Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate RR42_RS33305 RR42_RS33305 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__Cup4G11:RR42_RS33305 Length = 579 Score = 363 bits (933), Expect = e-105 Identities = 215/571 (37%), Positives = 324/571 (56%), Gaps = 21/571 (3%) Query: 4 TPERRLRSEQWFNDPAHADMTAL-YVERYMNYGMTREELQSGRPIIGIAQTGSDLTPCNR 62 TPE LRS +WF A D+ + + R M G + +E RPII I T SD+ PC+ Sbjct: 7 TPET-LRSARWF---APDDLRSSGHRSRIMQMGYSPDEWLD-RPIIAIINTWSDINPCHS 61 Query: 63 HHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGV 122 H + VK GI AGG P+E P ++E + +PT L RN+ + E++ +P+DG Sbjct: 62 HFKQRVDDVKRGILQAGGFPIELPAISLSESAVKPTTMLYRNMLAMEAEELIRSHPVDGA 121 Query: 123 VLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEI 182 VL GCDKTTP LM A++ +PAI + GPML G+ KG ++GSG+ W + AG I Sbjct: 122 VLMGGCDKTTPGLLMGASSAGVPAIYVPAGPMLRGNWKGNVLGSGSDAWKFWDERRAGNI 181 Query: 183 DYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATG 242 ++ + + S G C TMGTA +M A+AEA+GM+LPG +SIPA +M G Sbjct: 182 SKTEWIGIEGGIARSHGTCMTMGTASTMTAIAEAIGMTLPGASSIPAADANHIRMCSEAG 241 Query: 243 KRICELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQR 302 +RI ++V +D+ P +I TR +FENAIAVA A+G S+N H+IA+AR G ++ L+D+ + Sbjct: 242 RRIVDMVWEDLTPQRIQTRASFENAIAVAMAMGCSTNAIIHVIAMARRAGHDIGLEDFDK 301 Query: 303 IGEDVPLLVNCMPAG-KYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGRTIGEIVSS 361 VP++ N P+G KYL E F AGG+P++M+ + + +L+ D TV+GRT+GE ++ Sbjct: 302 TSRHVPVIANIRPSGDKYLMEDFFYAGGLPALMNRI--SDKLNLDALTVTGRTLGENIAG 359 Query: 362 SLTSNADVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENSFE 420 + N DVI + L VL GN D ++K S A K + G Sbjct: 360 AEVYNDDVIRTKENALYQEGALAVLKGNIAPDGCVIKPS----ACEKRFFKHTGP----- 410 Query: 421 ARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGID 480 A+VF+ ++ LD+ IL++R G G PG E + P L++QG+ Sbjct: 411 --ALVFDDYPSMKEAVERDDLDVTADHILILRNAGPQGGPGMPEWGMLPIPKKLVQQGVR 468 Query: 481 SLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMA 540 + + D R SGTS IL++SPE+ +GG AL++T D + VD++ R+++L + DEE+A Sbjct: 469 DMLRMSDARMSGTSYGACILHVSPESYIGGPFALVRTGDMISVDIDRRSIHLEVSDEELA 528 Query: 541 RRRLEWTPNIPPSQTPWQELYRQLVGQLSTG 571 RR+ WTP P + ++ + + Q + G Sbjct: 529 RRKAAWTPPPPRFGRGYGWMFSKHIRQANDG 559 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: 966 Number of extensions: 48 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: 579 Length adjustment: 37 Effective length of query: 557 Effective length of database: 542 Effective search space: 301894 Effective search space used: 301894 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