Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate BPHYT_RS28510 BPHYT_RS28510 dioxygenase
Query= curated2:P39160 (486 letters) >FitnessBrowser__BFirm:BPHYT_RS28510 Length = 492 Score = 363 bits (933), Expect = e-105 Identities = 207/460 (45%), Positives = 259/460 (56%), Gaps = 10/460 (2%) Query: 11 VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIE 70 V P++D + L IVHLG GAFHRAHQALYT H L + D WGI V+L + E Sbjct: 19 VVVPAYDRASLAPGIVHLGLGAFHRAHQALYTEHALRAGDHRWGIVGVSLRRADTS---E 75 Query: 71 NLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEK 130 L Q LY V + + L++IG++ +L +L+AM P+ IVSLT+TEK Sbjct: 76 ALTAQDHLYAVDVRDGTADSLQVIGALIASLVAP-QSPAAVLDAMTDPRCHIVSLTITEK 134 Query: 131 GYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRE 190 GYC + ASG L ++P I HDL AP+SAIG++V AL LRR GL FTV+SCDN+ Sbjct: 135 GYCRNPASGALQFDHPDIAHDLRAAAAPRSAIGFVVRALALRRAAGLGPFTVLSCDNLPS 194 Query: 191 NGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPC 250 NG + L A+ DP LA WIE FP TMVDRIVP T +A QLG D Sbjct: 195 NGDTMRALTLAFARETDPALADWIELEAAFPNTMVDRIVPLTTDADRLRVAKQLGADDAW 254 Query: 251 AIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGG 310 + EPF QWVIED F RP W++ GA V D P+E KLRMLNG+HS LAYLG L G Sbjct: 255 PVITEPFSQWVIEDRFAGPRPAWERAGATLVGDARPYEQAKLRMLNGAHSALAYLGSLIG 314 Query: 311 YETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQI 370 Y+T+ + PA +++ E PTLS P L Y L RF N +L HR QI Sbjct: 315 YDTVDQAIGAPAVLNFVESMLRDEVEPTLSRPA---LATYRAELFARFRNTALDHRLQQI 371 Query: 371 AMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPM---L 427 A DGSQKLPQR L+ VR +L++G LA +AGW+ Y G DE G + DP+ L Sbjct: 372 ATDGSQKLPQRWLESVRANLKSGAPTERLAFALAGWIAYLGGHDETGRTYAIADPLADRL 431 Query: 428 AEFQKINAQYQGADRVKALLGLSGIFADDLPQNADFVGAV 467 E + AD V+ L + IF DL + FV V Sbjct: 432 TEAVRATLHADAADAVRTLFEIEPIFGRDLCAHPRFVAQV 471 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: 657 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 486 Length of database: 492 Length adjustment: 34 Effective length of query: 452 Effective length of database: 458 Effective search space: 207016 Effective search space used: 207016 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