Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate N515DRAFT_2409 N515DRAFT_2409 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__Dyella79:N515DRAFT_2409 Length = 574 Score = 457 bits (1177), Expect = e-133 Identities = 252/574 (43%), Positives = 353/574 (61%), Gaps = 19/574 (3%) Query: 4 TPERRLR-SEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTPCNR 62 +P++ LR S++WF Y ++ ++ GRP+IGI T S+LTPCN Sbjct: 3 SPKKPLRRSQEWFG---REGKQGFYYRSWLKGLGLPNDMFDGRPVIGICNTWSELTPCNS 59 Query: 63 HHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGV 122 ELA+ VK G+ +AGG P+EFPV + E RPTA L RNLA + + E + P+DGV Sbjct: 60 SFRELAEHVKRGVYEAGGFPLEFPVMSLGETQMRPTAMLFRNLASMDVEESIRANPIDGV 119 Query: 123 VLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEI 182 VL GCDKTTPA +M AA+ +LP I LSGGP L G+ +G+ IGSGT + ++ AGE+ Sbjct: 120 VLLMGCDKTTPALMMGAASVNLPTIGLSGGPSLSGNWRGQPIGSGTGVIRMSEMVRAGEL 179 Query: 183 DYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATG 242 E F+E S G C TMGTA +M ++ EALG+SLP A+IPA R ++A+ +G Sbjct: 180 AQEEFVEAEACMQRSKGSCMTMGTASTMASMVEALGLSLPENAAIPAVDSRRFRLAHLSG 239 Query: 243 KRICELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQR 302 +RI E+V +D+R S+I+TR AFENAI +A+G S+N HL+A+A +GVEL+LDDW R Sbjct: 240 RRIVEMVHEDLRMSKILTRAAFENAIRANAAIGGSTNAVIHLLALAGRLGVELALDDWDR 299 Query: 303 IGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGRTIGEIVSSS 362 +G +P LVN P+G YL E F+ AGG+P+V+ E+ A LH T +GRT+G+ ++++ Sbjct: 300 LGSHLPCLVNLKPSGDYLMEDFYYAGGLPAVLREI--APHLHLGALTANGRTLGDNIATA 357 Query: 363 LTSNADVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENSFEA 421 N DVI P + PLK AG VL GN D A++K S + Sbjct: 358 PCWNRDVIRPIEEPLKREAGIAVLRGNLAPDGAVIKPSAASAHLLQ-----------HRG 406 Query: 422 RAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDS 481 RA+VFE +D+ ARIDD ALDIDE C++V++ G GYPG AEV NM P L+++GI Sbjct: 407 RAVVFENIDDFKARIDDEALDIDETCVMVLKNCGPRGYPGMAEVGNMPLPPKLLRRGITD 466 Query: 482 LPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMAR 541 + + D R SGT+ +L+ SPEAA GG LAL++ D +++D+ R ++L + D+E+AR Sbjct: 467 IVRISDARMSGTAYGTVVLHASPEAAAGGNLALVRDGDFIELDVPGRRLHLDLADDELAR 526 Query: 542 RRLEWTPNIPPSQTPWQELYRQLVGQLSTGGCLE 575 RR W PP + W +LY V Q G L+ Sbjct: 527 RRAAWKAP-PPPERGWAKLYVDHVQQAHLGADLD 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: 992 Number of extensions: 55 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: 574 Length adjustment: 36 Effective length of query: 558 Effective length of database: 538 Effective search space: 300204 Effective search space used: 300204 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