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_077243786.1 B1A74_RS03615 aconitate hydratase AcnA
Query= SwissProt::O53166 (943 letters) >NCBI__GCF_001995255.1:WP_077243786.1 Length = 917 Score = 1069 bits (2765), Expect = 0.0 Identities = 551/937 (58%), Positives = 672/937 (71%), Gaps = 37/937 (3%) Query: 14 TLKVGEKSYQIYRLDAVPNTAKLPYSLKVLAENLLRNEDGSNITKDHIEAIANWDPKAEP 73 TL G Q + LP++LKVL ENL+R+EDG +T+D IE + +WDP AEP Sbjct: 11 TLSAGGHECQYVPIADDRRAQTLPFALKVLLENLMRHEDGRTVTRDDIEGLLDWDPAAEP 70 Query: 74 SIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAPADLVIDHSVIADL 133 S EI + PARV++QDFTGVP +VDLA MR+A+ DLGG+P K+ PL PA+LVIDHSV D Sbjct: 71 SREIAFRPARVLLQDFTGVPAVVDLAAMRDAMEDLGGDPAKIAPLQPAELVIDHSVQVDS 130 Query: 134 FGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTGIVHQVNIEYLASVVMTR 193 +G A++ N E+EY RN ERY FL+WGQ AF+ FKVVPP TGIVHQVN+EYLA V Sbjct: 131 YGEANSMNLNAELEYSRNRERYSFLKWGQQAFETFKVVPPDTGIVHQVNLEYLARTVFLE 190 Query: 194 DG-----VAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSMLIPRVVGFRL 248 D +AYPDT VGTDSHTTM+NGLGVLGWGVGGIEAEAAMLGQP+SMLIP+VVGFRL Sbjct: 191 DRADGSCMAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPISMLIPQVVGFRL 250 Query: 249 TGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRATLGNMSPEFGSTA 308 TG++ G TATD+VL + E LR+HGVVGKFVEF+G+G+A++PLA+RAT+ NM+PE+G+T Sbjct: 251 TGKLAEGATATDLVLVIVEQLRKHGVVGKFVEFFGDGLADLPLADRATIANMAPEYGATC 310 Query: 309 AIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDPKHE-PEFSEYLELNLSDVVPS 367 IFPID+ET++YLR TGR + +EAYA+ QG+W D +S+ LEL+LS V PS Sbjct: 311 GIFPIDDETLEYLRLTGREESHIQFIEAYARGQGLWRDDSAPVARYSDLLELDLSTVEPS 370 Query: 368 IAGPKRPQDRIALAQAKSTFREQIYHYVGNGSPDSPHDPHSKLDEVVEETFPASDPGQLT 427 +AGPKRPQDRI L+QA G+ S H LD V++E D Sbjct: 371 LAGPKRPQDRIPLSQA--------------GAEISRH-----LDTVLKERVSGKDEP--- 408 Query: 428 FANDDVATDETVHSAAAHADGRVSNPVRVKSDELGE-FVLDHGAVVIAAITSCTNTSNPE 486 + + E H+A + + P + GE F LDHG VVIAAITSCTNTSNP Sbjct: 409 -SEAERFATEGGHTAVG-VEHQAEEPHHTAIEMGGETFTLDHGDVVIAAITSCTNTSNPS 466 Query: 487 VMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLEKLGFYLVGYGCT 546 VMLGA L+AR A E+GL KPWVKT++APGS+VV DY +GL LE LGFY+VGYGCT Sbjct: 467 VMLGAGLVARKARERGLKVKPWVKTSLAPGSRVVTDYLQNAGLLEDLEDLGFYVVGYGCT 526 Query: 547 TCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYLASPPLVIAYALAG 606 TCIGNSGPLPE IS+A+ +DL V++VLSGNRNFEGRI+ +V+MN+LASPPLV+AYALAG Sbjct: 527 TCIGNSGPLPEAISEAIVKDDLVVSSVLSGNRNFEGRIHSEVQMNFLASPPLVVAYALAG 586 Query: 607 TMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTRNYADVFKGDDRWR 666 + D PLG D DG V+L+DIWP+ Q+V D +A + FT Y D++ G++RWR Sbjct: 587 RSNLDLYNDPLGDDADGNPVYLKDIWPTSQEVRDEVARHVGAGSFTTAYGDLYTGENRWR 646 Query: 667 NLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALLGDSVTTDHISPAG 726 NL PSG+ F+W +STYVRKPPYF+GM P +I GARVLALLGDSVTTDHISPAG Sbjct: 647 NLEAPSGDRFDWQEDSTYVRKPPYFDGMGMTPAETPDIEGARVLALLGDSVTTDHISPAG 706 Query: 727 AIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRNQLLDDVSGGYTRD 786 +I +PAARYL+E GV D+NS+GSRRGNHEVM+RGTFAN+RLRN L GG TR Sbjct: 707 SIASDSPAARYLEEQGVKPADFNSYGSRRGNHEVMMRGTFANVRLRNLLAPGTQGGVTRH 766 Query: 787 FTQPGGPQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTLLLGVRAVIAESFE 846 P G Q IYDA+ Y A+ PLVV GKEYG+GSSRDWAAKGTLLLGV+AVI ES+E Sbjct: 767 L--PDGEQMSIYDASMRYQAEGTPLVVIAGKEYGTGSSRDWAAKGTLLLGVKAVIVESYE 824 Query: 847 RIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKTPKTVCVQATKGDG 906 RIHRSNL+GMGV+PLQF +G++A SLGL G E + ITGI G+ K V AT DG Sbjct: 825 RIHRSNLVGMGVLPLQFHDGENAESLGLTGEETYTITGI---RSGEA-KEATVTATADDG 880 Query: 907 ATIEFDAVVRIDTPGEADYYRNGGILQYVLRNILKSG 943 + EF VR+DTP E DYYR+GGIL YVLR + G Sbjct: 881 SRKEFRVRVRLDTPQEIDYYRHGGILPYVLRQLAGEG 917 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: 2348 Number of extensions: 113 Number of successful extensions: 6 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: 943 Length of database: 917 Length adjustment: 43 Effective length of query: 900 Effective length of database: 874 Effective search space: 786600 Effective search space used: 786600 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 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