Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate CCNA_01554 CCNA_01554 D-mannonate oxidoreductase
Query= ecocyc::MANNONOXIDOREDUCT-MONOMER (486 letters) >FitnessBrowser__Caulo:CCNA_01554 Length = 482 Score = 316 bits (810), Expect = 1e-90 Identities = 197/466 (42%), Positives = 260/466 (55%), Gaps = 11/466 (2%) Query: 11 VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIE 70 VA P++D +L+ +VH G GAFHRAHQA Y LL + D WG+C V+L R + Sbjct: 25 VAIPTYDRDKLQIGVVHFGPGAFHRAHQAHYFDQLL-AHDPRWGVCAVSLKSPGVR---D 80 Query: 71 NLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEK 130 LK Q LYT+A+ AE+T +I+GS+ E L D + +A P T +V+LTVTEK Sbjct: 81 ALKPQDGLYTLAQLDAETT-FRIVGSILEVLVAPEDP-PSVFARLAAPTTRLVTLTVTEK 138 Query: 131 GYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRE 190 GY +A+G LD ++P I HDL NP P+SA+GY+VE LR R GL + V++CDN+ + Sbjct: 139 GYTL-SANGGLDESHPDIVHDLANPREPRSAVGYLVEGLRRRFAAGLAPYAVVACDNLAD 197 Query: 191 NGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPC 250 NG K AV+ A D LAAWI+ FP TMVD I PA G+ D Sbjct: 198 NGWRLKAAVVAYAAKLDESLAAWIDREGRFPRTMVDSITPATDDALRARTLAATGLEDAW 257 Query: 251 AIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGG 310 I E F QWV+ED PD VG DV FE KLR+LNG HS LAY+G L G Sbjct: 258 PIQREAFAQWVVEDVLPADGPDLASVGVIMTDDVRGFERAKLRLLNGVHSTLAYVGILRG 317 Query: 311 YETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQI 370 +ET+ + V++P A +M ++ PTL+ P G DL AYA ++ RF NP +RH QI Sbjct: 318 HETVFEAVSDPTLAALASDMMAKDIIPTLTPPRGLDLQAYADAILGRFRNPEIRHLLAQI 377 Query: 371 AMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEF 430 A DGSQKLP R+L + L+ G S LA+ +A WMR+ + G AI VDP+ Sbjct: 378 AWDGSQKLPFRILGTLTETLEAGRSIERLAVPLAAWMRFVALRAKAGEAI--VDPLQDRL 435 Query: 431 QKIN--AQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQL 474 + A + + V A L L +F L + FV A+ AY L Sbjct: 436 LALGLAATGEASADVAAFLALDSVFPASLAGDPRFVSALEKAYADL 481 Lambda K H 0.320 0.135 0.408 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: 612 Number of extensions: 35 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: 486 Length of database: 482 Length adjustment: 34 Effective length of query: 452 Effective length of database: 448 Effective search space: 202496 Effective search space used: 202496 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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