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 WP_036133359.1 N800_RS00150 aconitate hydratase AcnA
Query= SwissProt::Q8NQ98 (939 letters) >NCBI__GCF_000768355.1:WP_036133359.1 Length = 926 Score = 1044 bits (2700), Expect = 0.0 Identities = 539/947 (56%), Positives = 671/947 (70%), Gaps = 43/947 (4%) Query: 6 NSFNAKSTLEVGDKSYDYFALSAVP---GMEKLPYSLKVLGENLLRTEDGA-NITNEHIE 61 +SF+ + L V KS Y++L A+ + KLPYS+K+L ENLLR EDG + EHIE Sbjct: 3 DSFSTRRQLSVNGKSLTYYSLPALGEHFDLSKLPYSMKILLENLLRHEDGGMTVGREHIE 62 Query: 62 AIANWDASSDPSIEIQFTPARVLMQDFTGVPCVVDLATMREAVAALGGDPNDVNPLNPAE 121 A+A WDA+ DP EI F PARV++QDFTGVPCVVDLA MR+AV LGG+ +NPL P+E Sbjct: 63 AVAQWDATKDPDTEIAFMPARVVLQDFTGVPCVVDLAAMRDAVTRLGGNARQINPLIPSE 122 Query: 122 MVIDHSVIVEAFGRPDALAKNVEIEYERNEERYQFLRWGSESFSNFRVVPPGTGIVHQVN 181 +VIDHSV V+ FGRPDAL N +IE+ERN ERY FLRWG ++F NF+VVPP TGIVHQVN Sbjct: 123 LVIDHSVQVDVFGRPDALDLNGKIEFERNMERYSFLRWGQKAFENFKVVPPNTGIVHQVN 182 Query: 182 IEYLARVVFDNEGL---------AYPDTCIGTDSHTTMENGLGILGWGVGGIEAEAAMLG 232 +E LARVV + E A+PDT GTDSHTTM NG+G+LGWGVGGIEAEAAMLG Sbjct: 183 LENLARVVVEREVKTDDGASELQAFPDTVFGTDSHTTMINGIGVLGWGVGGIEAEAAMLG 242 Query: 233 QPVSMLIPRVVGFKLTGEIPVGVTATDVVLTITEMLRDHGVVQKFVEFYGSGVKAVPLAN 292 QP SMLIP+VVGFKLTG++P G TATD+VLT+T+MLR GVV KFVEFYG G++ +PLA+ Sbjct: 243 QPSSMLIPQVVGFKLTGKLPEGTTATDLVLTVTQMLRKLGVVGKFVEFYGEGLQHLPLAD 302 Query: 293 RATIGNMSPEFGSTCAMFPIDEETTKYLRLTGRPEEQVALVEAYAKAQGMWLDEDTVEAE 352 RATI NM+PE+G+TC +FPID E YLRL+GR E Q+ALVEAYAKAQG+W + EA Sbjct: 303 RATIANMAPEYGATCGIFPIDAEALNYLRLSGRSEAQIALVEAYAKAQGLWHEPGAPEAT 362 Query: 353 YSEYLELDLSTVVPSIAGPKRPQDRILLSEAKEQFRKDLPTYTDDAVSVDTSIPATRMVN 412 YS L LDL V PS+AGPKRPQDR+LL + + F +L T + Sbjct: 363 YSATLSLDLGDVKPSLAGPKRPQDRVLLEDMQVNFNDNL-TGLIVGRKARVGCAESDFKE 421 Query: 413 EGGGQPEGGVEADNYNASWAGSGESLATGAEGRPSKPVTVASPQGGEYTIDHGMVAIASI 472 EGG QP+ A +KP + + + G V IA+I Sbjct: 422 EGGAQPQ----------------------ASHLAAKPQSKIRIHDQDAYLHDGSVVIAAI 459 Query: 473 TSCTNTSNPSVMIGAGLIARKAAEKGLKSKPWVKTICAPGSQVVDGYYQRADLWKDLEAM 532 TSCTNTSNP+VM+GAGL+AR AA+ GLK+KPWVKT PGS VV Y ++A L DLE + Sbjct: 460 TSCTNTSNPAVMLGAGLLARNAAKLGLKAKPWVKTSLGPGSLVVTDYLRKAGLLDDLEQL 519 Query: 533 GFYLSGFGCTTCIGNSGPLPEEISAAINEHDLTATAVLSGNRNFEGRISPDVKMNYLASP 592 GFY+ G+GCTTCIGNSGPLP+ +S I E+DL +VLSGNRNFEGR+ P+VKMNYLASP Sbjct: 520 GFYVVGYGCTTCIGNSGPLPDVVSKGIAENDLVVASVLSGNRNFEGRVHPEVKMNYLASP 579 Query: 593 IMVIAYAIAGTMDFDFENEALGQDQDGNDVFLKDIWPSTEEIEDTIQQAISRELYEADYA 652 +V+AYAIAGT+D D + L DG V+L+D+WPS +EI D I + EL+ +YA Sbjct: 580 PLVVAYAIAGTVDIDLTRDPLATTADGTPVYLRDLWPSNKEIGDLIAATVGPELFAQNYA 639 Query: 653 DVFKGDKQWQELDVPTGDTFEWDENSTYIRKAPYFDGMPVEPVAVTDIQGARVLAKLGDS 712 DVFKGD +W ++ P G++F WDE STYI+ PYFDGM + + DI+GARV+ GDS Sbjct: 640 DVFKGDNRWNQIASPEGESFRWDEASTYIKNPPYFDGMTMAVGHIADIEGARVMGLFGDS 699 Query: 713 VTTDHISPASSIKPGTPAAQYLDEHGVERHDYNSLGSRRGNHEVMMRGTFANIRLQN-QL 771 +TTDHISPA +IK +PA ++L GV+ D+NS GSRRGN +VM+RGTFANIR++N L Sbjct: 700 ITTDHISPAGNIKKDSPAGRFLQARGVQPADFNSYGSRRGNDDVMVRGTFANIRIKNLML 759 Query: 772 VDIAGGYTRDFTQEGA--PQAFIYDASVNYKAAGIPLVVLGGKEYGTGSSRDWAAKGTNL 829 GG T ++ GA + IYDA++ YKA G+PLVV GKEYGTGSSRDWAAKGTNL Sbjct: 760 GGEEGGNTLYYSPGGAAPEKLAIYDAAMKYKADGVPLVVFAGKEYGTGSSRDWAAKGTNL 819 Query: 830 LGIRAVITESFERIHRSNLIGMGVVPLQFPAGESHESLGLDGTETFDITGLTALNEGETP 889 LG+RAV+ ESFERIHRSNL+GMGV+PLQF AGE+ ++LGLDG+ET ITGL +G + Sbjct: 820 LGVRAVVAESFERIHRSNLVGMGVLPLQFQAGENAQTLGLDGSETISITGLV---DGAS- 875 Query: 890 KTVKVTATKENGDVVEFDAVVRIDTPGEADYYRHGGILQYVLRQMAA 936 +T V A + +G F+ V + TP E +Y+RHGGIL YVLRQ+AA Sbjct: 876 RTATVVARRADGSEKRFEVKVLLLTPKEVEYFRHGGILHYVLRQLAA 922 Lambda K H 0.314 0.133 0.390 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: 2304 Number of extensions: 127 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: 939 Length of database: 926 Length adjustment: 43 Effective length of query: 896 Effective length of database: 883 Effective search space: 791168 Effective search space used: 791168 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: 42 (22.0 bits) S2: 57 (26.6 bits)
This GapMind analysis is from Sep 24 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