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 RR42_RS14490 RR42_RS14490 aconitate hydratase
Query= SwissProt::Q5SMF6 (902 letters) >FitnessBrowser__Cup4G11:RR42_RS14490 Length = 901 Score = 965 bits (2494), Expect = 0.0 Identities = 503/905 (55%), Positives = 638/905 (70%), Gaps = 21/905 (2%) Query: 3 NSFQTLKTLTTKSGTYG-YYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTRED 61 N +TLK + G +Y L +L + V RLP SIRV+LES+LRN DG +VT E Sbjct: 4 NLNKTLKEFKIGPSSKGQFYSLPQLGKALGVAVERLPVSIRVVLESVLRNCDGKKVTEEH 63 Query: 62 IEALARWRPDPGEIN-VPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVP 120 + LA W+P ++ +P +ARV+LQDFTGVP + DLAAMR+ + G +PK+I P+VP Sbjct: 64 VRQLAHWKPVAERVDEIPFVVARVVLQDFTGVPLLADLAAMRNVAEKMGKNPKKIEPLVP 123 Query: 121 ADLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQ 180 DLV+DHSVQ+D F A N++ E++RN ERY +KW A + F VV PG GIVHQ Sbjct: 124 VDLVVDHSVQIDHFREKNALDLNMKLEFQRNNERYQFMKWGMQAFDTFGVVQPGFGIVHQ 183 Query: 181 VNIEYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPY 240 VN+EYL + V K+DG+ +PD+LVGTDSHTTM+NG+GV+GWGVGGIEAEA MLGQP Sbjct: 184 VNLEYLARGVH--KKDGVY--YPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPV 239 Query: 241 YMLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRAT 300 Y L P VVG +L G L EG TATDLVLT+TEMLR+ VVGKFVEF+G G A L+ PDRAT Sbjct: 240 YFLTPDVVGVELKGRLREGVTATDLVLTITEMLRREKVVGKFVEFFGEGTASLALPDRAT 299 Query: 301 IANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYS 360 I NMAPEYGATMGFFPVDE+T++Y + TGR EE + E Y +A +F P+A E + Y+ Sbjct: 300 IGNMAPEYGATMGFFPVDEKTIDYFKGTGRTEEEIAAFEGYFRAQKMFGVPKAGE-IDYT 358 Query: 361 EYLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVK 420 + LDL V PSLAGPKRPQDR+ + VK +F + KP E GF +L + Sbjct: 359 NVVTLDLGTVAPSLAGPKRPQDRIEIGNVKSTFASLFAKPTAENGFNKDIAELDKTYTTA 418 Query: 421 RRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSK 480 + + G V+IAAITSCTNTSNPSV+L AGLLAKKAVEAGL P +KTSLAPGS+ Sbjct: 419 ---DGVNVKSGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVAPHIKTSLAPGSR 475 Query: 481 VVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNR 540 VVT+YL+ +GL+P+LE LGF + YGCTTCIGN+G L ++ +A+ +LV AAVLSGNR Sbjct: 476 VVTEYLQAAGLLPYLEKLGFGVTAYGCTTCIGNAGDLTPELNEAITRNDLVAAAVLSGNR 535 Query: 541 NFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEI 600 NFE RI+P+++AN+LASP LVVAYA+AG + D TEP+G G+ IYL DIWP+ EEI Sbjct: 536 NFEARIHPNIRANFLASPPLVVAYAIAGNVTRDLMTEPVGTGKGGREIYLGDIWPTSEEI 595 Query: 601 REAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGERK 660 ++ +D ++FK Y +V + + W + G++Y W P+STYI PPFF+ G Sbjct: 596 HALMKYAMDSKVFKINYEQVKKPSKLWAKVKGTKGQVYDW-PKSTYIAEPPFFDGFGMEP 654 Query: 661 V---EDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGN 717 +R AR L V GDSVTTDHISPAG+I SPAG+YL++ GV DFNSYGSRRGN Sbjct: 655 AATQSSVRNARALGVFGDSVTTDHISPAGSIKESSPAGKYLLANGVLKADFNSYGSRRGN 714 Query: 718 HEVMMRGTFANIRIKNLML----DG--IEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLV 771 HEVMMRGTFAN+RIKNLML DG +EGG P G+ +Y+ AM+Y AEGTP +V Sbjct: 715 HEVMMRGTFANVRIKNLMLPVKADGSRVEGGVTLHQPSGEALSIYDAAMKYIAEGTPTVV 774 Query: 772 IAGKEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLG 831 G+EYGTGSSRDWAAKGT LLG++AV+ SFERIHRSNLVGMGVLPL+F ++ +TLG Sbjct: 775 FGGEEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGSDSVQTLG 834 Query: 832 LTGYEVYDILGLE-DLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTV 890 + G E +DI G+E +LKP++ V +V +R +G R + R+DTP+EVDYY +GGIL V Sbjct: 835 IVGDETFDIEGIEGELKPQQDVTLVIKRANGDVQRVPLLLRIDTPIEVDYYNHGGILPFV 894 Query: 891 LLNML 895 L +L Sbjct: 895 LRQLL 899 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: 2178 Number of extensions: 98 Number of successful extensions: 9 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: 901 Length adjustment: 43 Effective length of query: 859 Effective length of database: 858 Effective search space: 737022 Effective search space used: 737022 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