Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_036833329.1 N784_RS06120 aconitate hydratase AcnA
Query= BRENDA::P09339 (909 letters) >NCBI__GCF_000775615.1:WP_036833329.1 Length = 904 Score = 1409 bits (3648), Expect = 0.0 Identities = 681/903 (75%), Positives = 788/903 (87%), Gaps = 1/903 (0%) Query: 8 AAKDVFQARKTFTTNGKTYHYYSLKALEDSGIGKVSKLPYSIKVLLESVLRQVDGFVIKK 67 A KD FQA K F NGK Y+YY LK LE++G+GK+S+LPYSI+VLLESVLRQ DG VI+K Sbjct: 2 AVKDTFQAHKQFELNGKKYNYYKLKTLEEAGLGKISRLPYSIRVLLESVLRQHDGEVIQK 61 Query: 68 EHVENLAKWGTAELKDIDVPFKPSRVILQDFTGVPAVVDLASLRKAMAAVGGDPDKINPE 127 EH+E LAKWG+ E + +DVPFKPSRVILQDFTGVPAVVDLASLRKAM +GG PDKINPE Sbjct: 62 EHIEKLAKWGSKEAESVDVPFKPSRVILQDFTGVPAVVDLASLRKAMVDMGGSPDKINPE 121 Query: 128 IPVDLVIDHSVQVDKAGTEDALAVNMDLEFERNAERYKFLSWAKKAFNNYQAVPPATGIV 187 +PVDLVIDHSVQVD+ GT AL NM+LEFERN ERY+FL+WAKKAF+NYQAVPPATGIV Sbjct: 122 VPVDLVIDHSVQVDEYGTAKALDANMELEFERNKERYEFLNWAKKAFDNYQAVPPATGIV 181 Query: 188 HQVNLEFLASVVHAIE-EDGELVTYPDTLVGTDSHTTMINGIGVLGWGVGGIEAEAGMLG 246 HQVNLE+LA+VVHAIE E GE YPDTLVGTDSHTTMING+GVLGWGVGGIEAEAGMLG Sbjct: 182 HQVNLEYLANVVHAIENEKGEYDAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAGMLG 241 Query: 247 QPSYFPVPEVIGAKLVGKLPNGTTATDLALKVTQVLREKGVVGKFVEFFGPGIAELPLAD 306 QPSYFP PEVIG KL G LP GTTATDLALKVTQ LREK VVGKFVEFFGPG+ E+PLAD Sbjct: 242 QPSYFPAPEVIGVKLTGTLPKGTTATDLALKVTQKLREKNVVGKFVEFFGPGLTEMPLAD 301 Query: 307 RATIANMAPEYGATCGFFPVDEEALNYLRLTGRDPEHIDVVEAYCRSNGLFYTPDAEDPQ 366 RATI+NMAPEYGATCGFFPVD+E+L YLRLTGR E I +VEAYC+ N LFYTPD EDP Sbjct: 302 RATISNMAPEYGATCGFFPVDQESLEYLRLTGRSEEQIQLVEAYCKENDLFYTPDQEDPT 361 Query: 367 FTDVVEIDLSQIEANLSGPKRPQDLIPLSAMQETFKKQLVSPAGNQGFGLNAEEENKEIK 426 FTD+VEI L ++E NLSGPKRPQDLIPL+ M+E+F K L +P GNQGFGL+ +E++K++ Sbjct: 362 FTDLVEIKLDELEPNLSGPKRPQDLIPLTEMKESFNKALTAPEGNQGFGLDEKEKDKKVS 421 Query: 427 FKLLNGEETVMKTGAIAIAAITSCTNTSNPYVLIGAGLVAKKAVELGLKVPNYVKTSLAP 486 + +G+ + MKTGA+AIAAITSCTNTSNPYV++GAGL+AKKAVE GL+VP YVKTSLAP Sbjct: 422 VQHPSGKSSTMKTGAVAIAAITSCTNTSNPYVMLGAGLLAKKAVEKGLEVPEYVKTSLAP 481 Query: 487 GSKVVTGYLVNSGLLPYMKELGFNLVGYGCTTCIGNSGPLSPEIEEAVAKNDLLITSVLS 546 GSKVVT YL +SGL+ Y+++LGFN VGYGCTTCIGNSGPLSPE+E+A+A NDL ++SVLS Sbjct: 482 GSKVVTRYLEDSGLMTYLEKLGFNTVGYGCTTCIGNSGPLSPEVEQAIADNDLTVSSVLS 541 Query: 547 GNRNFEGRIHPLVKGNYLASPPLVVAYALAGTVNINLKTDPIGVGKDGQNVYFNDIWPSM 606 GNRNFEGRIHPLVK NYLASPPLVVAYALAGTV+I+L+ + +G DG++V+F+DIWPSM Sbjct: 542 GNRNFEGRIHPLVKANYLASPPLVVAYALAGTVDIDLRKESLGKDHDGKDVHFDDIWPSM 601 Query: 607 DEINALVKQTVTPELFRKEYETVFDDNKRWNEIETTDEALYKWDNDSTYIQNPPFFEEMS 666 DEI A V + V PE+FRKEYE VFD N++WN+I+TTDE LY WD++STYIQNPPFF +S Sbjct: 602 DEIKAEVDKHVNPEIFRKEYEDVFDSNEKWNQIQTTDEPLYNWDDESTYIQNPPFFVGLS 661 Query: 667 VEPGKVEPLKGLRVVGKFGDSVTTDHISPAGAIGKDTPAGKYLQEKGVSPRDFNSYGSRR 726 +P +V+ L GLRV+GKFGDSVTTDHISPAGAI KD PAGKYLQ+KGVSPR FNSYGSRR