Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate HSERO_RS16705 HSERO_RS16705 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__HerbieS:HSERO_RS16705 Length = 578 Score = 451 bits (1159), Expect = e-131 Identities = 248/576 (43%), Positives = 348/576 (60%), Gaps = 19/576 (3%) Query: 3 DTPERRLRSEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTPCNR 62 DT + RS+ WF +Y N G+ ++ GRP+IGI T S+LTPCN Sbjct: 4 DTKKSTRRSQAWFGRQDRDGF--IYRSWVKNRGIPHDQFD-GRPVIGICNTYSELTPCNS 60 Query: 63 HHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGV 122 H LA++VK GI +AGG P+EFPV + E RPTA L RNLA + + E + PLDGV Sbjct: 61 HFRALAEQVKIGIWEAGGFPLEFPVMSLGETLLRPTAMLYRNLASMDVEESIRANPLDGV 120 Query: 123 VLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEI 182 VL GCDKTTPA LM AA+ D+P I +SGGPML G ++G +GSGT +W + AG++ Sbjct: 121 VLLMGCDKTTPALLMGAASVDVPTIGVSGGPMLSGKYRGRELGSGTGVWQMSEDVRAGKM 180 Query: 183 DYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATG 242 E F E + S GHC TMGTA +M ++ EALG+ LP A+IPA R +A G Sbjct: 181 TQEEFFEAESCMHRSHGHCMTMGTASTMASMVEALGVGLPHNAAIPAVDARRNVLARNAG 240 Query: 243 KRICELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQR 302 +RI ++V +D+ S+I+TRQAFENAI V +A+G S+N HL+AIA +G++L L DW Sbjct: 241 RRIVQMVEEDLVLSKILTRQAFENAIRVNAAIGGSTNAVIHLLAIAGRIGIKLDLKDWDD 300 Query: 303 IGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGRTIGEIVSSS 362 IG+ +P L++ P+GK+L E F+ AGG+P+V+ +L+ + + T +G+T+ E + Sbjct: 301 IGQQLPCLLDLQPSGKFLMEDFYYAGGLPAVIRQLESV--IDKTALTANGKTLWENCQDA 358 Query: 363 LTSNADVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENSFEA 421 N +VI FD P K AG +L GN D A++K S A K Sbjct: 359 PNWNEEVIRSFDKPFKEAAGIAILKGNLAPDGAVIKPSAATPALLK-----------HRG 407 Query: 422 RAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDS 481 RA+VFE +D H RIDD LD+DE C+LV++ G GYPG AE NM P ++++GI Sbjct: 408 RAVVFENSDDLHKRIDDENLDVDETCVLVLKNCGPKGYPGMAEAGNMPLPPKILRKGITD 467 Query: 482 LPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMAR 541 + + D R SGT+ +L++SPEAA GG LA++Q D +++D+ R ++L + DEE+AR Sbjct: 468 MVRVSDARMSGTAYGTVVLHVSPEAAAGGPLAVVQNGDFIELDVEARKLHLDVSDEELAR 527 Query: 542 RRLEW-TPNIPPS-QTPWQELYRQLVGQLSTGGCLE 575 RR +W P +PP Q W +LY V Q + G L+ Sbjct: 528 RRAQWQKPELPPQMQRGWVKLYVDHVQQANQGADLD 563 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: 974 Number of extensions: 59 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: 578 Length adjustment: 37 Effective length of query: 557 Effective length of database: 541 Effective search space: 301337 Effective search space used: 301337 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