Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate 15664 b1542 predicted mannonate dehydrogenase (NCBI)
Query= ecocyc::MANNONOXIDOREDUCT-MONOMER (486 letters) >FitnessBrowser__Keio:15664 Length = 486 Score = 531 bits (1369), Expect = e-155 Identities = 274/472 (58%), Positives = 336/472 (71%), Gaps = 4/472 (0%) Query: 14 PSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIENLK 73 P +D + L RIVHLG GAFHRAHQ +Y L SDWG EVNL+ G + I +L+ Sbjct: 13 PVYDLNNLAPRIVHLGFGAFHRAHQGVYADILATEHFSDWGYYEVNLIGGEQQ--IADLQ 70 Query: 74 KQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYC 133 +Q LYTVAE A+ +++G +K+ALH +IDG E +L AM PQ AIVSLT+TEKGY Sbjct: 71 QQDNLYTVAEMSADVWTARVVGVVKKALHVQIDGLETVLAAMCEPQIAIVSLTITEKGYF 130 Query: 134 ADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENGH 193 A+GQL L++P++ D++NP PK+A G IVEAL R+ GL AFTVMSCDN+ ENGH Sbjct: 131 HSPATGQLMLDHPMVAADVQNPHQPKTATGVIVEALARRKAAGLPAFTVMSCDNMPENGH 190 Query: 194 VAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIA 253 V + V AQA D +LA WIE+NVTFP TMVDRIVPA T +TL +I GV DP +A Sbjct: 191 VMRDVVTSYAQAVDVKLAQWIEDNVTFPSTMVDRIVPAVTEDTLAKIEQLTGVRDPAGVA 250 Query: 254 CEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYET 313 CEPFRQWVIEDNFV GRP+W+K GA+ V+DV+P+E MKLRMLNGSHSFLAYLGYL GY+ Sbjct: 251 CEPFRQWVIEDNFVAGRPEWEKAGAELVSDVLPYEEMKLRMLNGSHSFLAYLGYLAGYQH 310 Query: 314 IADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMD 373 I D + + YR AA+ LM+QEQAPTL + +G DL YA LI R+SNP+LRHRTWQIAMD Sbjct: 311 INDCMEDEHYRYAAYGLMLQEQAPTLKV-QGVDLQDYANRLIARYSNPALRHRTWQIAMD 369 Query: 374 GSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEFQK- 432 GSQKLPQR+LD VR HL + + LALGVAGWMRY GVDEQGN I++ DP+L QK Sbjct: 370 GSQKLPQRMLDSVRWHLAHDSKFDLLALGVAGWMRYVGGVDEQGNPIEISDPLLPVIQKA 429 Query: 433 INAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGARECVA 484 + + +G RV++LL + IF DDLP N+ F VT Y L GA+ VA Sbjct: 430 VQSSAEGKARVQSLLAIKAIFGDDLPDNSLFTARVTETYLSLLAHGAKATVA 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: 703 Number of extensions: 25 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: 486 Length adjustment: 34 Effective length of query: 452 Effective length of database: 452 Effective search space: 204304 Effective search space used: 204304 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