Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate H281DRAFT_06210 H281DRAFT_06210 aconitate hydratase
Query= SwissProt::P37032 (891 letters) >FitnessBrowser__Burk376:H281DRAFT_06210 Length = 898 Score = 879 bits (2270), Expect = 0.0 Identities = 448/873 (51%), Positives = 594/873 (68%), Gaps = 24/873 (2%) Query: 23 YYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTKDIKAIADWLHNKTSQHEIA 82 Y LK AE + F ++ LP SL++LLEN +R D+ AI DWL + S EI+ Sbjct: 23 YADLKRAEAQGFAPLSELPVSLRILLENAMRRGG-----VDDVAAIRDWLTRRESDREIS 77 Query: 83 FRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLSPVDLVIDHSVMVDKFASAD 142 F P RVLM D + VP V DLAAMR A+ K GG++ +++PL PVD+V+DHS + D +D Sbjct: 78 FFPVRVLMPDSSAVPLVADLAAMRDAVRKKGGDSWRVNPLIPVDIVVDHSAITDHAGRSD 137 Query: 143 ALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICHQVNLEYLGKTVWNSENDGQ 202 A ++N +E +RN ERY FL+W Q AF N +VVPP TGI HQVNLE+L V D Sbjct: 138 AFDLNLALEYQRNHERYAFLKWAQNAFDNVRVVPPATGIVHQVNLEFLAAGVQTVVIDDV 197 Query: 203 LYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLSGKLKE 262 + PDTLVG DSHTTM+N +GVLGWGVGGIEA AA+LGQP+SML+P VIG ++SG+ + Sbjct: 198 TFVVPDTLVGMDSHTTMVNSIGVLGWGVGGIEAAAAILGQPISMLLPRVIGCRISGRPRS 257 Query: 263 GITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADRATISNMAPEYGATCGFFPVD 322 G+T TD+VL++T+ LR K VVG FVEF+G GL++LP++DRATI+NMAPE GAT FFP D Sbjct: 258 GVTCTDIVLSLTEFLRGKKVVGCFVEFFGEGLDNLPVSDRATIANMAPEAGATMCFFPPD 317 Query: 323 KETIKYLELTGRDKHTIALVEAYAKAQGMWYDK---DNEEPVFTDSLHLDLGSVEPSLAG 379 TI+YL TGR + +A+ EA KAQG+W + D E ++D L DL +V PS+AG Sbjct: 318 AATIEYLHATGRSREQVAVAEAVLKAQGIWRPEAGADEERIAYSDRLEFDLSAVTPSMAG 377 Query: 380 PKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDFQMKHGHVVIAAITSCTNTS 439 PKRPQD+V+L + F+ + F + + + +G VVIAAITSCTNTS Sbjct: 378 PKRPQDRVDLKDVSARFH-------------REFGLTAEGRGLTNGSVVIAAITSCTNTS 424 Query: 440 NPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRHAGLQTYLDQLGFNLVGY 499 N ++ AGL+A+ +G++ K WVK+SL+PGS+VVTDYLR +GLQ LD LGFNL GY Sbjct: 425 NARAMIGAGLIARNLRARGVKPKAWVKTSLSPGSRVVTDYLRESGLQDDLDSLGFNLTGY 484 Query: 500 GCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHPQVRANWLASPPLVVAYA 559 GC TC G+SG L +++ + LVV++VLSGNRNFEGR HP RAN+L SP LVVAYA Sbjct: 485 GCMTCAGSSGQLDAEVARRILSEGLVVATVLSGNRNFEGRTHPLARANFLGSPALVVAYA 544 Query: 560 LCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEVAK-VSGTMFRKEYAEVFKGDA 618 GT DL+ EPI + +G V L D+WP + +I A + V+ TMF++ YA F+G+A Sbjct: 545 CAGTILRDLTTEPIADEADGQPVMLADVWPDDADIDAIFRRIVTLTMFKRVYATAFQGEA 604 Query: 619 HWQAIQTSSGQTYEWNPDSTYIQHPPFFE-NLSLKPEPLKPIKQAYVLALFGDSITTDHI 677 WQ I +SG ++W+ STYI+ PP+F+ + + I A L + GDSITTDHI Sbjct: 605 RWQRIAAASGDHFDWDQASTYIRRPPYFDAGFADDGFGMANIVGARALLMLGDSITTDHI 664 Query: 678 SPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTFANIRIRNEMTPGQEGG 737 SP G I++ + AG +L GV DFN+ SRR NH+VMMRGTFAN+R+RNEMTP +EG Sbjct: 665 SPVGVIRSETEAGRFLHGAGVAPSDFNTLLSRRANHDVMMRGTFANVRLRNEMTPDREGP 724 Query: 738 VTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWAAKGTNLLGVKAVITES 797 +R+VP+G+ M ++ AA RY++ + L++IAG +YG GSSRDWAAKG LLGV+AVI ES Sbjct: 725 WSRHVPSGDVMRVFQAASRYRDERVPLIVIAGADYGAGSSRDWAAKGPRLLGVRAVIAES 784 Query: 798 FERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISI-EISDKLTPGAMVPVTIERQDG 856 FERIHRSNL+GMGILPLQF GTTRKTL L G E +I I L P + + R +G Sbjct: 785 FERIHRSNLVGMGILPLQFPPGTTRKTLGLTGEESFTIFGIEGALQPHQRIECEVSRANG 844 Query: 857 DIEKIETLCRIDTADELEYYKNGGILQYVLRKI 889 + I +CR+D E+ +Y++GG+LQY+ ++ Sbjct: 845 ARDSITLICRLDIPREIAWYRHGGVLQYIAAQL 877 Lambda K H 0.316 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: 1782 Number of extensions: 70 Number of successful extensions: 7 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: 891 Length of database: 898 Length adjustment: 43 Effective length of query: 848 Effective length of database: 855 Effective search space: 725040 Effective search space used: 725040 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 Apr 09 2024. 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