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 AZOBR_RS02985 AZOBR_RS02985 aconitate hydratase
Query= SwissProt::P37032 (891 letters) >FitnessBrowser__azobra:AZOBR_RS02985 Length = 896 Score = 1201 bits (3107), Expect = 0.0 Identities = 593/890 (66%), Positives = 706/890 (79%), Gaps = 3/890 (0%) Query: 4 GQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTK 63 GQDSL T+ L+V GK+Y+Y+S+K AE+ ++RLPYS+KVLLENLLRFEDG TV+T Sbjct: 6 GQDSLKTRRSLSVGGKSYDYFSIKAAEDAGLGDLSRLPYSMKVLLENLLRFEDGRTVSTD 65 Query: 64 DIKAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLS 123 D+KA+A WLH+K S EIA+RP RVLMQDFTGVPAV DLAAMR A+ +GG+ KI+PL Sbjct: 66 DVKAVAQWLHDKRSDREIAYRPARVLMQDFTGVPAVCDLAAMREAMAALGGDPKKINPLV 125 Query: 124 PVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICH 183 PVDLVIDHSVMVD F + A E N ++E ERN ERY FLRWGQKAF NF+VVPPGTGICH Sbjct: 126 PVDLVIDHSVMVDYFGNPSAFEKNVELEFERNLERYAFLRWGQKAFDNFRVVPPGTGICH 185 Query: 184 QVNLEYLGKTVW-NSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 242 QVN+EYL + VW +++ G+L AYPDTLVGTDSHTTM+NGLGVLGWGVGGIEAEAAMLGQ Sbjct: 186 QVNVEYLAQGVWTDTDPAGKLVAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQ 245 Query: 243 PVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADR 302 P+SMLIPEV+GFKL+G+LKEG TATDLVLTVTQMLRKKGVVGKFVEFYGPGL+ L LADR Sbjct: 246 PISMLIPEVVGFKLTGRLKEGTTATDLVLTVTQMLRKKGVVGKFVEFYGPGLDHLTLADR 305 Query: 303 ATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVF 362 ATI NMAPEYGATCG FP+D ETI+YL TGRD +A+VEAYA+AQGMW D +PVF Sbjct: 306 ATIGNMAPEYGATCGIFPIDAETIRYLTFTGRDADRVAMVEAYARAQGMWRDAGTPDPVF 365 Query: 363 TDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDFQM 422 TD+L LD+ +VEPSLAGPKRPQD+V LS F L+ K ++ +++ VK + + Sbjct: 366 TDALELDMTTVEPSLAGPKRPQDRVPLSQAAQSFGTDLVGAFKAEDADRSVPVKGCGYNL 425 Query: 423 KHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRH 482 G VVIAAITSCTNTSNP+VL+AAGL+A+KA+EKGL+ KPWVK+SLAPGS+VVTDYL Sbjct: 426 DQGAVVIAAITSCTNTSNPAVLVAAGLLARKAVEKGLKSKPWVKTSLAPGSQVVTDYLAK 485 Query: 483 AGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHP 542 AGLQ YLDQLGFN+VGYGCTTCIGNSGPLPD I+ V E +LVV++VLSGNRNFEGRV+P Sbjct: 486 AGLQPYLDQLGFNIVGYGCTTCIGNSGPLPDPIAAAVEEGNLVVAAVLSGNRNFEGRVNP 545 Query: 543 QVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEV-AKV 601 RAN+LASPPL VAYAL G DL+++PIG +G VYLKD+WP+N+E+ + A + Sbjct: 546 HTRANYLASPPLCVAYALAGNMKIDLAKDPIGTGHDGQPVYLKDVWPTNQEVQDAIDASL 605 Query: 602 SGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIKQ 661 S MFR Y VF+G W+ IQT+ GQTYEW STY++ PPFF ++ P+ + ++ Sbjct: 606 SAEMFRSRYGNVFEGPEQWRGIQTAEGQTYEWQAGSTYVKLPPFFADMPKTPDAVSDVRG 665 Query: 662 AYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTF 721 A LA+ GDSITTDHISPAGSIK +SPAG YL S V +DFNSYG+RRGNHEVMMRGTF Sbjct: 666 ARALAVLGDSITTDHISPAGSIKKTSPAGEYLLSHQVRPQDFNSYGARRGNHEVMMRGTF 725 Query: 722 ANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWA 781 ANIRIRNEM G EGG TR+ P+GE + IY AAMRY + LV+IAGKEYGTGSSRDWA Sbjct: 726 ANIRIRNEMLAGVEGGETRHYPSGEQLPIYTAAMRYAQEGVPLVVIAGKEYGTGSSRDWA 785 Query: 782 AKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIE-ISDK 840 AKGT LLG++AVI ESFERIHRSNL+GMGILPLQFK+G TR L LDG+E I+ I Sbjct: 786 AKGTKLLGIRAVIAESFERIHRSNLVGMGILPLQFKDGLTRNDLALDGTETFDIDGIEQD 845 Query: 841 LTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKIS 890 L P V +TI R DG ++ L RIDT DE+EYY+NGG+L +VLR ++ Sbjct: 846 LRPRKDVTMTITRADGQTRQVPLLLRIDTVDEVEYYRNGGVLNFVLRNLA 895 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: 2142 Number of extensions: 82 Number of successful extensions: 4 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: 896 Length adjustment: 43 Effective length of query: 848 Effective length of database: 853 Effective search space: 723344 Effective search space used: 723344 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