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 HSERO_RS14940 HSERO_RS14940 aconitate hydratase
Query= SwissProt::P70920 (906 letters) >FitnessBrowser__HerbieS:HSERO_RS14940 Length = 903 Score = 957 bits (2473), Expect = 0.0 Identities = 506/915 (55%), Positives = 643/915 (70%), Gaps = 25/915 (2%) Query: 3 SLDSFKCKKTLKV-GAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVKK 61 S ++ K K+ G+K +YSLP +K+ IS+LP S++++LE++LRN DG+ V + Sbjct: 2 SRNTLNTLKEFKISGSKKGKFYSLPALQKSLGVNISRLPVSIRIVLESVLRNCDGQKVTE 61 Query: 62 ADIVAVSKWLRKKSLEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPL 121 + ++ W K + EI F ARV++QDFTGVP + DLAAMRN KLG + + I PL Sbjct: 62 EHVKQLANWGAKAARVDEIPFVVARVVLQDFTGVPLLADLAAMRNVASKLGKNPKNIEPL 121 Query: 122 VPVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGIC 181 VPVDLV+DHSV ++ F + KA N+ E+ +N ERY+F+KWG AF F VVPPG GI Sbjct: 122 VPVDLVVDHSVQIDHFREKKALDLNMKLEFSRNNERYQFMKWGMQAFDTFGVVPPGFGIV 181 Query: 182 HQVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIE 241 HQVNLEYL++ V K TG + YPD+LVGTDSHTTM+NG+ V+GWGVGGIE Sbjct: 182 HQVNLEYLARGVHNK---------TGVY---YPDTLVGTDSHTTMINGIGVVGWGVGGIE 229 Query: 242 AEACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGL 301 AEA MLGQP+ L P+VVG L GA++EGVTATDLVLT+T++LR+ VVGKFVEFFG G Sbjct: 230 AEAGMLGQPVYFLTPDVVGVNLTGALREGVTATDLVLTITELLRQTKVVGKFVEFFGEGT 289 Query: 302 DHLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRT 361 + LS+ D+ATIANMAPEYGAT GFFPVD A I+Y K +GR + +AY KAQ L+ Sbjct: 290 ESLSLTDRATIANMAPEYGATMGFFPVDDATIEYFKGTGRTKAEIDAFEAYFKAQELYGV 349 Query: 362 AKSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALA-----NEYKKTEE 416 K+ +T+ ++LDL V PS+AGPKRP+ RI + +V FS N + K E Sbjct: 350 PKAGQIDYTQEVSLDLGTVAPSLAGPKRPQDRIEIGNVKSTFSDLFTKPTAENGFNKKAE 409 Query: 417 PAKRFAVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTS 476 ++ +GDV+IAAITSCTNTSNPSVL+ AGLLA+ A GLK P +KTS Sbjct: 410 DLGASYKNADGVDLHNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVAPHIKTS 469 Query: 477 LAPGSQVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAA 536 LAPGS+VV YL +GL +L+K+GF + +GCTTCIGN+G L ++++I N +VAAA Sbjct: 470 LAPGSRVVTKYLEAAGLLPYLEKLGFGVTAYGCTTCIGNAGDLTPAMNEAIVKNDVVAAA 529 Query: 537 VLSGNRNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIW 596 VLSGNRNFE R+ P+++AN+LASPPLVVA+A+AG+VT++L EP+G+GK GK +YL DIW Sbjct: 530 VLSGNRNFEARIHPNIRANFLASPPLVVAYAIAGNVTRDLMTEPVGKGKGGKDIYLGDIW 589 Query: 597 PTSKEINAFMKKFVTASIFKKKYADVFKGDTN--WRKIKTV-ESETYRWNMSSTYVQNPP 653 PTS+EI +K + A FK+ YADV KG W IK V + E Y W SSTY+ PP Sbjct: 590 PTSQEIEKLLKFAMNAKTFKENYADV-KGAPGKLWEAIKGVAKGEVYNW-PSSTYIAEPP 647 Query: 654 YFEGMKKEPE-PVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADF 712 +FE +EP+ I AR L +FGD ITTDHISPAGSIK +SPAGK+L + V ADF Sbjct: 648 FFENFSEEPKAAAAGITGARALGVFGDSITTDHISPAGSIKESSPAGKWLQANGVLKADF 707 Query: 713 NQYGTRRGNHEVMMRGTFANIRIKNFMLKG-ADGNIPEGGLTKHWPDGEQMSIYDAAMKY 771 N YG+RRGNHE+MMRGTFAN+RIKN M+ DG+ EGG+T H P GE+MSIYDAAMKY Sbjct: 708 NSYGSRRGNHEIMMRGTFANVRIKNLMIPAKEDGSRVEGGITIHQPSGEEMSIYDAAMKY 767 Query: 772 QQEQVPLVVFAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFE 831 E P +VF G EYG GSSRDWAAKGT+LLGV+AVI +SFERIHRSNLVGMGVLPL F Sbjct: 768 VAEGTPTMVFGGEEYGTGSSRDWAAKGTQLLGVKAVIARSFERIHRSNLVGMGVLPLQFL 827 Query: 832 EGTSWSSLGLKGDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYY 891 S SLG+ GDE L+GL G++KP+Q+ T I +G + V LL RIDT E+DYY Sbjct: 828 GNDSVQSLGITGDETFDLKGLEGEIKPQQEATLVIHRKNGETKEVKLLLRIDTPIEVDYY 887 Query: 892 RNGGILHYVLRKLAA 906 ++GGIL +VLR+L A Sbjct: 888 KHGGILPFVLRQLLA 902 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: 2164 Number of extensions: 102 Number of successful extensions: 6 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: 903 Length adjustment: 43 Effective length of query: 863 Effective length of database: 860 Effective search space: 742180 Effective search space used: 742180 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