Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate GFF1288 HP15_1258 isoquinoline 1-oxidoreductase, beta subunit
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__Marino:GFF1288 Length = 734 Score = 394 bits (1011), Expect = e-113 Identities = 260/748 (34%), Positives = 377/748 (50%), Gaps = 48/748 (6%) Query: 14 LSRRRFL--ASTAVGALVIGFGLPLGAGRVQAATSAERGTQVP-AFLEIRPDGTVRLLSP 70 ++RR FL ++ A G+L++ LP G +Q + G P A+LE+ D V Sbjct: 3 MNRRNFLKVSAGASGSLMVSITLP-GCAGIQTGYEPDTGEWRPDAWLELTADDEVFFTLA 61 Query: 71 FMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMSYPT 130 +E GQGT+T + ++ EEL+ P AP Y L++TGGS SV S+ Sbjct: 62 RVEMGQGTYTGLTTLIAEELEIQPERITPRFAPVAPEYRNPLYKLQLTGGSTSVATSWEP 121 Query: 131 MRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVPDP 190 +R GA AR ML+ A A+ W V E GRVVH S+ YG+L A + Sbjct: 122 LRTAGAEARQMLVMAAARVWNVEATECRASEGRVVHPNGIDSMAYGQLVELAAKEVLR-- 179 Query: 191 ASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGSL 250 I L+ S++++IGK +LDA KSTG A+Y ID+ + +M++ V PR G V Sbjct: 180 GDIALKPQSEWKYIGKQRGKLDARAKSTGTAVYGIDVDLPDMVYGVVSRPPRRGGRVRDF 239 Query: 251 RNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEAAADSALRVMPADFS 310 N QV M GV V + VAVVA+++W A++A +A+++DW + A S + Sbjct: 240 -NADQVRAMTGVLDVFKIERGVAVVADKYWRARKAQDALKIDWDFSDAVS----LSTGDV 294 Query: 311 SDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALARFNP 370 D +R AA P + +EG A A++ VEA Y YL HA LEP +A A + Sbjct: 295 FDSYRA--AADDDPGESERSEGSFASAMEEGDRVVEAEYAQPYLAHATLEPMNATAWYRE 352 Query: 371 DGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIAL 430 DG +E+W P QAPD+ R A+ T L P IT+++ LGG FGR D +A A+ Sbjct: 353 DG-MEVWAPTQAPDLGRIAAARVTNLGPDDITINTTFLGGGFGRRLTQDYIE---EAAAV 408 Query: 431 AKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGL-------------------- 470 A V RP+K+IWSREE+ D+ RP + + +A+L L Sbjct: 409 AYRVGRPVKVIWSREEDTRHDLYRPAMLHRMKASLSGAELKGWHHQIVGPQILDWYVRNA 468 Query: 471 -----PVAIEAVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPM 525 P A + + T G +A D +A+EG Y +PN I + Sbjct: 469 APAQYPWAPKFMYDTLGSVGLMAEGIATPKDHSAIEGAIEYPYRVPNIDIRHTHTDPGIP 528 Query: 526 LGYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWK 585 + +WRSVG S N F E+F+DELA + G DPY R L+ PR +L L+ Sbjct: 529 ITWWRSVGFSHNGFAVETFMDELAHEAGEDPYRFRRRLIAHEPRHLEVLDRVVRLADWQS 588 Query: 586 RGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVE 645 P RARG+A+ FG++ A + E IENG ++V+ + ++D G +VNP IVE Sbjct: 589 PVP------EGRARGLALFRSFGTYVAQVVEAGIENGAIRVYKVTCSVDCGQVVNPRIVE 642 Query: 646 AQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIG 705 Q+ G + GL+ L E +G+ + N+ Y ++ + V V +V S E G+G Sbjct: 643 DQIEGGILFGLTAALYGEITLENGEVQQSNFHDYRLMRQYERPEVLVDIVASSESPTGVG 702 Query: 706 EPPLPAVAPAVANAVAQLTGQRVRSLPL 733 EP +P V PA+ NA+ L G+R RSLPL Sbjct: 703 EPGVPPVIPALGNALFALNGKRQRSLPL 730 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: 1293 Number of extensions: 64 Number of successful extensions: 9 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: 734 Length adjustment: 40 Effective length of query: 699 Effective length of database: 694 Effective search space: 485106 Effective search space used: 485106 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