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 N515DRAFT_1419 N515DRAFT_1419 aconitate hydratase
Query= SwissProt::O53166 (943 letters) >FitnessBrowser__Dyella79:N515DRAFT_1419 Length = 916 Score = 1110 bits (2871), Expect = 0.0 Identities = 569/946 (60%), Positives = 704/946 (74%), Gaps = 49/946 (5%) Query: 6 VNSFGAHDTLKVGEKSYQIYRLDAVP---NTAKLPYSLKVLAENLLRNEDGSNITKDHIE 62 ++SF DTLKV SYQI L + + LPYS+K+L ENLLR+EDG N+T IE Sbjct: 2 LDSFATRDTLKVNGSSYQIASLAKLGQRFDIKHLPYSMKILLENLLRHEDGVNVTAKEIE 61 Query: 63 AIANWDPKAEPSIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAPAD 122 A+A W+PKAEP EI + PARVV+QDFTGVPC+VDLA MR+A+ LGG+ ++NPLAPA+ Sbjct: 62 AVARWNPKAEPDTEIAFMPARVVLQDFTGVPCVVDLAAMRDAVVKLGGDAKQINPLAPAE 121 Query: 123 LVIDHSVIADLFGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTGIVHQVN 182 LVIDHSV D++G A E+NV IE+QRN ERY FLRWGQ AFD+FKVVPP TGIVHQVN Sbjct: 122 LVIDHSVQVDVYGSESALEQNVAIEFQRNQERYAFLRWGQKAFDNFKVVPPRTGIVHQVN 181 Query: 183 IEYLASVVMT--RDGV--AYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM 238 +EYL VV T +DG AYPDT GTDSHTTM+NG+GVLGWGVGGIEAEAAMLGQP SM Sbjct: 182 LEYLGRVVFTGEKDGQSWAYPDTVFGTDSHTTMINGVGVLGWGVGGIEAEAAMLGQPSSM 241 Query: 239 LIPRVVGFRLTGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRATLG 298 LIP+VVGF+LTG++ GVTATD+VLTVT+MLR+ GVVGKFVEF+G G+ ++ LA+RAT+G Sbjct: 242 LIPQVVGFKLTGKLAEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLKDLALADRATIG 301 Query: 299 NMSPEFGSTAAIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDPKH-EPEFSEYL 357 NM+PE+G+T IFP+D+E + YLR +GR+ E + LV+AYA+AQG+WHD +F+ L Sbjct: 302 NMAPEYGATCGIFPVDQEALNYLRLSGRSEEHIELVKAYAQAQGLWHDENTPHAQFTTTL 361 Query: 358 ELNLSDVVPSIAGPKRPQDRIALAQAKSTFREQIYHYVGNGSPDSPHDPHSKLDEVVEET 417 EL+L DV PS+AGPKRPQDR+ L + +FR+ + N P Sbjct: 362 ELDLGDVRPSLAGPKRPQDRVLLQDVEKSFRDALGPLTANRRP----------------- 404 Query: 418 FPASDPGQLTFANDDVATDETVHSAAAHADGRVSNPVR---VKSDELGE-FVLDHGAVVI 473 N D T ++ + A G +N V V ++ GE F L GAVVI Sbjct: 405 -----------RNGD--TSNFINEGGSAAIGNPANAVSESGVLVEKNGESFRLGDGAVVI 451 Query: 474 AAITSCTNTSNPEVMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYL 533 AAITSCTNTSNP VMLGA LLA+ A KGL ++PWVKT++ PGS+VV DY +++GL L Sbjct: 452 AAITSCTNTSNPAVMLGAGLLAKKAAAKGLKAQPWVKTSLGPGSKVVTDYLEKTGLLQEL 511 Query: 534 EKLGFYLVGYGCTTCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYL 593 EK+GFY+VGYGCTTCIGNSGPLP EISK + + DL+V +VLSGNRNFEGR++P+VKMNYL Sbjct: 512 EKVGFYVVGYGCTTCIGNSGPLPAEISKGIAEGDLAVASVLSGNRNFEGRVHPEVKMNYL 571 Query: 594 ASPPLVIAYALAGTMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTR 653 ASPPLV+AYALAG++D D PLG DG+ V+LRDIWPS Q++SDTIA AIN MF + Sbjct: 572 ASPPLVVAYALAGSLDVDLSKDPLGTGSDGQPVYLRDIWPSNQEISDTIAGAINPAMFAK 631 Query: 654 NYADVFKGDDRWRNLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALL 713 NYADVF+GDDRW ++ +P G+ ++W +STY++ PPYF+GMT + V +I GARVL L Sbjct: 632 NYADVFQGDDRWNHIASPDGSVYQWG-DSTYIKNPPYFDGMTREVGKVEDIHGARVLGLF 690 Query: 714 GDSVTTDHISPAGAIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRN 773 GDS+TTDHISPAG+IK +PA R+L GV+ KD+NS+GSRRGN +VM+RGTFANIR+RN Sbjct: 691 GDSITTDHISPAGSIKKDSPAGRFLIGKGVEPKDFNSYGSRRGNDDVMVRGTFANIRIRN 750 Query: 774 QLLDDVSGGYTRDFTQPGGPQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTL 833 +LD V GGYT P G Q IYDAA Y A+H PLVV GKEYG+GSSRDWAAKGTL Sbjct: 751 LMLDGVEGGYT--LHVPSGEQLAIYDAAMKYKAEHTPLVVLAGKEYGTGSSRDWAAKGTL 808 Query: 834 LLGVRAVIAESFERIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKT 893 LLGV+AVIAESFERIHRSNL+GMGV+P QF +G+SA +LGL G EVFDITG LNDG++ Sbjct: 809 LLGVKAVIAESFERIHRSNLVGMGVLPCQFEDGQSAQTLGLTGKEVFDITG---LNDGES 865 Query: 894 PKTVCVQATKGDGATIEFDAVVRIDTPGEADYYRNGGILQYVLRNI 939 K V AT DG+ EF V + TP E +++R+GGILQYVLR + Sbjct: 866 -KVAKVTATAPDGSRKEFIVKVLLLTPKEREFFRHGGILQYVLRQL 910 Lambda K H 0.316 0.136 0.403 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: 2418 Number of extensions: 137 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: 943 Length of database: 916 Length adjustment: 43 Effective length of query: 900 Effective length of database: 873 Effective search space: 785700 Effective search space used: 785700 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: 57 (26.6 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