Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate SM_b20115 SM_b20115 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__Smeli:SM_b20115 Length = 573 Score = 370 bits (950), Expect = e-107 Identities = 216/542 (39%), Positives = 308/542 (56%), Gaps = 20/542 (3%) Query: 9 LRSEQWFNDPAHADMTAL-YVERYMNYGMTREELQSGRPIIGIAQTGSDLTPCNRHHLEL 67 LRS +WF A D+ + + R M G ++ +PII I T SDL PC+ H Sbjct: 5 LRSARWF---APDDLRSSGHRSRLMQMGYDAKDWGE-KPIIAILNTWSDLNPCHAHFKHR 60 Query: 68 AQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGVVLTTG 127 VK G+ AGG P+E PV ++E S +PT L RN + E+L G+P+DG VL G Sbjct: 61 IDDVKRGVLQAGGFPVELPVQSLSESSLKPTTMLYRNFLAMEAEELLRGHPIDGAVLMGG 120 Query: 128 CDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGF 187 CDKTTPA +M A + LP I L GPML GH+KGE +GSG+ W + AG I E + Sbjct: 121 CDKTTPALVMGAISAGLPMIFLPSGPMLRGHYKGEHLGSGSDAWKYWDERRAGTITDEQW 180 Query: 188 MEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICE 247 + + + S GHC T GTA +M A+AE+LG++LPG +SIPA +M+ G+RI E Sbjct: 181 IGVEEGIARSYGHCMTFGTASTMTAIAESLGLTLPGASSIPAADANHIRMSTRCGRRIVE 240 Query: 248 LVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDV 307 +V + + P +I+T ++ NA AVA A G S+N HLIA+AR GV L+L+D I Sbjct: 241 MVHEKLGPEKIITEKSVANASAVAMATGCSTNAVVHLIAMARRAGVPLTLEDLDGISRTT 300 Query: 308 PLLVNCMPAGK-YLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGRTIGEIVSSSLTSN 366 P++ N P+GK YL E F+ AGG+ ++M E+++ LH D TVSG +G + + N Sbjct: 301 PVIANIRPSGKQYLMEDFYYAGGLRALMAEMKEL--LHLDAMTVSGFPLGATLEGAEVHN 358 Query: 367 ADVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIV 425 +DVI P P+ H VL GN D ++K S E R E A+V Sbjct: 359 SDVIRPLSNPIYHEGSLAVLKGNLAPDGCVVKPSACEERLR-----------VHEGPALV 407 Query: 426 FEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDSLPCL 485 F+ + A IDD LD+ +L++R G G PG E + P ++KQG + + Sbjct: 408 FDSYPEMKAAIDDEDLDVTPDHVLILRNAGPKGGPGMPEWGMLPIPKKILKQGYRDMLRI 467 Query: 486 GDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRRLE 545 D R SGTS IL+++PE+ VGG L+L++T D ++VD+ RT+++L+D+E +A RR Sbjct: 468 SDARMSGTSYGACILHVAPESHVGGPLSLVRTGDIIRVDVANRTIDMLVDEEILAMRRAA 527 Query: 546 WT 547 WT Sbjct: 528 WT 529 Lambda K H 0.319 0.135 0.407 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: 893 Number of extensions: 36 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: 594 Length of database: 573 Length adjustment: 36 Effective length of query: 558 Effective length of database: 537 Effective search space: 299646 Effective search space used: 299646 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