Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate RR42_RS18585 RR42_RS18585 dihydroxy-acid dehydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__Cup4G11:RR42_RS18585 Length = 577 Score = 454 bits (1168), Expect = e-132 Identities = 250/573 (43%), Positives = 349/573 (60%), Gaps = 18/573 (3%) Query: 4 TPKHRLRSEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTPCNRH 63 TP R RS+ WF LY N G+ ++ GRP+IGI T S+LTPCN H Sbjct: 7 TPPTR-RSQAWFGRLDRDGF--LYRSWLKNRGIPHDQFD-GRPVIGICNTYSELTPCNSH 62 Query: 64 HLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGVV 123 LA++VK G+ +AGG P+EFPV + E RPTA L RNLA + + E + G P+DGVV Sbjct: 63 FRTLAEQVKIGVWEAGGFPLEFPVMSLGETMLRPTAMLFRNLASMDVEESIRGNPIDGVV 122 Query: 124 LTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEID 183 L GCDKTTPA +M AA+ DLP I +SGGPML G +G +GSGT +W + AG++ Sbjct: 123 LLMGCDKTTPALMMGAASCDLPTIGVSGGPMLSGKFRGGELGSGTDVWKMSEQVRAGQMS 182 Query: 184 YEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGK 243 E F E + S GHC TMGTA +M ++ EALGMSLPG A+IPA R +A A+G+ Sbjct: 183 QEDFFEAESCMHRSHGHCMTMGTASTMASMVEALGMSLPGNAAIPAVDGRRNVLARASGR 242 Query: 244 RICDLVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRI 303 RI ++V+ ++ S+I+TR AFENAI V +A+G S+N HL+AIA +GVEL LEDW + Sbjct: 243 RIVEMVKDNLVMSKILTRDAFENAIRVNAAIGGSTNAVIHLLAIAGRIGVELKLEDWDAL 302 Query: 304 GEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVSNSL 363 G ++P L++ P+G++L E F+ AGG+P+V+ EL+ L D TV+GKT+ + ++ Sbjct: 303 GHELPCLLDLQPSGRHLMEDFYYAGGLPAVIRELESV--LARDALTVNGKTLWDNCKDAP 360 Query: 364 TSNTDVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENSFEAR 422 N +VIH F P K AG VL GN D A++K S A K R Sbjct: 361 NWNREVIHAFGAPFKANAGIAVLRGNLCPDGAVIKPSAATPALLK-----------HTGR 409 Query: 423 AIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDSL 482 A+VFE E H R+DD +LD+DE C+LV++ G GYPG AE NM P ++++GI + Sbjct: 410 AVVFENSEHMHQRLDDESLDVDETCVLVLKNCGPRGYPGMAEAGNMPLPPKVLRKGITDM 469 Query: 483 PCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDDAEMAQR 542 + D R SGT+ +L+++PEAA GG LAL+K D +++D+ R ++L +D+AE+ +R Sbjct: 470 VRVSDARMSGTAYGTVVLHVAPEAAAGGPLALVKDGDMVELDVPMRKLHLHVDEAELQRR 529 Query: 543 RREWIPNIPPSQTPWQELYRQLVGQLSTGGCLE 575 R W P W LY + V Q + G ++ Sbjct: 530 RAAWQAPALPMARGWTRLYVEHVQQANLGADMD 562 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: 1015 Number of extensions: 53 Number of successful extensions: 3 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: 577 Length adjustment: 37 Effective length of query: 557 Effective length of database: 540 Effective search space: 300780 Effective search space used: 300780 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