Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_065400933.1 BBI00_RS21750 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683 (865 letters) >NCBI__GCF_001684965.1:WP_065400933.1 Length = 927 Score = 328 bits (842), Expect = 7e-94 Identities = 285/928 (30%), Positives = 444/928 (47%), Gaps = 114/928 (12%) Query: 3 EEYRKHVAERAAEGIAPKPLD-ANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEAA 61 ++Y K + ER +G+ PKP+D A ++ ++ +K+ + L PG AA Sbjct: 5 KDYIKEIEERKTQGLHPKPIDSAELLSEIIAQIKDSGNADRTDSLQFFIYNTLPGTTSAA 64 Query: 62 YVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDAL--DDAKLAPIAAKAL 119 VKA FL I GE+ +TP+ A ELL M+GG +I L+D +D +A AA L Sbjct: 65 GVKAQFLKEIILGESVVEEITPDFAFELLSHMKGGKSIEVLLDLALGNDTAIAQQAADVL 124 Query: 120 SHTLLMFD-NFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKL-TVTVFKVTGET 177 + +++ + +++ +GN AK++++S+A AE+F P +AE++ VT G+ Sbjct: 125 KTQVFLYEADTNRLKDAYNSGNAIAKEILESYAKAEFFTKLPEVAEEIKVVTYIAGEGDI 184 Query: 178 NTDDLSPAPDAWSRPDIPLHALAMLK-NAREGIEPDQPGVVGPIKQIEALQQKGFPLAYV 236 +TD LSP A SR D LH M+ A++ I+ Q P + + +KG Sbjct: 185 STDLLSPGNQAHSRSDRELHGKCMITPEAQQEIKALQ--AQHPDASVMLIAEKG------ 236 Query: 237 GDVVGTGSSRKSATNSV-LWFMGDDIPHVPNKRGGGLCLGGK-IAPIFFNTMEDAGALPI 294 +G GSSR S N+V LW P+VP + G I+PIF T++ G + I Sbjct: 237 --TMGVGSSRMSGVNNVALWTGKQASPYVPFVNIAPIVGGTNGISPIFLTTVDVTGGIGI 294 Query: 295 EV------------------------DVSNLNMGDVIDVYPYKGEVRNHETGELLATFEL 330 ++ + ++ G V+ + + ++ N + EL+ + Sbjct: 295 DLKNWVKKVDENGNPVRNEAGEVILEEAYSVATGTVLTINTKEKKLYNGDQ-ELIDLTKS 353 Query: 331 KTDVLIDEVRAGGRIPLIIGRGLTTKAREALGLPHSDVFRQAKDVAESDRGFSLAQKMVG 390 T ++ ++AGG ++ G+ L T A + LG+ VF +K+++ +G + +K+ Sbjct: 354 FTPQKMEFIKAGGSYAIVFGKKLQTFAAQTLGIEAPVVFAPSKEISHEGQGLTAVEKIFN 413 Query: 391 R-ACGV---KGIRPGAYCEPKMTSVGSQDTTGPMTRDELKDLACLGFS--ADLVMQSFCH 444 R A G K + G+ K+ VGSQDTTG MT EL+ +A S D QS CH Sbjct: 414 RNAVGTTPGKVLHAGSDVRVKVNIVGSQDTTGLMTAQELESMAATVISPTVDGAYQSGCH 473 Query: 445 TAA-YPKPVDVNTHHTLPDFIMNRGGVSLRPGDG-------VIHSWLNRMLLPD-TVGTG 495 TA+ + K N L F+ + G ++ R G VIH LN + + + + G Sbjct: 474 TASVWDKKAQANIPK-LMKFMNDFGLITARDPKGEYHSMTDVIHKVLNDITVDEWAIIIG 532 Query: 496 GDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVHAIPL 555 GDSHTR G++F A SG VA A ATG + +PESV V FKG+M+P + RD+VHA Sbjct: 533 GDSHTRMSKGVAFGADSGTVALALATGEASMPIPESVKVTFKGEMKPHMDFRDVVHATQA 592 Query: 556 YAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTIKLNKEP 615 +KQ G +N+F GRI+E+ + L +QAF TD +AE A Sbjct: 593 QMLKQ-------FGGENVFQGRIIEVH-IGTLPADQAFTFTDWTAEMKAKASINISEDNT 644 Query: 616 IIEYLNSNIVLLKWMIAEGYGD-RRTLERRIQGMEKWL-----ANPELLEADADAEYAAV 669 +IE L ++ MI +G + + L+ I K + L DA+A+Y A Sbjct: 645 LIESLEIAKGRIQIMIDKGMDNHNKVLQGLIDKANKRIEEIRSGEKPALTPDANAKYYAE 704 Query: 670 IDIDLADIKEPILCAPN----------DPDDARPLSAVQGE-KIDEVFIGSCMTNIGHFR 718 + +DL I EP++ P+ D R LS GE K+D F+GSCM + G + Sbjct: 705 VVVDLDVIVEPMIADPDVNNEDVSKRYTHDTIRDLSYYGGEKKVDLGFVGSCMVHKGDLK 764 Query: 719 AAGKLL-----DAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGK-SGAR--------- 763 ++L K + L VA PT +L EG + + K SG Sbjct: 765 IVSQMLRNLEKQQGKVEFNAPLVVAAPTYNIIDELKAEGDWELLEKYSGFEFNDNAPKGE 824 Query: 764 ----------IEIPGCSLCMGNQARVADGATVVSTSTRNFPNRLGTGA-----NVFLASA 808 +E PGC+LCMGNQ + A G TV++TSTR F R+ + LAS Sbjct: 825 ARTQYENVMYLERPGCNLCMGNQEKAAKGDTVLATSTRLFQGRVVEDSERKKGESLLAST 884 Query: 809 ELAAVAALIGKLPTPEEYQTYVAQVDKT 836 + ++A+IG++P+ +EY+ V +D T Sbjct: 885 PVVVLSAIIGRIPSIDEYKAAVEGIDLT 912 Lambda K H 0.317 0.136 0.400 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: 1785 Number of extensions: 100 Number of successful extensions: 13 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: 865 Length of database: 927 Length adjustment: 43 Effective length of query: 822 Effective length of database: 884 Effective search space: 726648 Effective search space used: 726648 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 (21.7 bits) S2: 56 (26.2 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