Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate AO356_26900 AO356_26900 carbon monoxide dehydrogenase
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_26900 Length = 747 Score = 353 bits (905), Expect = e-101 Identities = 265/741 (35%), Positives = 379/741 (51%), Gaps = 38/741 (5%) Query: 9 DAPVNLSRRRFLASTAVGALVIGF--GLPLGAGRVQAATSAERGTQVP-AFLEIRPDGTV 65 D P L RR FL +G L +G L L A + + TQ P AF++I P+G V Sbjct: 24 DGPAALPRRSFLKIVGIGGLALGAFPHLALAQEANGAVAAPLKPTQQPSAFVQIAPNGEV 83 Query: 66 RLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVR 125 + +E GQG T + I+ EELDAD + AY+ G+ +TGGS +++ Sbjct: 84 TVTINRLEFGQGVQTGLPMILAEELDADWSLVRSRNGSNDAAYMDPAFGIHLTGGSNTIK 143 Query: 126 MSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDM 185 SY R LGA ARAMLL A A +W V V L+TQ G V+ A GR YGELA +A+ M Sbjct: 144 NSYTQYRELGARARAMLLSAAAARWNVDVASLSTQAGMVLGPA-GRKASYGELAQAAMAM 202 Query: 186 PVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGM 245 PVP+ ITL+DP FR IG+ R+DA KS+G+ + ID+ + L A V P G Sbjct: 203 PVPE--QITLKDPKDFRIIGQATTRIDAKAKSSGQQDFGIDMHLPGQLTAVVARPPVFGA 260 Query: 246 TVGSLRNQSQVEGMKGVHSVHVLP---GA--VAVVAERWWHAKRAVEAIQVDWQEAAADS 300 + +L + S KGV +V +P GA VAVVA+ +W AK A +A++V+W S Sbjct: 261 RIAAL-DDSAARATKGVKAVLRVPLDGGAEGVAVVADSYWQAKLARDALKVEWNA----S 315 Query: 301 ALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLE 360 A+ + ++ ++RE LA+Q GP D + +A A ++EA + YL HA +E Sbjct: 316 AVEKLDSEKQLAQYRE-LASQPGPLHFDADMTPLA----TAPHRLEAEFLFPYLAHAPME 370 Query: 361 PPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDS 420 P + + ++W+ Q P A AK L P QI ++ GG FGR + + Sbjct: 371 PLNCTVQLAGKNGAQLWVGTQFPGGDAAAAAKVLDLKPEQIQVNVQTAGGGFGRRGV-PT 429 Query: 421 ANPYPQAIALAKA-----VSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIE 475 + A +AKA V PI+ +WSRE++ RP+ + + R DD G +A + Sbjct: 430 NDFVVLACEVAKAARTAGVDAPIRTLWSREDDIKGGYYRPMHLHRARIGFDDSGKVLAWD 489 Query: 476 --AVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVG 533 V + G+ + IDPTA EGL Y +P + P+L +WRSVG Sbjct: 490 HALVGQSIITGTVFGGRVKNGIDPTATEGLR-DPYPLPMRLTVHHPKLNVPVL-WWRSVG 547 Query: 534 NSLNDFFYESFLDELADKGGHDPYELRLHLLRD-NPRLTTLLQAAGELSGGWKRGPFTAE 592 ++ F E+ +DE+A DP R+ L D +PR LQ A + S KR + Sbjct: 548 STHTAFVMETLIDEIARTTKQDPVAYRMKLFGDQSPRHRAALQLAVDKSEYGKR-----Q 602 Query: 593 DGTRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAV 652 RA GVA+ F S A + E S+++G+ +H++ + VNP VEAQV GA Sbjct: 603 LPAGRAWGVAVHESFSSVVAYVVEASVQDGRPVLHNVTAGVHCNLAVNPRSVEAQVQGAA 662 Query: 653 ALGLSQTLLEEAVYV-DGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPA 711 +GLS L A+ + DG + N+ + + M V +V S E G+GEP LPA Sbjct: 663 LMGLSMCLPGGAITLKDGVVQQSNFADFSVPRITDMPEFAVHIVPSAEPPTGMGEPGLPA 722 Query: 712 VAPAVANAVAQLTGQRVRSLP 732 +APA ANAVA LTG+ +R LP Sbjct: 723 LAPAFANAVASLTGKPMRELP 743 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: 1440 Number of extensions: 85 Number of successful extensions: 12 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: 747 Length adjustment: 40 Effective length of query: 699 Effective length of database: 707 Effective search space: 494193 Effective search space used: 494193 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