Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate AZOBR_RS31260 AZOBR_RS31260 dihydroxy-acid dehydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__azobra:AZOBR_RS31260 Length = 608 Score = 767 bits (1981), Expect = 0.0 Identities = 380/608 (62%), Positives = 464/608 (76%), Gaps = 14/608 (2%) Query: 1 MSDT---PKH-------RLRSEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGI 50 MSDT P+H RLRS WF++P + DMTALY+ERY+N+G+TREELQSG PIIGI Sbjct: 1 MSDTKPSPQHPEIGSGRRLRSRAWFDNPDNPDMTALYLERYLNFGLTREELQSGAPIIGI 60 Query: 51 AQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGL 110 AQTGSDL+PCNRHHL LA+R++ GIR AGGI +EFPVHPI E +RPTA++DRNLAYLGL Sbjct: 61 AQTGSDLSPCNRHHLVLAERLREGIRTAGGIAIEFPVHPIQETGKRPTASIDRNLAYLGL 120 Query: 111 VEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVL 170 VE+LHGYPLDGVVLT GCDKTTPACLMAAAT ++PAI LS GPML+G +GE GSGT++ Sbjct: 121 VEVLHGYPLDGVVLTIGCDKTTPACLMAAATVNIPAIALSVGPMLNGWFRGERTGSGTIV 180 Query: 171 WHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAP 230 W AR +MAAGEIDY+GF+E+ +++PS G+CNTMGTA +MN+LAE LGM LPG A+IPAP Sbjct: 181 WKARQMMAAGEIDYQGFIELVASSAPSTGYCNTMGTASTMNSLAEVLGMQLPGSAAIPAP 240 Query: 231 YRERGQMAYATGKRICDLVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARH 290 YRER Q Y TGKRI ++VR+D++PS I+TR AF NAI V SA+G S+N P H+ AIA+H Sbjct: 241 YRERQQADYETGKRIVEMVREDLKPSDILTRDAFLNAIVVNSAIGGSTNAPIHINAIAKH 300 Query: 291 MGVELSLEDWQRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATV 350 +GV L++EDWQ G DVPLLVN PAG+YLGE FHRAGGVP+V+ +L G + E TV Sbjct: 301 IGVPLTVEDWQTHGHDVPLLVNLQPAGEYLGEDFHRAGGVPAVVAQLMGKGLIREGAPTV 360 Query: 351 SGKTIGEIVSNSLTSNTDVIHPFDTPLKHRAGFIVLSGNFFDSAIMKMSVVGEAFRKTYL 410 +G+TIGE +T VIHP D PL AGF+VL GN F +AIMK SV+ + FR+ YL Sbjct: 361 NGRTIGENCRRQPILDTRVIHPIDEPLMPNAGFVVLRGNLFGAAIMKTSVISDEFRERYL 420 Query: 411 SEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAP 470 S P +FE + +VF+GPEDYH RIDDP+L ID ILVIRG G +GYPG+AEVVNM P Sbjct: 421 SNPQDPEAFEGKVVVFDGPEDYHHRIDDPSLGIDAYTILVIRGTGPIGYPGAAEVVNMRP 480 Query: 471 PAALIKQGIDSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTV 530 PA LIKQG+ SLPC+GDGRQSGTS SPSILN SPEAA GGGLALL++ DR+++DL + Sbjct: 481 PATLIKQGVHSLPCIGDGRQSGTSGSPSILNASPEAAAGGGLALLRSGDRVRIDLRRGSA 540 Query: 531 NLLIDDAEMAQRRREWIP----NIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIAR 586 ++LI + E+A RR IPPSQTPWQE+ R +V QL G L+PA + RV Sbjct: 541 DILIPEGELADRRAALEAAGGYPIPPSQTPWQEIQRGIVDQLDEGMVLKPAVKYQRVAQT 600 Query: 587 SGEPRHSH 594 G PR +H Sbjct: 601 MGIPRDNH 608 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: 1191 Number of extensions: 56 Number of successful extensions: 2 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: 608 Length adjustment: 37 Effective length of query: 557 Effective length of database: 571 Effective search space: 318047 Effective search space used: 318047 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