Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate CCNA_03781 CCNA_03781 aconitate hydratase
Query= SwissProt::P70920 (906 letters) >FitnessBrowser__Caulo:CCNA_03781 Length = 895 Score = 1209 bits (3128), Expect = 0.0 Identities = 614/907 (67%), Positives = 718/907 (79%), Gaps = 17/907 (1%) Query: 1 MTSLDSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVK 60 M S+DS K ++ LKVG ++YVYYSL AE+ GL +S LP SMKVLLENLLRNEDG SV Sbjct: 1 MASVDSLKARRELKVGKQSYVYYSLRAAEEAGLADVSSLPVSMKVLLENLLRNEDGVSVN 60 Query: 61 KADIVAVSKWLRKK-SLEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKIN 119 + D+ AV+ WL K S+EHEI+FRPARVLMQDFTGVPAVVDLAAMR+AM LG D KIN Sbjct: 61 EDDLKAVAAWLNNKGSVEHEISFRPARVLMQDFTGVPAVVDLAAMRDAMVALGADPAKIN 120 Query: 120 PLVPVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTG 179 PL PVDLVIDHSV+V+ FG+ KA+ NV EY++N ERY FL+WG +AF+NF VVPPGTG Sbjct: 121 PLNPVDLVIDHSVMVDNFGNPKAYDDNVKREYERNIERYRFLRWGSSAFNNFRVVPPGTG 180 Query: 180 ICHQVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGG 239 ICHQVNLEYL+QTVWT EVAYPD++VGTDSHTTMVNGLAVLGWGVGG Sbjct: 181 ICHQVNLEYLAQTVWTNT--------VDGAEVAYPDTVVGTDSHTTMVNGLAVLGWGVGG 232 Query: 240 IEAEACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGP 299 IEAEA MLGQP+ ML+P V+GFKL GAM EG TATDLVLTVTQMLRK GVVGKFVEF+G Sbjct: 233 IEAEAAMLGQPIPMLIPEVIGFKLTGAMPEGATATDLVLTVTQMLRKKGVVGKFVEFYGD 292 Query: 300 GLDHLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLF 359 L +L++ D+ATIANMAPEYGATCGFFP+ AA I YLK +GRAA RVALV+AYAK QGL+ Sbjct: 293 ALANLTLEDQATIANMAPEYGATCGFFPISAATIAYLKGTGRAAERVALVEAYAKEQGLW 352 Query: 360 RTAKSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAK 419 A+P FT+TL LDL+ V+PS+AGPKRP+ R+ L A F+ +LA E+ K E P Sbjct: 353 WEPGVAEPTFTDTLELDLSTVLPSLAGPKRPQDRVLLSDAAAKFAESLAGEFGKAENPEL 412 Query: 420 RFAVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAP 479 R VEG+ +++GHGDVVIAAITSCTNTSNPSVLI AGLLA+NA AKGLKAKPWVKTSLAP Sbjct: 413 RAPVEGEDFDVGHGDVVIAAITSCTNTSNPSVLIAAGLLAKNAVAKGLKAKPWVKTSLAP 472 Query: 480 GSQVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLS 539 GSQVV YLA +GL HLD +GFNLVG+GCTTCIGNSGPLPE ISK+INDN +VA +VLS Sbjct: 473 GSQVVTDYLAKAGLTKHLDALGFNLVGYGCTTCIGNSGPLPEAISKTINDNDLVACSVLS 532 Query: 540 GNRNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTS 599 GNRNFEGRV+PDV+ANYLASPPLVVA+ALAGS+ +LA +P+G+ K G V+LKDIWP++ Sbjct: 533 GNRNFEGRVNPDVRANYLASPPLVVAYALAGSLKIDLATQPIGQDKKGNDVFLKDIWPSN 592 Query: 600 KEINAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMK 659 ++I A +K + +F +Y DVFKGD NW+ IK +TY W STYVQNPPYF M Sbjct: 593 EDIAALQRKAINEKMFATRYGDVFKGDKNWQGIKVTGGQTYAWEADSTYVQNPPYFPNMS 652 Query: 660 KEPEPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRR 719 P PVTDIVEARILA+FGD ITTDHISPAGSIK +SPAGK+L ++ V P DFN YG RR Sbjct: 653 MTPAPVTDIVEARILAVFGDSITTDHISPAGSIKASSPAGKFLIDNGVEPVDFNGYGARR 712 Query: 720 GNHEVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLV 779 GNH+VMMRGTFANIRI+N + EGG+TKH+P GE MSIYDAAMKYQ+E P V Sbjct: 713 GNHQVMMRGTFANIRIRNRITPDI-----EGGVTKHFPTGEVMSIYDAAMKYQEEGRPAV 767 Query: 780 VFAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSL 839 VF G EYG GSSRDWAAKGT+LLGVRAVIC+SFERIHRSNLVGMGVLPL F + W L Sbjct: 768 VFGGKEYGTGSSRDWAAKGTKLLGVRAVICESFERIHRSNLVGMGVLPLQFVQ-DGWQKL 826 Query: 840 GLKGDEKVTLRGLVGDLKPRQKLTAEIV-SGDGSLQRVSLLCRIDTLDELDYYRNGGILH 898 L G+E V++RGL DL PR++L E+ DG + R + CRIDT EL+Y++NGG+L+ Sbjct: 827 ELTGEEIVSIRGLT-DLAPRKQLIVELYRPTDGRIARFPVRCRIDTPTELEYFKNGGVLN 885 Query: 899 YVLRKLA 905 YVLR LA Sbjct: 886 YVLRNLA 892 Lambda K H 0.317 0.134 0.393 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: 2183 Number of extensions: 84 Number of successful extensions: 5 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: 906 Length of database: 895 Length adjustment: 43 Effective length of query: 863 Effective length of database: 852 Effective search space: 735276 Effective search space used: 735276 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 (21.6 bits) S2: 56 (26.2 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