Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate GFF372 Psest_0373 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily
Query= SwissProt::P42206 (451 letters) >FitnessBrowser__psRCH2:GFF372 Length = 463 Score = 605 bits (1559), Expect = e-177 Identities = 294/462 (63%), Positives = 360/462 (77%), Gaps = 19/462 (4%) Query: 7 SQAATGAPVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEG 66 SQ + P + ++V+PVAGHDSMLLNL GAH P FTRN+++LTD++G+ G+GEVPGGEG Sbjct: 2 SQPFSATPHVKSMQVIPVAGHDSMLLNLCGAHAPYFTRNLVLLTDNAGNTGIGEVPGGEG 61 Query: 67 IRKTLEDARHLLINQSIGNYQSLLNKVRNAFADRDVGG----RGLQTFDLRIAV------ 116 IR+ LE R L+I Q IG Y LN +R+A A G R T + AV Sbjct: 62 IRQALERCRALVIGQPIGLYNRTLNSLRSAIASNAAGTPQATRHEVTSEAEAAVLKQPHE 121 Query: 117 ------HAVTAVESALLDLLGQHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGY 170 + +TAVE+ALLDLLGQHL VPVA LLG GQQRDAV ML YLFY+GDR +TDL Y Sbjct: 122 INLRLDNVITAVEAALLDLLGQHLDVPVAELLGSGQQRDAVPMLAYLFYIGDRQRTDLPY 181 Query: 171 RSEHEADNEWFRLRNKEALTPESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALS 230 + D W+ LR+++ALTP+++ LAEAA RYGF DFKLKGGV+RGE+E+ A+ A+ Sbjct: 182 LASTGED--WYHLRHQQALTPDAIARLAEAARARYGFADFKLKGGVMRGEEEMQAIAAIK 239 Query: 231 ERFPDARITLDPNGAWSLKEAVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGL 290 RFPDAR+TLDPNGAWSL EA+ALC+ Q H+LAYAEDPCG ENGYSGRE+MAEF+R+TG+ Sbjct: 240 ARFPDARVTLDPNGAWSLDEAIALCKGQGHLLAYAEDPCGPENGYSGREIMAEFKRATGI 299 Query: 291 RTATNMIATDWRQMGHAIQLQSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHF 350 TATNM+ATDWRQMGH+++L++VDIPLADPHFWTMQGSVR+AQMC ++GLTWGSHSNNHF Sbjct: 300 PTATNMVATDWRQMGHSLRLEAVDIPLADPHFWTMQGSVRLAQMCEQFGLTWGSHSNNHF 359 Query: 351 DISLAMFTHVAAAAPGNITAIDTHWIWQDGQ-RLTKEPLQIKGGLVEVPKKPGLGVELDW 409 D+SLAMFTH AAAAPG ITAIDTHWIWQ+GQ RLT+EPLQI G V VP++PGLG+E D Sbjct: 360 DVSLAMFTHAAAAAPGRITAIDTHWIWQEGQERLTREPLQIVDGQVRVPERPGLGIEPDM 419 Query: 410 DALMKAHEVYKSMGLGARDDATAMRYLVSGWEFNNKRPCMVR 451 D +M AHE+YK + G+RDDA AMRYLV GW ++ K+P + R Sbjct: 420 DRIMAAHELYKKVASGSRDDAMAMRYLVPGWTYDPKKPSLGR 461 Lambda K H 0.319 0.135 0.410 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: 641 Number of extensions: 24 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: 451 Length of database: 463 Length adjustment: 33 Effective length of query: 418 Effective length of database: 430 Effective search space: 179740 Effective search space used: 179740 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: 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