Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate Ga0059261_1453 Ga0059261_1453 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__Korea:Ga0059261_1453 Length = 740 Score = 280 bits (715), Expect = 2e-79 Identities = 221/725 (30%), Positives = 340/725 (46%), Gaps = 70/725 (9%) Query: 48 ERGTQVPAFLEIRPDGTVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEA 107 ++ T A+L+I +G V + P E GQG T + Q++ ++L AD VE AP Sbjct: 42 DKETAFGAWLKIAENGQVTVAIPQCEYGQGVFTTLPQLLADQLGADWRMVGVEQAPLNPI 101 Query: 108 YV---------------------VMENGLRITGGSMSVRMSYPTMRRLGALARAMLLQAG 146 Y N +TGGS S+R +R GA ARA+L +A Sbjct: 102 YANSLALDALFPGVFPERLKRIWAERNLAMLTGGSTSMRSFETPLRSAGAGARALLCKAA 161 Query: 147 AKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVPDPASITLRDPSQFRWIGK 206 A++WGV E T G VVH + L +GELA+ A +PD + R+ R G Sbjct: 162 ARRWGVDWQECDTANGHVVH--DQKRLRFGELAAEAAGEKLPD--DLPFREGETGRLTGT 217 Query: 207 PVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGSLRNQSQVEGMKGVHSVH 266 P RLD K G A ++ D+++ M+ AA++ P +G + +++ + G+ +H Sbjct: 218 PAPRLDGPGKVDGSANFAADIRLPGMVFAALRQGP-IGTVKLAAIDEAAAAKVPGM--LH 274 Query: 267 VLPGA--VAVVAERWWHAKRAVEAIQVDWQEAA---ADSALRVMPADFSSDKHREFLAAQ 321 ++ VA VA WW A +A++AI ++ AA +++ + A SD R A Sbjct: 275 IVKNELWVATVANNWWAASQALDAISPRFEVAAKVESETIQAALDAALESDGERMASA-- 332 Query: 322 QGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQ 381 GD+A K A+ V A Y HA +EP A A + +G + +WLP Q Sbjct: 333 ----------GDLAPVFKDARV-VAAEYRVGLALHAAIEPICATAVWE-EGRVRLWLPTQ 380 Query: 382 APDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIALAKAVSRPIKLI 441 AP R +A G+ + + +H L GG FG++ + +A QA +A+ V +P++L+ Sbjct: 381 APGFARDAVANVLGVSASDVVIHPMLAGGSFGQNLEHQAA---AQAALIAREVKKPVQLM 437 Query: 442 WSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEALA-------GKQGDK 494 WSR E ++D RP AV + A L G A A LA G G Sbjct: 438 WSRGETCVQDRFRPPAVGRMTARLGANGSISGWLAKIAAPRTGHELARRLTGGGGATGAA 497 Query: 495 IDPTAVEGLSGKSYAIPNKRIAQIYVKGAPM-----LGYWRSVGNSLNDFFYESFLDELA 549 + + + + A P RI + + P+ GYWRS +S FF ESF+DELA Sbjct: 498 LATGGIGDAAAVAGARPPYRIPALAIDHHPVEIVVPTGYWRSGAHSYTAFFTESFIDELA 557 Query: 550 DKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGS 609 + + R+ +L PRL L L GGW+ G +G+A + GS Sbjct: 558 HVADIEAFSFRIAMLGGEPRLARCLSTVTSL-GGWQGGL------PGSGQGLACHAFGGS 610 Query: 610 HTAAIAEVSIENG-KVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVD 668 + A +AE S+ +V+V + A+D G +VNP++VE Q+ G + G++ L Sbjct: 611 YIAVMAEASVGGDQRVQVDRLIAAVDCGRVVNPSVVEQQIEGGLIFGMAAALGATTGITA 670 Query: 669 GKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRV 728 +P AR++ + A ++ V ++ S GG E +P VAPA+ANA+ TG R+ Sbjct: 671 NRPEARSFRDLELPRLADCPQIMVELIASDADPGGASELAVPPVAPAIANALYAATGVRL 730 Query: 729 RSLPL 733 R LPL Sbjct: 731 RQLPL 735 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: 1308 Number of extensions: 78 Number of successful extensions: 7 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: 740 Length adjustment: 40 Effective length of query: 699 Effective length of database: 700 Effective search space: 489300 Effective search space used: 489300 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