Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate Pf6N2E2_1904 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1904 Length = 752 Score = 1038 bits (2684), Expect = 0.0 Identities = 512/732 (69%), Positives = 601/732 (82%), Gaps = 4/732 (0%) Query: 11 PVNLSRRRFLASTA---VGALVIGFGLPLGAGRV-QAATSAERGTQVPAFLEIRPDGTVR 66 PVN+SRRRFL ++A GALVI FG+PLG R + A + G +VPAFLEIRPD TVR Sbjct: 19 PVNVSRRRFLQASAGVTAGALVISFGIPLGPLRAAERAQALPPGARVPAFLEIRPDNTVR 78 Query: 67 LLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRM 126 L SPF+EGGQG T MAQ+VGEELD DPA+F+VE A PG + VME G+R TGGS S+R Sbjct: 79 LQSPFIEGGQGIFTGMAQVVGEELDIDPASFLVENAAPGNDFKVMEGGMRFTGGSRSMRA 138 Query: 127 SYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMP 186 SY TMRRLGA AR MLLQA + W VP+ +LTT+PGRV+HAAS RS+ YGELA LD+P Sbjct: 139 SYMTMRRLGASARLMLLQAASSHWKVPLAQLTTEPGRVIHAASNRSITYGELAPLTLDLP 198 Query: 187 VPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMT 246 +PDP ++TLRDP+ FRWIGKPV+R+D YDKSTGKA Y+ID +V+ MLHAAVQHAPRLG+ Sbjct: 199 IPDPQTVTLRDPATFRWIGKPVQRIDVYDKSTGKAQYTIDTRVEGMLHAAVQHAPRLGLQ 258 Query: 247 VGSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEAAADSALRVMP 306 VG +RN+ Q+ +KGVHSVH L GAVAVVA+RWW AKRAVEA+QV+W E DS +R MP Sbjct: 259 VGLVRNEDQIRNLKGVHSVHRLEGAVAVVAQRWWVAKRAVEALQVEWTEPGGDSTVRYMP 318 Query: 307 ADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALA 366 A+F + + E L+ + E EGD+ L GAK V ATYH QYLNHAQLEPPSALA Sbjct: 319 ANFDTQAYAEQLSKTTDAGDEAEREGDLQQGLAGAKKVVSATYHTQYLNHAQLEPPSALA 378 Query: 367 RFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQ 426 RF+ +G L++WLPNQAPD+F AD+AKRTGLDP++ITLHSPLLGGFFGRHFLY +A+PYPQ Sbjct: 379 RFDAEGNLDLWLPNQAPDLFLADVAKRTGLDPSKITLHSPLLGGFFGRHFLYPNASPYPQ 438 Query: 427 AIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEA 486 AI LA++ RPIK+IWSREEEFLRDVLRP AVV+FRA LD++G+PVA EA+SATEGPTE Sbjct: 439 AIQLAQSTGRPIKVIWSREEEFLRDVLRPSAVVRFRAGLDEQGMPVAFEAISATEGPTEG 498 Query: 487 LAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLD 546 +A KQGDKIDPTAVEGL+GK YAI ++RIAQ+Y + MLGYWRSVGNS+NDF YE+FLD Sbjct: 499 IANKQGDKIDPTAVEGLAGKKYAIAHRRIAQLYSQTPVMLGYWRSVGNSINDFMYEAFLD 558 Query: 547 ELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASP 606 E+AD GG DPYELR LL+ N RL+ LL+ +LSGGWKRGPFTA+DGT+RARGVAMASP Sbjct: 559 EVADAGGQDPYELRAKLLQGNERLSHLLKVVADLSGGWKRGPFTAQDGTKRARGVAMASP 618 Query: 607 FGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVY 666 FG+ TA IAEVSI NG VKVHDIWQAIDPGSIVNPAI+EAQVN AVALGLSQTL+E+A+Y Sbjct: 619 FGTETAVIAEVSISNGAVKVHDIWQAIDPGSIVNPAIIEAQVNSAVALGLSQTLVEQAIY 678 Query: 667 VDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQ 726 G P ARNYDLY IL P MARVHVRVVESG MGGIGEPPLPAVAPAVANAV++LTGQ Sbjct: 679 KGGTPVARNYDLYRILTPEMMARVHVRVVESGAPMGGIGEPPLPAVAPAVANAVSRLTGQ 738 Query: 727 RVRSLPLSRHTF 738 R+RS+PLS++ F Sbjct: 739 RIRSMPLSQYRF 750 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: 1645 Number of extensions: 62 Number of successful extensions: 4 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: 752 Length adjustment: 40 Effective length of query: 699 Effective length of database: 712 Effective search space: 497688 Effective search space used: 497688 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