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_099018782.1 CCS90_RS06680 aconitate hydratase AcnA
Query= SwissProt::O53166 (943 letters) >NCBI__GCF_002591915.1:WP_099018782.1 Length = 933 Score = 946 bits (2445), Expect = 0.0 Identities = 477/948 (50%), Positives = 658/948 (69%), Gaps = 24/948 (2%) Query: 1 MTSKSVNSFGAHDTLKVGEKSYQIYRLDAVPNTA----KLPYSLKVLAENLLRNEDGSNI 56 M + ++ F A L++G + ++ + L A+ KLP+S+++L EN +RN DG + Sbjct: 1 MNTLDLDPFKAKKILQIGAEEHEYFSLKALQKQGYAIEKLPFSIRILLENAVRNFDGFGV 60 Query: 57 TKDHIEAIANWDPKAEPSIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVN 116 TK HIE + NW PK +I + PARV+MQDFTGVP +VDLA +R +A G D +N Sbjct: 61 TKAHIETLLNWQPKGGTD-DIPFKPARVLMQDFTGVPAVVDLAAIRAEVARKGKQVDLIN 119 Query: 117 PLAPADLVIDHSVIADLFGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTG 176 PL P DLVIDHSV D FG D+++RN+E+EY RN ERYQ L+W Q AF +F VVPPG G Sbjct: 120 PLIPVDLVIDHSVQIDYFGTEDSYQRNIELEYSRNRERYQLLKWAQNAFTNFSVVPPGMG 179 Query: 177 IVHQVNIEYLASVVMTRDGVAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPV 236 I HQVN+EYL+ V+ RDG +PDT VGTDSHT MVNG+GV+GWGVGGIEAEAA+LGQP+ Sbjct: 180 ICHQVNLEYLSQGVIARDGQLFPDTLVGTDSHTPMVNGIGVVGWGVGGIEAEAAILGQPI 239 Query: 237 SMLIPRVVGFRLTGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRAT 296 ++P V+G +L+G + G TATD+VLTV E+LR HGVVGKFVE +G+G+ + + +RAT Sbjct: 240 YFIMPEVIGLKLSGTLPVGSTATDLVLTVAELLRTHGVVGKFVEVFGQGLDTLSVPDRAT 299 Query: 297 LGNMSPEFGSTAAIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDPKHEPEFSEY 356 LGNMSPEFG T FPID++T++Y+R + R+ EQ+ VE Y K +W + + ++ Sbjct: 300 LGNMSPEFGCTITYFPIDDKTLEYMRNSNRSDEQIERVERYCKENMLWRENEEAINYTTV 359 Query: 357 LELNLSDVVPSIAGPKRPQDRIALAQAKSTFREQIYHYVGNGSPDSPHDPHSKLDEVVEE 416 LEL++S + P+IAGPK PQ +I L AK+ F E ++ G + + + +E +E+ Sbjct: 360 LELDVSGIKPTIAGPKLPQQKILLENAKAKFGELLHGGFGRSYVE---EKDRETEEELEK 416 Query: 417 TFPASDPGQLTFANDDVATDETVHSAAAHADGRVSNPVRV--KSDELGEFVLDHGAVVIA 474 F Q+ +N+D T + +H G+ N ++ +E ++ L G++ IA Sbjct: 417 RFVDEGGDQIEKSNED-KTIKQIHR------GKTINGLKSVWVDEERLKYKLADGSIAIA 469 Query: 475 AITSCTNTSNPEVMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLE 534 AITSCTNTSNP VM+GA L+ARNA++KG+ KPWVKT++APGS+VV DY +++GL E Sbjct: 470 AITSCTNTSNPFVMIGAGLVARNAIKKGIDVKPWVKTSLAPGSKVVTDYLNKAGLMTDFE 529 Query: 535 KLGFYLVGYGCTTCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYLA 594 L F+LVGYGCT+CIGNSGPL + +AV D DL VT+VLSGNRNFE RI+P VKMN+L Sbjct: 530 ALQFHLVGYGCTSCIGNSGPLLPAVEQAVKDYDLVVTSVLSGNRNFEARIHPLVKMNFLM 589 Query: 595 SPPLVIAYALAGTMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTRN 654 SP LV+A+ALAG +D D + + LG ++G V+LRDIWPS +++ +A + + F +N Sbjct: 590 SPMLVVAFALAGRVDIDMENEALGHTRNGDPVYLRDIWPSDDEINAIMAEVLTPKYFAKN 649 Query: 655 YADVFKGDDRWRNLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALLG 714 Y ++F G+ W+++P GN ++W+ +STY+++ P+F+ + +P + NI AR L LG Sbjct: 650 YGEIFAGNQIWQDMPVAKGNLYQWEESSTYIQEIPFFKDLPEQPAAMQNIIDARALLKLG 709 Query: 715 DSVTTDHISPAGAIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRNQ 774 D+ +TDHISPAG+ + A +YL GV R D+NS+GSRRGN EVM+RGTFAN+R++NQ Sbjct: 710 DNTSTDHISPAGSFNETSAAGQYLISKGVKRADFNSYGSRRGNDEVMLRGTFANVRIKNQ 769 Query: 775 LLDDVSGGYTRDFTQPGGPQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTLL 834 L+ + GG T P + +Y+AA+ Y +IPLVV GGKEYGSGSSRDWAAKGT L Sbjct: 770 LV-ETEGGVT--LYLPTQEEMSVYEAAKKYRENNIPLVVLGGKEYGSGSSRDWAAKGTSL 826 Query: 835 LGVRAVIAESFERIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKTP 894 LGV+AV+ +S+ERIHRSNL+ MGV+PLQ+ G++A SL LDGTE F+ITGI +G P Sbjct: 827 LGVKAVLVDSYERIHRSNLVYMGVLPLQYLPGQNADSLSLDGTETFNITGI---AEGLEP 883 Query: 895 -KTVCVQATKGDGATIEFDAVVRIDTPGEADYYRNGGILQYVLRNILK 941 K V V+A K DG + F+A R+D+ E YY++GGILQYVLR+ LK Sbjct: 884 RKKVSVKAIKADGEVVSFEAEARLDSAIEVAYYQHGGILQYVLRDFLK 931 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: 2232 Number of extensions: 113 Number of successful extensions: 5 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: 933 Length adjustment: 43 Effective length of query: 900 Effective length of database: 890 Effective search space: 801000 Effective search space used: 801000 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