Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 6937660 Sama_1810 phosphogluconate dehydratase (RefSeq)
Query= reanno::ANA3:7024896 (586 letters) >FitnessBrowser__SB2B:6937660 Length = 608 Score = 189 bits (481), Expect = 2e-52 Identities = 155/518 (29%), Positives = 253/518 (48%), Gaps = 50/518 (9%) Query: 54 IGICNTWSELTPCNG---HLRELAQRVKNGI----REAGGIPVEFPVFSNGESNLRPSAM 106 IGI ++++ + H EL + N + + AGG+P + G+ + S + Sbjct: 68 IGIVTAFNDMLSAHQPYEHYPELLKAACNEVGSVAQVAGGVPAMCDGVTQGQPGMELS-L 126 Query: 107 LTRNLAAMDTEEAIRGNPIDGVVLLVGCDKTTPALLMGAASCD-LPTIVVTGGPMLNG-- 163 L+R + AM T + N DG +LL CDK P LL+GA S LP + V GPM +G Sbjct: 127 LSREVIAMATAVGLSHNMFDGALLLGVCDKIVPGLLIGAMSFGHLPMLFVPAGPMRSGIP 186 Query: 164 -KHKGKDVGSGTLVWELHQEYKAGNISLAAFMNAEADMSRSTGTCNTMGTASTMACMVET 222 K K + + Q++ G + A + AEA S GTC GTA++ ++E Sbjct: 187 NKEKAR----------VRQKFAEGKVDREALLEAEASSYHSAGTCTFYGTANSNQLVLEV 236 Query: 223 LGVSLPHNATIPAVDSRRQVLAHMSGMRIVDMVKEDLTLS---KILSRDAFINAIKVNAA 279 +G+ LP ++ + D R L+ M+ ++ + + L S +I++ + +N I A Sbjct: 237 MGLQLPGSSFVNPDDPLRTELSKMAAKQVCRLTENGLQYSPIGEIVNEKSVVNGIVALLA 296 Query: 280 IGGSTNAVIHLKAIAGRIGVELSLDDWRH-GYTVPTIVNLKPSGQYLMEDFYYAGGLPAV 338 GGSTN +H+ A A G+ ++ DD+ VP + + P+G + F+ AGG+ + Sbjct: 297 TGGSTNLTMHIVAAARAAGIIINWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFL 356 Query: 339 LRQLFEHDLLSKNTLTVNAASLWDNVKE--------------APCYNQEVIMSLENPLVE 384 +++L + L+ ++ TV L +E +QEV+ + P Sbjct: 357 MKELLDAGLIHEDVNTVAGYGLRRYTQEPRLIDGQLTWVDGPVTSLDQEVLRGVAEPFQS 416 Query: 385 NGGIRVLRGNLAPRGAVIKPSAASAHLMQHRGKAVVFESFDDYNARIGDPELDIDENSIM 444 NGG+++++GNL AVIK SA AVV + + +A ELD D ++ Sbjct: 417 NGGLKLMKGNLG--RAVIKVSAVQEQHRIVEAPAVVIDDQNKLDALFKAGELDRD--CVV 472 Query: 445 VLKNCGPKGYPGMAEVGNM-GLPPKLLKKGIKDMVRISDARMSGTAFGTV--VLHVAPEA 501 V+K GPK GM E+ + + L +G K + ++D RMSG A G V +H+ PEA Sbjct: 473 VVKGQGPKA-NGMPELHKLTPILGTLQDRGFK-VALMTDGRMSG-ASGKVPAAIHLTPEA 529 Query: 502 QALGPLAAVQNGDMIALDTYAGTLQLEISDQELQARLA 539 G +A VQ+GD+I ++ G L L +S EL++R A Sbjct: 530 LDGGLIAKVQDGDLIRINAITGELSLLVSAPELESRTA 567 Lambda K H 0.318 0.135 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: 789 Number of extensions: 33 Number of successful extensions: 6 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: 586 Length of database: 608 Length adjustment: 37 Effective length of query: 549 Effective length of database: 571 Effective search space: 313479 Effective search space used: 313479 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 (21.7 bits) S2: 53 (25.0 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