG V S Sbjct: 180 ADSLRLKAVKDFKQIGASRQIVDMQAMLTGKAVYGYDIQVDNMLYASIVRPPVLGSDVAS 239 Query: 250 LRNQSQVEGMKGVHSVHVLP-----------GAVAVVAERWWHAKRAVEAIQVDWQEAAA 298 L + + ++GV V+ LP G VAVVA W A + +A++V W ++A Sbjct: 240 L-DDTAARKVQGVVDVYRLPTPKGAPAFQALGGVAVVATNTWSALQGRKALKVTWTQSAN 298 Query: 299 DSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQ 358 S S +E + Q P + GD A A T ++A Y YL H+ Sbjct: 299 SS-------HDSKTYLQELVDKVQAPGKVVRQVGDEVKAWPEANT-LKAIYTVPYLIHSS 350 Query: 359 LEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLY 418 +EPP A A G EIW Q P + ++A G+ + ++ LLGG FGR Sbjct: 351 IEPPVATANVTEKG-CEIWASTQTPQSTQQNVAAALGIAEDAVKVNVTLLGGGFGRKSKP 409 Query: 419 DSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVS 478 D + +A L+K + RP+K+ WSRE+E ++ ++A D P A+ A + Sbjct: 410 DFS---VEAALLSKQLKRPVKVSWSREDEIQNGYYHAISAQCYQALFDTNNQPTALLART 466 Query: 479 ATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLND 538 + A D G +A+P+ R + +G+ RSV N + Sbjct: 467 GFPSISSTFAEGVEYPSDGELDLGFVDVPFALPHLRYEAVKATAHSRIGWMRSVCNIQHG 526 Query: 539 FFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQA--AGELSGGWKRGPF------- 589 F SF+DE+A K ++ LL R T Q G R P Sbjct: 527 FGVGSFVDEMAHKAQLSCPDMWRSLLGQPRRETFDNQGFKYGNYGEELTRHPVDIGRYLK 586 Query: 590 -----------TAEDGTRRARGVAMASPFGSHTAAIAEVSI-ENGKVKVHDIWQAIDPGS 637 + G + G A+ F S A V + E+ ++KV + AID G+ Sbjct: 587 VIEAVEQAQAKAPKAGKNQGWGFAVHRSFVSVVAVAMRVEVSEDKQLKVLNAIAAIDAGT 646 Query: 638 IVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVES 697 +VNP V+AQ GA+ GLS L+ E Y +GK N+ YP+L Q+ + + +++S Sbjct: 647 VVNPDRVKAQTEGAIVFGLSLALMGEISYQEGKVVQSNFHDYPLLRLPQVPEIEIIIIDS 706 Query: 698 GEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPLSR 735 G+GEP +P VAP++ NA+ TG R+R LP+++ Sbjct: 707 DAPPAGVGEPGVPPVAPSLTNAIFAATGVRIRDLPVNK 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: 1183 Number of extensions: 69 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