Sbjct: 662 EDPSEVKDLDGLRVIGKFGDSVTTDHISPAGAIAKDMPAGKYLQDKGVSPRHFNSYGSRR 721 Query: 727 GNHEVMMRGTFANIRIKNQIAPGTEGGFTTYWPTGEVTSIYDACMKYKEDKTGLVVLAGK 786 GNHEVMMRGTFANIRI+N+IAPGTEGG+TT+WPT EV IYDA MKY+E TGL+V+AG Sbjct: 722 GNHEVMMRGTFANIRIRNKIAPGTEGGYTTFWPTDEVMPIYDAAMKYQEQGTGLLVIAGN 781 Query: 787 DYGMGSSRDWAAKGTNLLGIRTVIAESFERIHRSNLVFMGVLPLQFKQGENADTLGLTGK 846 DYGMGSSRDWAAKGTNLLGI+TVIAESFERIHRSNLV MGVLPLQFK G++AD+LGL+GK Sbjct: 782 DYGMGSSRDWAAKGTNLLGIKTVIAESFERIHRSNLVMMGVLPLQFKDGDSADSLGLSGK 841 Query: 847 EVIEVDVDETVRPRDLVTVRAINEDGNVTTFEAVVRFDSEVEIDYYRHGGILQMVLREKM 906 E ++ +DETV+PRDLV V AI+E GN T F+ + RFDS VEIDYYRHGGILQ VLR+K+ Sbjct: 842 ETFDIKIDETVKPRDLVDVIAIDEAGNKTEFQVIARFDSGVEIDYYRHGGILQKVLRDKL 901 Query: 907 KQS 909 + + Sbjct: 902 QSN 904 Lambda K H 0.316 0.135 0.394 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: 2427 Number of extensions: 93 Number of successful extensions: 2 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: 909 Length of database: 904 Length adjustment: 43 Effective length of query: 866 Effective length of database: 861 Effective search space: 745626 Effective search space used: 745626 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 (21.5 bits) S2: 56 (26.2 bits)
Align candidate WP_036833329.1 N784_RS06120 (aconitate hydratase AcnA)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01341.hmm # target sequence database: /tmp/gapView.3248502.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01341 [M=876] Accession: TIGR01341 Description: aconitase_1: aconitate hydratase 1 Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1478.9 0.0 0 1478.7 0.0 1.0 1 NCBI__GCF_000775615.1:WP_036833329.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000775615.1:WP_036833329.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1478.7 0.0 0 0 1 876 [] 18 901 .. 18 901 .. 0.99 Alignments for each domain: == domain 1 score: 1478.7 bits; conditional E-value: 0 TIGR01341 1 kkvyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlq 72 kk++yy lk+lee+ l+kis+lp+s+r+llesvlr+ dg++i++e++e+l+kw ++e + ++++fkp+rv+lq NCBI__GCF_000775615.1:WP_036833329.1 18 KKYNYYKLKTLEEAgLGKISRLPYSIRVLLESVLRQHDGEVIQKEHIEKLAKWGSKEAESVDVPFKPSRVILQ 90 689*********99789******************************************************** PP TIGR01341 73 dftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkw 145 dftGvpavvdla+lr+a+ ++g+ p+kinp+vpvdlvidhsvqvd++g+ +al+an+elefernkery+fl+w NCBI__GCF_000775615.1:WP_036833329.1 91 DFTGVPAVVDLASLRKAMVDMGGSPDKINPEVPVDLVIDHSVQVDEYGTAKALDANMELEFERNKERYEFLNW 163 ************************************************************************* PP TIGR01341 146 akkafknlkvvppgtGivhqvnleylakvvfeae.kdgellaypdslvGtdshttminGlGvlGwGvGGieae 217 akkaf n+++vpp+tGivhqvnleyla+vv+++e ++ge aypd+lvGtdshttminGlGvlGwGvGGieae