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 H281DRAFT_06606 H281DRAFT_06606 aconitase
Query= SwissProt::Q5SMF6 (902 letters) >FitnessBrowser__Burk376:H281DRAFT_06606 Length = 905 Score = 965 bits (2495), Expect = 0.0 Identities = 495/905 (54%), Positives = 638/905 (70%), Gaps = 17/905 (1%) Query: 3 NSFQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDI 62 N +TLK + SG +Y L +L + ++ RLP SIR++LES+LRN DG ++ E I Sbjct: 4 NLHKTLKEFDSGSGKGKFYSLPQLGKALNIKIDRLPVSIRIVLESVLRNYDGKKIAEEHI 63 Query: 63 EALARWRPDPGEIN-VPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPA 121 LA W+P ++ +P ++RV+LQDFTGVP + D+AAMR + G +PK I P+VP Sbjct: 64 TQLANWKPTAPRVDEIPFVVSRVVLQDFTGVPLLADIAAMRGVAQRVGKNPKSIEPLVPV 123 Query: 122 DLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQV 181 DLV+DHSVQ+D F A N++ E++RN ERY +KW A + F+VVPPG GIVHQV Sbjct: 124 DLVVDHSVQIDHFREKNALDLNMKLEFQRNNERYQFMKWGMQAFDTFKVVPPGVGIVHQV 183 Query: 182 NIEYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYY 241 N+EYL + V T+ +PDSLVGTDSHTTM+NG+GV+GWGVGGIEAEA MLGQP Y Sbjct: 184 NLEYLARGVHKKAEGADTVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPVY 243 Query: 242 MLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATI 301 L P VVG L G+L EG TATDLVLT+TE+LRK VVGKFVEF+G G LS PDRATI Sbjct: 244 FLTPDVVGVNLKGKLREGVTATDLVLTITELLRKEKVVGKFVEFFGEGTRSLSLPDRATI 303 Query: 302 ANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSE 361 NMAPEYGATMGFFPVDE+T++Y + TGR + + + Y KA LF P+ E + +++ Sbjct: 304 GNMAPEYGATMGFFPVDEKTIDYFKGTGRTDAEISAFQNYFKAQNLFGIPK-EGDIDFTK 362 Query: 362 YLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVKR 421 + LDL V PSLAGPKRPQDR+ + VK +F +KPV E GF E L + Sbjct: 363 VVTLDLGTVAPSLAGPKRPQDRIEIGNVKSTFSDLFSKPVAENGFAKKEADLDAQYTT-- 420 Query: 422 RDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSKV 481 + +G V+IAAITSCTNTSNPSV+L AGLLAKKAVEAGL P +KTSLAPGS++ Sbjct: 421 -SNGVNVKNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVAPHIKTSLAPGSRI 479 Query: 482 VTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNRN 541 VT+YL +GL+P+L+ LGF L YGCTTCIGN+G L ++ +A+ + ++V AAVLSGNRN Sbjct: 480 VTEYLTKTGLLPYLDKLGFTLAAYGCTTCIGNAGDLTPELNEAITKNDIVAAAVLSGNRN 539 Query: 542 FEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEIR 601 FE RI+P+++AN+LASP LVVAYA+AG + D TEP+G GK +YL DIWP+ +E+ Sbjct: 540 FEARIHPNIRANFLASPPLVVAYAIAGNITRDLMTEPVGKGKGGKDVYLGDIWPTSDEVN 599 Query: 602 EAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFF-EDLGERK 660 + ++ LD + F+K Y+ + + + W + G++Y W P+STYI PPFF D Sbjct: 600 DLLKFALDADAFRKNYASLTKKGDLWSKIEGEEGQVYDW-PKSTYIAEPPFFGNDFSMTP 658 Query: 661 VEDI---RGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGN 717 + I + AR L + GDSVTTDHISPAG+I SPAG++L GV+ DFNSYGSRRGN Sbjct: 659 ADSIAAVKNARALGIFGDSVTTDHISPAGSIKEDSPAGKWLKENGVQKADFNSYGSRRGN 718 Query: 718 HEVMMRGTFANIRIKNLML----DG--IEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLV 771 H+VMMRGTFAN+RIKNLM+ DG +EGG P G+ +Y+ AM+Y GTP +V Sbjct: 719 HDVMMRGTFANVRIKNLMIPAKADGSRVEGGLTIHQPSGEQLSIYDAAMKYIDAGTPTIV 778 Query: 772 IAGKEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLG 831 AG+EYGTGSSRDWAAKGT LLG++AV+A SFERIHRSNLVGMGVLPL+F ++ ++LG Sbjct: 779 FAGEEYGTGSSRDWAAKGTQLLGVKAVVARSFERIHRSNLVGMGVLPLQFKGSDSVQSLG 838 Query: 832 LTGYEVYDILGL-EDLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTV 890 +TG E YDI GL D KP++ V +V R +DGSE R + R+DTP+EVDYYK+GGIL V Sbjct: 839 ITGEETYDIEGLGADFKPQQEVTLVIRGKDGSEKRVPVLLRIDTPIEVDYYKHGGILPFV 898 Query: 891 LLNML 895 L ++L Sbjct: 899 LRSLL 903 Lambda K H 0.317 0.137 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: 2197 Number of extensions: 106 Number of successful extensions: 8 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: 902 Length of database: 905 Length adjustment: 43 Effective length of query: 859 Effective length of database: 862 Effective search space: 740458 Effective search space used: 740458 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