Align glucarate dehydratase (EC 4.2.1.40) (characterized)
to candidate 16872 b2788 predicted glucarate dehydratase (NCBI)
Query= BRENDA::Q6FFQ2 (444 letters) >FitnessBrowser__Keio:16872 Length = 446 Score = 591 bits (1524), Expect = e-173 Identities = 283/443 (63%), Positives = 344/443 (77%), Gaps = 4/443 (0%) Query: 4 STPIIQSVRAIPVAGHDSMLLNLSGAHAPYFTRNLLVIEDNSGNIGVGEIPGGEKILATL 63 S+P+I ++ IPVAGHDSMLLN+ GAH YFTRN++V+ DN+G+ G+GE PGG+ I TL Sbjct: 5 SSPVITDMKVIPVAGHDSMLLNIGGAHNAYFTRNIVVLTDNAGHTGIGEAPGGDVIYQTL 64 Query: 64 NDAKSLILGQPIGEYKNLLKKIHQ--TFADRDSGGRGNQTFDLRTTVHVVTAYESALLDL 121 DA ++LGQ + +++++H+ AD D+ G+G TF+LR V+ V A E+ALLDL Sbjct: 65 VDAIPMVLGQEVARLNKVVQQVHKGNQAADFDTFGKGAWTFELR--VNAVAALEAALLDL 122 Query: 122 LGKHLNVNVASLLGDGQQRDEVEVLGYLFFIGDRKQTSLDYATSTHLNHDWYQVRHEKAL 181 LGK LNV V LLG G+QR+ + VLGYLF+IGDR +T L Y +T NH+WYQ+RH+KA+ Sbjct: 123 LGKALNVPVCELLGPGKQREAITVLGYLFYIGDRTKTDLPYVENTPGNHEWYQLRHQKAM 182 Query: 182 TPEAIQRLAEASYDRYGFKDFKLKGGVLHGEQEAEAVTAIARRFPDARVTLDPNGAWYLD 241 EA+ RLAEAS DRYGFKDFKLKGGVL GEQE + V A+ +RFPDAR+T+DPNGAW LD Sbjct: 183 NSEAVVRLAEASQDRYGFKDFKLKGGVLPGEQEIDTVRALKKRFPDARITVDPNGAWLLD 242 Query: 242 EAIGLGKHLKGVLAYAEDPCGAEQGYSSREIMAEFKRATGLPTATNMIATDWREMSHSIQ 301 EAI L K L VL YAEDPCGAEQG+S RE+MAEF+RATGLP ATNMIAT+WREM H++ Sbjct: 243 EAISLCKGLNDVLTYAEDPCGAEQGFSGREVMAEFRRATGLPVATNMIATNWREMGHAVM 302 Query: 302 LQAVDIPLADPHFWTLEGSVRVSQLCNMYNLTWGSHSNNHFDVSLAMFTHVAAAAVGNVT 361 L AVDIPLADPHFWTL G+VRV+QLC+ + LTWG HSNNHFD+SLAMFTHV AAA GN T Sbjct: 303 LNAVDIPLADPHFWTLSGAVRVAQLCDDWGLTWGCHSNNHFDISLAMFTHVGAAAPGNPT 362 Query: 362 AIDTHWIWQEGTDHLTKQPLEIKGGKIQVPSVPGLGVELDWDNINRAHELYKAKGLGARN 421 AIDTHWIWQEG LT+ PLEIK GKI VP PGLGVELDW+ + +AHE YK GARN Sbjct: 363 AIDTHWIWQEGDCRLTQNPLEIKNGKIAVPDAPGLGVELDWEQVQKAHEAYKRLPGGARN 422 Query: 422 DADAMQFMVPNWKFDHKKPCLVR 444 DA MQ+++P W FD K+P R Sbjct: 423 DAGPMQYLIPGWTFDRKRPVFGR 445 Lambda K H 0.318 0.135 0.409 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: 637 Number of extensions: 18 Number of successful extensions: 2 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: 444 Length of database: 446 Length adjustment: 32 Effective length of query: 412 Effective length of database: 414 Effective search space: 170568 Effective search space used: 170568 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: 51 (24.3 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