Align 2-methylisocitrate dehydratase (EC 4.2.1.99) (characterized)
to candidate WP_011386009.1 AMB_RS18485 aconitate hydratase AcnA
Query= reanno::acidovorax_3H11:Ac3H11_1140 (980 letters) >NCBI__GCF_000009985.1:WP_011386009.1 Length = 903 Score = 1120 bits (2898), Expect = 0.0 Identities = 585/949 (61%), Positives = 689/949 (72%), Gaps = 71/949 (7%) Query: 32 QFYSLPAL-AKQFPEIKRLPVSIRIVLESVLRNCDGRKVTPEHVEQLARWAPNAERKDEI 90 ++Y+L AL A + RLPVSIRIVLESVLRNCDG+++T EHV QLA W P+A R EI Sbjct: 21 RYYALAALDAVTDGPVSRLPVSIRIVLESVLRNCDGKRITEEHVRQLANWRPDAPRTQEI 80 Query: 91 PFVVSRVVLQDFTGVPLLADLAAMRSVAAKLGKNPKKIEPLVPVDLVVDHSIMIDHYGKK 150 PFVV+R+VLQDFTGVPLL DLAAMR VA GKNPK IEPLVPVDLVVDHS+ +DHYG+ Sbjct: 81 PFVVARIVLQDFTGVPLLCDLAAMRGVAQAFGKNPKIIEPLVPVDLVVDHSVQVDHYGEA 140 Query: 151 NSLDLNMKLEFQRNRERYEFMKWGMQAFDTFGVVPPGFGIVHQVNLEYLARGVHKRKDGV 210 +SLDLNM+ EFQRN ERY F+KWGMQAFDTF VVPPG GIVHQVNLE+LARGV + KDG+ Sbjct: 141 DSLDLNMRREFQRNAERYRFIKWGMQAFDTFRVVPPGIGIVHQVNLEFLARGVLE-KDGI 199 Query: 211 FYPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAAMLGQPVYFLTPDVVGFEMTGRLREGV 270 YPDTLVGTDSHTTMIN +GV GWGVGGIEAEA MLGQP+ FLTPDVVG + GRL EG Sbjct: 200 TYPDTLVGTDSHTTMINALGVAGWGVGGIEAEAGMLGQPLVFLTPDVVGVHLHGRLPEGA 259 Query: 271 TATDLVLTVTELLRKHKVVGKFVEFFGEGTRTLALPDRATIGNMAPEYGATMGFFPVDEK 330 TATDLVL +TE LR+ KVVGKFVEFFGEGTR+LA+PDRATI NMAPEYGATMGFFPVD++ Sbjct: 260 TATDLVLFLTERLRRAKVVGKFVEFFGEGTRSLAVPDRATIANMAPEYGATMGFFPVDKE 319 Query: 331 TIDYFQGTGRTKAEIEAFEAYFKAQGLFGVPLAGEVDYSQVVTLDLGSVTPSLAGPKRPQ 390 T+ Y + TGRT +EIE F AY+ AQGLFG+P+ G++DYS+V+ DLGSV PS+AGPKRPQ Sbjct: 320 TVRYLEATGRTDSEIEVFRAYYSAQGLFGMPMPGDIDYSEVIEFDLGSVQPSIAGPKRPQ 379 Query: 391 DRIELGQVSRQFADLFSQPAAHNGFNRPAELLHTRFHIHRAAEVVADVTPDGKPTPAGAP 450 DR+ L + R F LFS PA +G+ RPAE L R + A AD Sbjct: 380 DRLNLSDMRRAFTSLFSAPAKDDGYGRPAEALGRRHRVETTA--AAD------------- 424 Query: 451 RSVVEMEANKPALATAHAEARSATLPARGADPTVGNGDVLIAAITSCTNTSNPSVLLAAG 510 +G+GDVLIAAITSCTNTSNP V+LAAG Sbjct: 425 ---------------------------------IGHGDVLIAAITSCTNTSNPGVMLAAG 451 Query: 511 LLAKKAVEAGLKVQPHIKTSLAPGSRIVTEYLSETGLLPYLEKLGFSIAGYGCTTCIGNA 570 LLA+KAV GLKV P +KTSLAPGSR+VTEYL++ GLL LE LGF + YGCTTCIGN+ Sbjct: 452 LLARKAVALGLKVGPRVKTSLAPGSRVVTEYLAKAGLLGDLESLGFGVVAYGCTTCIGNS 511 Query: 571 GDLTPELNEAITQNDLVCAAVLSGNRNFEARIHPNLKANFLASPPLVVAYAIAGTVLKDL 630 G L P+L +AI +DLVCAAVLSGNRNFEARIHP +KANFL SPPLVVA+AIAG + D+ Sbjct: 512 GPLMPDLEQAIAADDLVCAAVLSGNRNFEARIHPAIKANFLMSPPLVVAFAIAGRIAIDM 571 Query: 631 MTEPVGQGKGGKDIYLGDIWPSSDEVHALLKFAMKGKAFRDNYAKVATDPGKLWEKIQGV 690 EP+G GK GK + L DIWPS EV L A + +R Y+ LW I Sbjct: 572 TQEPLGTGKDGKPVMLKDIWPSGREVADALLVATDPELYRRLYSDF-VHGNPLWNDIPTQ 630 Query: 691 SGTAYTWPASTYIAEPPFFAQFALEKGANKASGTRGEGQKDAQLPSVMGARIMALFGDSI 750 +G AY W STYIAEPPFF +F+ + A + ++GAR +A+FGDS+ Sbjct: 631 TGPAYAWETSTYIAEPPFFERFS---------------PQPAGVGDIIGARALAIFGDSV 675 Query: 751 TTDHISPAGSIKESSPAGQWLLQHGVQKADFNSYGARRGNHDVMVRGTFANVRIKNLMIP 810 TTDHISPAGSI SSPAGQ+LL HGV DFNSYGARRGNH+VM+RGTFANVRI+NLM+P Sbjct: 676 TTDHISPAGSIAVSSPAGQYLLAHGVAAGDFNSYGARRGNHEVMMRGTFANVRIRNLMLP 735 Query: 811 PTADGSREEGGVTVFQNEGALQGEKMFIFDAAMQYMAQGTPTVVFAGEEYGTGSSRDWAA 870 DGSR EGG+T+ Q EG+ +M IFDAA +Y G P++VFAG EYGTGSSRDWAA Sbjct: 736 AKVDGSRVEGGLTLHQPEGS----EMPIFDAASRYQEAGIPSIVFAGTEYGTGSSRDWAA 791 Query: 871 KGTQLLGIKAVVARSFERIHRSNLVGMGVLPLQFKAGDSWETLGLTGNEVIDVLP-DPAL 929 KG +LLG++AVVA+SFERIHRSNLVGMGVLPLQF+ G+S +LG+ G+E V L Sbjct: 792 KGPKLLGVRAVVAQSFERIHRSNLVGMGVLPLQFRDGESAASLGIAGDEEFHVRGLSGVL 851 Query: 930 TPQSDARLVIRRADGTVREVVVTLRIDTPIEVDYYRAGGILPFVLRQLL 978 P+ + L I G R + + LR+DT IE+DY GGILP+VLR LL Sbjct: 852 RPRQEVVLEIVNRQGRSRAISLQLRVDTAIELDYLSHGGILPYVLRDLL 900 Lambda K H 0.318 0.136 0.399 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: 2358 Number of extensions: 109 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 980 Length of database: 903 Length adjustment: 44 Effective length of query: 936 Effective length of database: 859 Effective search space: 804024 Effective search space used: 804024 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 57 (26.6 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