Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate PP_3622 PP_3622 putative Isoquinoline 1-oxidoreductase, beta subunit
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__Putida:PP_3622 Length = 751 Score = 1257 bits (3252), Expect = 0.0 Identities = 622/732 (84%), Positives = 673/732 (91%), Gaps = 4/732 (0%) Query: 12 VNLSRRRFLASTAVGALVIGFGLPLGAGRVQAATSA----ERGTQVPAFLEIRPDGTVRL 67 VNLSRRRFLA TAVGALV+GFGLP+G+ RVQAA +A ERGTQVPAFLEIRPDGTVRL Sbjct: 20 VNLSRRRFLAGTAVGALVLGFGLPMGSARVQAAAAAAATAERGTQVPAFLEIRPDGTVRL 79 Query: 68 LSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMS 127 LSPFMEGGQG TAMAQIVGEELD DPA F+V++APPGEAYVVMENG+RITGGSMSVRMS Sbjct: 80 LSPFMEGGQGPFTAMAQIVGEELDVDPAHFVVDSAPPGEAYVVMENGMRITGGSMSVRMS 139 Query: 128 YPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPV 187 YPTMRRLGALAR MLLQAGA+ GVPV EL+T PG VVH +GRS+ YGELA A+D+PV Sbjct: 140 YPTMRRLGALARGMLLQAGAEHLGVPVDELSTTPGNVVHTTTGRSVPYGELAGRAMDLPV 199 Query: 188 PDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTV 247 PDPAS+ LRDPSQFRWIGKPV+RLDAYDKSTGKA Y ID+KVD MLHAAVQHAPRLGMTV Sbjct: 200 PDPASVKLRDPSQFRWIGKPVRRLDAYDKSTGKAQYCIDIKVDGMLHAAVQHAPRLGMTV 259 Query: 248 GSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEAAADSALRVMPA 307 GSLRN+ Q++ MKGVHSVH LPGAVAVVAERWWHAKRAVEAIQVDW+E AADS +R MPA Sbjct: 260 GSLRNEDQIKAMKGVHSVHQLPGAVAVVAERWWHAKRAVEAIQVDWKEPAADSKVRPMPA 319 Query: 308 DFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALAR 367 DFSSD RE LA QGP+RD+ENEGD+AGAL AKT+VEA+YHNQYLNHAQLEPPSALAR Sbjct: 320 DFSSDAWREHLATVQGPSRDEENEGDIAGALANAKTKVEASYHNQYLNHAQLEPPSALAR 379 Query: 368 FNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQA 427 FNPDG+L++WLPNQAPDMFR DIA+RTGL+PAQI LHSPLLGGFFGRHFLYDSANPYPQA Sbjct: 380 FNPDGSLDVWLPNQAPDMFRDDIARRTGLEPAQINLHSPLLGGFFGRHFLYDSANPYPQA 439 Query: 428 IALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEAL 487 IALAKAV RP+KLIWSREEEFLRDVLRP+AVVKFRA LD G+PVA+EAVSATEGPTEAL Sbjct: 440 IALAKAVGRPVKLIWSREEEFLRDVLRPVAVVKFRAGLDADGMPVALEAVSATEGPTEAL 499 Query: 488 AGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLDE 547 AGKQG+KIDPTA+EGLSGKSYAI NKRIAQIYVKG MLGYWRSVGNSLNDFFYESFLDE Sbjct: 500 AGKQGEKIDPTALEGLSGKSYAIANKRIAQIYVKGPAMLGYWRSVGNSLNDFFYESFLDE 559 Query: 548 LADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPF 607 LADKGG DP+ELRLHLLRDNPRLT LL A +LSGGWKRGPFTAEDG++RARGVAMASPF Sbjct: 560 LADKGGKDPFELRLHLLRDNPRLTNLLNAVADLSGGWKRGPFTAEDGSKRARGVAMASPF 619 Query: 608 GSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYV 667 GS A IAEVSI+NG+V+VHDIWQAIDPGSIVNPAI+E QVNGAVALGLSQTL+EEAVYV Sbjct: 620 GSEAAVIAEVSIDNGQVRVHDIWQAIDPGSIVNPAIIEHQVNGAVALGLSQTLVEEAVYV 679 Query: 668 DGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQR 727 DGKPRARNYDLYPIL P++MARVHVR++ESG KMGGIGEPPLPAVAPAVANAVAQLTGQR Sbjct: 680 DGKPRARNYDLYPILPPSRMARVHVRIIESGAKMGGIGEPPLPAVAPAVANAVAQLTGQR 739 Query: 728 VRSLPLSRHTFS 739 VRSLPLSRHTFS Sbjct: 740 VRSLPLSRHTFS 751 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: 1843 Number of extensions: 81 Number of successful extensions: 2 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: 751 Length adjustment: 40 Effective length of query: 699 Effective length of database: 711 Effective search space: 496989 Effective search space used: 496989 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