Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate Ac3H11_954 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_954 Length = 567 Score = 326 bits (836), Expect = 1e-93 Identities = 202/553 (36%), Positives = 308/553 (55%), Gaps = 17/553 (3%) Query: 21 GKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGF 80 GK+ +RS G F +P++G+ N S +TPCN+ L+ LA+ G+ EAGG Sbjct: 21 GKSRAPNRSMYYAMGYEEGDFV-KPMVGVANGHSTITPCNSGLQKLADAAIAGIEEAGGN 79 Query: 81 PVEFPVFSTGESTLRPTAMMFRNLAAMDV-----EESIRGNPVDGVVLLGGCDKTTPSLL 135 F + + T M +L + +V E + G +DGV+++GGCDK P L Sbjct: 80 AQVFGTPTISDGMAMGTEGMKYSLVSREVISDCIETCVGGQWMDGVLVVGGCDKNMPGGL 139 Query: 136 MGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMAR 195 MG ++PAI V GG +L G ++GKD+ + E +G++S + + E+ Sbjct: 140 MGMLRANVPAIYVYGGTILPGHYQGKDLNIVSVFEAVGENA-AGKLSDFDLKEIEKRAIP 198 Query: 196 SAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKEDLKPS 255 GSC M TA+TM+S EALG++L ++ + + ++ + + ++E +K+D+KP Sbjct: 199 GTGSCGGMYTANTMSSAFEALGISLPYSSTMANPHDEKMNSAKESAKVLIEAIKKDIKPR 258 Query: 256 DILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQPS 315 DI+TK++ ENA+ V A GGSTNAVLH LA+A GV+ S+DD++R+ P + +L+PS Sbjct: 259 DIVTKKSIENAVAVIMATGGSTNAVLHFLAIAHAAGVEWSIDDFERVRVKTPVLCDLKPS 318 Query: 316 GKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKGVVNY---NEDVILPR 372 GKYL + + AGG+P V+K + GLLH D +T+ G T+ +K V + ++DVI P Sbjct: 319 GKYLAVDLHRAGGIPQVMKVLLNAGLLHGDCLTIEGKTVAEVLKDVPDQPRADQDVIRPI 378 Query: 373 EKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDI 432 + G +A+L+GNL+P GAV K + ++ G A VFE + I + Sbjct: 379 NNPMYAQGHLAILKGNLSPEGAVAKITGLKNPVI--TGPARVFEDEQSALEAILAGKIKA 436 Query: 433 DETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMI-RISDARMSGTAYGTVILHT 491 + +MVL+Y GPKG PGM E+ + ++ G+ + + I+D R SG +G V+ H Sbjct: 437 GD--VMVLRYLGPKGGPGMPEM--LAPTGALIGAGLGESVGLITDGRFSGGTWGMVVGHV 492 Query: 492 APEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGGLYI 551 APEAA GG +A V GD I +D L L+VS+EE+ARRRAAW +P T G + Sbjct: 493 APEAAAGGTIAFVHEGDSITIDARQLLLELNVSEEEIARRRAAWTAPAPRYTRGVQAKFA 552 Query: 552 KTVMQADAGADLD 564 A GA LD Sbjct: 553 FNASSASKGAVLD 565 Lambda K H 0.318 0.135 0.402 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: 957 Number of extensions: 51 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: 579 Length of database: 567 Length adjustment: 36 Effective length of query: 543 Effective length of database: 531 Effective search space: 288333 Effective search space used: 288333 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: 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