Align Galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (characterized)
to candidate PfGW456L13_3478 Altronate dehydratase (EC 4.2.1.7)
Query= SwissProt::P39829 (523 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3478 Length = 510 Score = 286 bits (733), Expect = 1e-81 Identities = 170/493 (34%), Positives = 265/493 (53%), Gaps = 21/493 (4%) Query: 16 IKVHDTDNVAIIVNDNGLKAGTRFP-DGLELIEHIPQGHKVALLDIPANGEIIRYGEVIG 74 I++ DNV + + + GT + L ++ +P GHK+A I +++Y VIG Sbjct: 10 IRLDPADNVVVARVE--IPTGTAITNESLTTLQDVPLGHKIAARMIEKGQPVLKYNTVIG 67 Query: 75 YAVRAIPRGSWIDESMVVLPEAPPLHTLPLATKVPEPLPPLEGYTFEGYRNADGSVGTKN 134 YA +P G+W+ + E + L + LP + TF+G DG V T+N Sbjct: 68 YASEDLPPGTWMHSHNIEFGETARDYRYGLDYVPTDLLPADKRATFQGIIREDGRVATRN 127 Query: 135 LLGITTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCGVAINAPAAVVPIRT 194 LGI +C A V + + + L +PN+DGVV H GCG+ + + RT Sbjct: 128 YLGIFVVGNCGATVARKIANHFDEERLAAFPNIDGVVPFVHEIGCGMEMTGEPMNLLRRT 187 Query: 195 IHNISLNPNFGGEVMVIGLGCEK------LQPERLLTGTDDVQAIPVESASIVSLQDEKH 248 I + N G ++ I LGCE+ ++ E+L+ G D ++++ ++ Sbjct: 188 IGGHIKHANTAGGLL-IALGCERNNIYGFIEQEQLVLG-DMLKSLVIQDVG--------- 236 Query: 249 VGFQSMVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGSDAFSGVTANPAVGYASD 308 G ++ V+ +++ + L + N QRET A L++GMQCGGSD FSG++ANPA+G A D Sbjct: 237 -GVKTAVDQGIKMIQAMLPQANAVQRETVSAEHLIIGMQCGGSDGFSGLSANPALGAAVD 295 Query: 309 LLVRCGATVMFSEVTEVRDAIHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGKTDRSANPS 368 +LVR G T + SE +E+ H LT RA EVG++L++ ++W+ Y T + S Sbjct: 296 ILVRHGGTAILSETSEIFGVEHTLTARAATPEVGRKLIDRIDWWLEYNKGRDTQINGRVS 355 Query: 369 PGNKKGGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKRGLIYAATPASDFVCGTQQVA 428 PGN GGLANV+EK+LG K G + +++V T GL++ TP D V T Q+A Sbjct: 356 PGNNAGGLANVLEKSLGGAKKGGNAPLMDVYEYAYPVTTHGLVFMDTPGYDPVSATGQIA 415 Query: 429 SGITVQVFTTGRGTPYGLMAVPVIKMATRTELANRWFDLMDINAGTIATGEETIEEVGWK 488 G + FTTGRG+ +G + P K+A+ + + NR D MDIN G I G++TI+++G + Sbjct: 416 GGANMIAFTTGRGSCFGSVPAPTFKLASNSPMFNRMSDDMDINCGQIIDGDKTIQQMGQE 475 Query: 489 LFHFILDVASGKK 501 +F +L ASG K Sbjct: 476 IFERLLTHASGDK 488 Lambda K H 0.317 0.136 0.403 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: 647 Number of extensions: 25 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: 523 Length of database: 510 Length adjustment: 35 Effective length of query: 488 Effective length of database: 475 Effective search space: 231800 Effective search space used: 231800 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: 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