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 Echvi_4039 Echvi_4039 aconitate hydratase 1
Query= SwissProt::Q5SMF6 (902 letters) >FitnessBrowser__Cola:Echvi_4039 Length = 925 Score = 1047 bits (2707), Expect = 0.0 Identities = 539/923 (58%), Positives = 682/923 (73%), Gaps = 42/923 (4%) Query: 9 KTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDIEALARW 68 K L T G+ Y+ L L+ +G +++ LPFSIR++LE+ LRN D + +T+E E L W Sbjct: 10 KQLDTAKGSLNYWSLAALQEQG-HKINELPFSIRILLENALRNYDDFAITKEHTETLLNW 68 Query: 69 RPDPGEINVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPADLVIDHS 128 +P+ + +VP K ARV++QDFTGVPAVVD+A++R KG DP++INP++P DLV+DHS Sbjct: 69 KPEASDKDVPYKPARVLMQDFTGVPAVVDIASLRAEAVRKGKDPQKINPLIPVDLVVDHS 128 Query: 129 VQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQVNIEYLTK 188 VQVD FGT Y++ NV+ EYERN ERY LKWAQ + +NF VVPPG GI HQVN+EYL K Sbjct: 129 VQVDYFGTNYSYKKNVDVEYERNGERYEFLKWAQKSFDNFSVVPPGMGICHQVNLEYLAK 188 Query: 189 VVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYYMLAPRVV 248 V+ +RDG FPD+LVGTDSHT MVNG+GV+GWGVGGIEAEA +LGQP Y + P+VV Sbjct: 189 GVI--ERDGNV--FPDTLVGTDSHTPMVNGIGVVGWGVGGIEAEAALLGQPIYFIMPQVV 244 Query: 249 GFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATIANMAPEY 308 G KL GELP G TATD+VLT+TE+LRKHGVVGKFVE +GPG+ L+ PDRATI+NM+PE+ Sbjct: 245 GLKLTGELPLGTTATDMVLTITELLRKHGVVGKFVEVFGPGLDTLTVPDRATISNMSPEF 304 Query: 309 GATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSEYLELDLS 368 G T+ +FP+D+ TL+Y+ +T R ++ ++LVE Y KA L+R E EE V+YS +ELDL Sbjct: 305 GCTVTYFPIDDRTLDYMSKTNRSKDQIKLVEDYAKANMLWR--EDEESVKYSSLVELDLG 362 Query: 369 AVEPSLAGPKRPQDRVPLKEVKKSF-----------LAHLTKPVKERGFG---------- 407 VEP+++GPKRPQD++ ++ K+ F + K K R F Sbjct: 363 TVEPTVSGPKRPQDKILVRNFKEKFGELLEEVHGREYIPIDKRDKSRWFSEGGGQPVDKP 422 Query: 408 --LSED-QLQRK-------VLVKRRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLA 457 L ED ++ K V VK +EEF L+ GS+VIAAITSCTNTSNPSVM+GAGL+A Sbjct: 423 GDLPEDVEIATKTKNGLKTVEVKINNEEFALSDGSIVIAAITSCTNTSNPSVMIGAGLVA 482 Query: 458 KKAVEAGLDRKPWVKTSLAPGSKVVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPL 517 +KA E GLD KPWVKTSLAPGSKVVTDYLE SGL+ LEAL FH+VGYGCT+CIGNSGPL Sbjct: 483 QKARERGLDVKPWVKTSLAPGSKVVTDYLEASGLLDDLEALRFHVVGYGCTSCIGNSGPL 542 Query: 518 PEDIAKAVEEGNLVVAAVLSGNRNFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTE 577 P+ IA AVEE +LVVA+VLSGNRNFE R++P VK NYL SPMLVVAYALAGR+D+D E Sbjct: 543 PKHIAHAVEENDLVVASVLSGNRNFEARVHPQVKMNYLMSPMLVVAYALAGRVDVDLNEE 602 Query: 578 PLGFDPNGKPIYLKDIWPSMEEIREAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGEL 637 PLGFDPN +P+YLKDIWPS +EI E + K L P F K Y ++FEG+E+W+ L AP+ ++ Sbjct: 603 PLGFDPNLEPVYLKDIWPSNDEIFEVMGKVLSPGDFDKNYGEIFEGNEQWKNLQAPSDKV 662 Query: 638 YQWDPESTYIQNPPFFEDLGER--KVEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAG 695 Y W +STYI+ PFF+ L + ++I+GARVLL LGDS+TTDHISPAGA SPAG Sbjct: 663 YNWSEKSTYIKEAPFFQGLSNEVPEPQNIQGARVLLKLGDSITTDHISPAGAFAESSPAG 722 Query: 696 QYLISKGVKPEDFNSYGSRRGNHEVMMRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFV 755 QYL+ +GV+ +DFNSYGSRRGN EVM+RGTFAN+RIKN L EGGY +P G+ V Sbjct: 723 QYLVGRGVEKKDFNSYGSRRGNDEVMVRGTFANVRIKN-QLASREGGYTTHIPSGEEMTV 781 Query: 756 YNVAMRYKAEGTPLLVIAGKEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMG 815 + + +Y+ + TPL+V+AGKEYG+GSSRDWAAKGT LLGI AV+AES+ERIHRSNLVGMG Sbjct: 782 FEASEKYQKDDTPLVVLAGKEYGSGSSRDWAAKGTTLLGIHAVIAESYERIHRSNLVGMG 841 Query: 816 VLPLEFLPGENRETLGLTGYEVYDILGL-EDLKPRKLVDIVARREDGSEVRFQAIARLDT 874 VLPL+F G++ +LGL G E I G+ E L P K + A+++ G+ V F + RLD+ Sbjct: 842 VLPLQFAEGQSASSLGLDGKEEITIEGITEGLTPLKNLKATAKKDGGAVVNFDVVCRLDS 901 Query: 875 PVEVDYYKNGGILQTVLLNMLKE 897 VE+ YYKNGGIL VL LK+ Sbjct: 902 EVEIAYYKNGGILHYVLREFLKQ 924 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: 2285 Number of extensions: 107 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 902 Length of database: 925 Length adjustment: 43 Effective length of query: 859 Effective length of database: 882 Effective search space: 757638 Effective search space used: 757638 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