Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate BWI76_RS15490 BWI76_RS15490 mannitol dehydrogenase family protein
Query= ecocyc::MANNONOXIDOREDUCT-MONOMER (486 letters) >FitnessBrowser__Koxy:BWI76_RS15490 Length = 487 Score = 551 bits (1419), Expect = e-161 Identities = 280/473 (59%), Positives = 343/473 (72%), Gaps = 4/473 (0%) Query: 14 PSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIENLK 73 P++D +RL RIVHLG GAFHRAHQA+Y L SDWG EVNL+ G + I +L+ Sbjct: 13 PAYDRNRLIPRIVHLGFGAFHRAHQAVYADILATEHGSDWGYTEVNLIGGEQQ--IADLQ 70 Query: 74 KQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYC 133 KQ LLYTVAE A++ +++G +K+A+H ++DG E +L M PQ AIVSLT+TEKGYC Sbjct: 71 KQDLLYTVAEMSADAWTARVVGVVKQAMHAQVDGLESVLAKMCEPQVAIVSLTITEKGYC 130 Query: 134 ADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENGH 193 ASG+L L++PLI DL+NP PKSA G +VEAL R+ GL AF+VMSCDN+ ENGH Sbjct: 131 HSPASGELQLDHPLIAADLQNPRQPKSAPGVVVEALARRKAAGLPAFSVMSCDNMPENGH 190 Query: 194 VAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIA 253 V + + A+A D LA WI NVTFP TMVDRIVPA T +TL +IA GV DP A+A Sbjct: 191 VMRNVICAYARAVDADLAEWITRNVTFPSTMVDRIVPAVTADTLDKIAQLTGVRDPAAVA 250 Query: 254 CEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYET 313 CEPFRQWVIEDNFV GRP W+K GA+ V+DV+PFE MKLRMLNGSHSFLAYLGYL GY+ Sbjct: 251 CEPFRQWVIEDNFVAGRPQWEKAGAELVSDVLPFEEMKLRMLNGSHSFLAYLGYLAGYQH 310 Query: 314 IADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMD 373 I D + + YR+AA LM+ EQAPTLS+ +G DL YA LLIER+SNP+L+HRTWQIAMD Sbjct: 311 INDCMQDANYRRAAHTLMLAEQAPTLSV-KGVDLARYAGLLIERYSNPALKHRTWQIAMD 369 Query: 374 GSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEF-QK 432 GSQKLPQR+LD +R HL +GG + LA+GVAGWMRY GVD+QG AI++ DPML Q Sbjct: 370 GSQKLPQRMLDSIRWHLADGGDFPLLAMGVAGWMRYVSGVDDQGQAIEISDPMLPVITQT 429 Query: 433 INAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGARECVAA 485 + G +RV+ALLG+ IF LP+ + FV AV AY L GA+ VAA Sbjct: 430 VQNSEDGEERVRALLGIEAIFGLSLPKESRFVNAVVRAYLSLQAHGAKATVAA 482 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: 721 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: 487 Length adjustment: 34 Effective length of query: 452 Effective length of database: 453 Effective search space: 204756 Effective search space used: 204756 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