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 GFF2473 Psest_2521 aconitate hydratase 1
Query= SwissProt::P37032 (891 letters) >FitnessBrowser__psRCH2:GFF2473 Length = 891 Score = 1246 bits (3224), Expect = 0.0 Identities = 618/885 (69%), Positives = 717/885 (81%), Gaps = 2/885 (0%) Query: 6 DSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTKDI 65 DSL + L V GKTY+YYSL +A + I+RLP SLKVLLENLLR+ED TV D+ Sbjct: 5 DSLKCRRSLEVAGKTYHYYSLPDAAAQ-LGDISRLPTSLKVLLENLLRWEDNQTVRADDL 63 Query: 66 KAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLSPV 125 K++ WL ++S EI +RP RVLMQDFTGVPAVVDLAAMR A+ K GG+ KI+PLSPV Sbjct: 64 KSLVSWLDTRSSTMEIQYRPARVLMQDFTGVPAVVDLAAMRDAVAKAGGDPQKINPLSPV 123 Query: 126 DLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICHQV 185 DLVIDHSVMVD+F S A E N +IE++RN ERYEFLRWGQ+AF NF VVPPGTGICHQV Sbjct: 124 DLVIDHSVMVDRFGSDQAFEQNVEIEMQRNGERYEFLRWGQQAFDNFAVVPPGTGICHQV 183 Query: 186 NLEYLGKTVWNSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVS 245 NLEYLG+ VW E +G+ +AYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVS Sbjct: 184 NLEYLGQVVWTREENGETFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVS 243 Query: 246 MLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADRATI 305 MLIPEVIGF+L+GKL EG+TATDLVLTVTQMLRK GVVGKFVEFYGPGL+ LPLADRATI Sbjct: 244 MLIPEVIGFRLTGKLNEGVTATDLVLTVTQMLRKHGVVGKFVEFYGPGLDHLPLADRATI 303 Query: 306 SNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVFTDS 365 NMAPEYGATCGFFPVD+ TI YL LTGR++ IALVEAY+KAQGMW D ++ P FT + Sbjct: 304 GNMAPEYGATCGFFPVDQVTIDYLRLTGRNEERIALVEAYSKAQGMWRDSNSPAPEFTAT 363 Query: 366 LHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDFQMKHG 425 L LDL V PS+AGPKRPQD+V L + F+ L G++++ + FAV + FQ+KHG Sbjct: 364 LELDLSQVRPSVAGPKRPQDRVTLGDIGANFDLLLETSGRQQQADTDFAVAAEQFQLKHG 423 Query: 426 HVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRHAGL 485 VVIAAITSCTNTSNP+VLMAAGLVAKKAIE+GLQRKPWVK+SLAPGSKVVTDYL AGL Sbjct: 424 AVVIAAITSCTNTSNPNVLMAAGLVAKKAIERGLQRKPWVKTSLAPGSKVVTDYLERAGL 483 Query: 486 QTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHPQVR 545 YLD+LGFNLVGYGCTTCIGNSGPLPD I + ++DL+VSSVLSGNRNFEGRVHP V+ Sbjct: 484 TRYLDELGFNLVGYGCTTCIGNSGPLPDAIGQAITDNDLIVSSVLSGNRNFEGRVHPLVK 543 Query: 546 ANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEVAKVSGTM 605 ANWLASPPLVVA+AL GTT D+ REP+G D + VYLKDIWPS+ EIA VA++ G M Sbjct: 544 ANWLASPPLVVAFALAGTTRIDMDREPLGYDAQNQPVYLKDIWPSSAEIAEAVARIDGEM 603 Query: 606 FRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIKQAYVL 665 FR YA+VF GD HWQ I S+G TY WN +S+Y+Q+PP+FE++ P P ++ A VL Sbjct: 604 FRSRYADVFSGDEHWQKIPVSAGDTYAWNANSSYVQNPPYFEDIGQPPTPPADVENARVL 663 Query: 666 ALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTFANIR 725 A+FGDSITTDHISPAG+IKASSPAGLYL+S GV +DFNSYGSRRGNHEVMMRGTFANIR Sbjct: 664 AVFGDSITTDHISPAGNIKASSPAGLYLQSLGVAPEDFNSYGSRRGNHEVMMRGTFANIR 723 Query: 726 IRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWAAKGT 785 IRNEM G+EGG T Y P+GE +SIYDAAMRYQ LV+IAGKEYGTGSSRDWAAKGT Sbjct: 724 IRNEMLGGEEGGNTLYQPSGEKLSIYDAAMRYQAEGVPLVVIAGKEYGTGSSRDWAAKGT 783 Query: 786 NLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIE-ISDKLTPG 844 NLLGVKAVI ESFERIHRSNLIGMG+L LQF TR++L L+G E++SI + + P Sbjct: 784 NLLGVKAVIAESFERIHRSNLIGMGVLALQFVNDQTRQSLGLNGMEKLSIRGLDADIKPR 843 Query: 845 AMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKI 889 M+ V +ER DG + + L RIDT +E++Y+K GGIL YVLR++ Sbjct: 844 QMLTVDVERADGSRDSFQVLSRIDTLNEVQYFKAGGILHYVLRQL 888 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: 2085 Number of extensions: 104 Number of successful extensions: 3 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: 891 Length adjustment: 43 Effective length of query: 848 Effective length of database: 848 Effective search space: 719104 Effective search space used: 719104 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