Align Galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (characterized)
to candidate AZOBR_RS31430 AZOBR_RS31430 galactarate dehydratase
Query= SwissProt::P39829 (523 letters) >FitnessBrowser__azobra:AZOBR_RS31430 Length = 507 Score = 342 bits (877), Expect = 2e-98 Identities = 203/496 (40%), Positives = 288/496 (58%), Gaps = 11/496 (2%) Query: 16 IKVHDTDNVAIIVNDNGLKAGTRFPD-GLELIEHIPQGHKVALLDIPANGEIIRYGEVIG 74 I++H DNV + D L GT PD G+ IP GHKVA+ I + +Y +VIG Sbjct: 6 IRLHPADNVVVAGAD--LPEGTTLPDTGVVARTTIPSGHKVAVQAIAVGEPVRKYNQVIG 63 Query: 75 YAVRAIPRGSWIDESMVVLPEAPPLHTLPLATKVPEPL-PPLEGYTFEGYRNADGSVGTK 133 +A I G + + + ++ A P L P E TF+G DG V T+ Sbjct: 64 FATAPIAPGDHVHVHNIGVGDSFERDYAFSADVHPTDLVPEAERATFQGIVRPDGRVATR 123 Query: 134 NLLGITTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCGVAINAPAAVVPIR 193 N +GI T+V+C A + D L YPN+DGVV L H YGCG+ A R Sbjct: 124 NYIGILTTVNCSATAARMIADQFRGDALAAYPNIDGVVALTHSYGCGMGSQGDAIDALRR 183 Query: 194 TIHNISLNPNFGGEVMVIGLGCEKLQPERLLTGTDDVQAIPVESASIVSLQDEKHVGFQS 253 TI + +PNF V+V+GLGCE Q ++L+ +V+ + + ++ +L ++ G + Sbjct: 184 TIAGYARHPNFAA-VLVLGLGCEVNQIDKLV----EVEGLTIGD-TLQTLAIQESGGTAA 237 Query: 254 MVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGSDAFSGVTANPAVGYASDLLVRC 313 V ++ L ++N +RET PAS L++ +QCGGSD +SG+TANPA+G+A DLL+R Sbjct: 238 TVRASVERIRALLPRVNDVKRETVPASHLILALQCGGSDGYSGITANPALGHAVDLLIRN 297 Query: 314 GATVMFSEVTEVRDAIHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGKTDRSANPSPGNKK 373 G T + SE EV A HLLT R+VN VG+ L+E + W+++Y + + + NPSPGNKK Sbjct: 298 GGTAVLSETPEVYGAEHLLTRRSVNPAVGETLVERIRWWEDYTSRTGGEMNNNPSPGNKK 357 Query: 374 GGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKRGLIYAATPASDFVCGTQQVASGITV 433 GGL ++EK+LG++AK+G + +VEV+ + T GL++ TP D V T QVA G V Sbjct: 358 GGLTTILEKSLGAVAKAGTTNLVEVVRYAEPITGPGLVFMDTPGYDPVSATGQVAGGANV 417 Query: 434 QVFTTGRGTPYGLMAVPVIKMATRTELANRWFDLMDINAGTIATGEETIEEVGWKLFHFI 493 FTTGRG+ +G P +K+AT T L + D MDI+ G IATG+ TIEEVG +F I Sbjct: 418 LCFTTGRGSVFGCKPTPSLKLATNTALFRKMPDDMDIDCGPIATGDATIEEVGRTIFQLI 477 Query: 494 LDVASGKKKTFSDQWG 509 LD ASG KKT S++ G Sbjct: 478 LDTASG-KKTKSEELG 492 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: 710 Number of extensions: 34 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: 523 Length of database: 507 Length adjustment: 35 Effective length of query: 488 Effective length of database: 472 Effective search space: 230336 Effective search space used: 230336 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