NCBI__GCF_000775615.1:WP_036833329.1 164 AKKAFDNYQAVPPATGIVHQVNLEYLANVVHAIEnEKGEYDAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAE 236 *******************************975278************************************ PP TIGR01341 218 aallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianma 290 a++lGqp+++ peviGvkltG l +G+tatdl+l+vt+ lr+k+vvgkfveffG+gl+e++ladrati+nma NCBI__GCF_000775615.1:WP_036833329.1 237 AGMLGQPSYFPAPEVIGVKLTGTLPKGTTATDLALKVTQKLREKNVVGKFVEFFGPGLTEMPLADRATISNMA 309 ************************************************************************* PP TIGR01341 291 peyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkr 362 peyGat++ffp+d+++l+ylrltgr+e++++lve+y+k ++lf++ d e+p++td+ve++l+++e++++Gpkr NCBI__GCF_000775615.1:WP_036833329.1 310 PEYGATCGFFPVDQESLEYLRLTGRSEEQIQLVEAYCKENDLFYTpDQEDPTFTDLVEIKLDELEPNLSGPKR 382 *********************************************999************************* PP TIGR01341 363 pqdrvalkevkaafksslesnagekglalrkeakekkle.....gkeaelkdgavviaaitsctntsnpsvll 430 pqd ++l+e+k++f+++l + g++g++l+ + k+kk+ gk+ ++k+gav+iaaitsctntsnp+v+l NCBI__GCF_000775615.1:WP_036833329.1 383 PQDLIPLTEMKESFNKALTAPEGNQGFGLDEKEKDKKVSvqhpsGKSSTMKTGAVAIAAITSCTNTSNPYVML 455 ******************************9999999877788899*************************** PP TIGR01341 431 gagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveea 503 gagllakkave Gl+v++yvktslapGskvvt yl +sgl++yle+lGfn vGyGcttciGnsGpl+ eve+a NCBI__GCF_000775615.1:WP_036833329.1 456 GAGLLAKKAVEKGLEVPEYVKTSLAPGSKVVTRYLEDSGLMTYLEKLGFNTVGYGCTTCIGNSGPLSPEVEQA 528 ************************************************************************* PP TIGR01341 504 ikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsa 576 i++ndl+vs+vlsGnrnfegrihplvkanylaspplvvayalaGtvdidl+ke +g d+dGk+v++ diwps+ NCBI__GCF_000775615.1:WP_036833329.1 529 IADNDLTVSSVLSGNRNFEGRIHPLVKANYLASPPLVVAYALAGTVDIDLRKESLGKDHDGKDVHFDDIWPSM 601 ************************************************************************* PP TIGR01341 577 keiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgar 649 +ei++ v+k+v++e+f+keye v+++ne+wn++++t+++ly+wd++styi++ppff +l+ +p+ev+d+ g+r NCBI__GCF_000775615.1:WP_036833329.1 602 DEIKAEVDKHVNPEIFRKEYEDVFDSNEKWNQIQTTDEPLYNWDDESTYIQNPPFFVGLSEDPSEVKDLDGLR 674 ************************************************************************* PP TIGR01341 650 illllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeG 722 ++ ++Gds+ttdhispaG+i+kd pa+kyl++kGv++r fnsyGsrrGnhevm+rGtfaniri+nk+++g+eG NCBI__GCF_000775615.1:WP_036833329.1 675 VIGKFGDSVTTDHISPAGAIAKDMPAGKYLQDKGVSPRHFNSYGSRRGNHEVMMRGTFANIRIRNKIAPGTEG 747 ************************************************************************* PP TIGR01341 723 gltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgm 795 g+t+++p++ev+ +ydaamky+++g++l+v+aG++yG+Gssrdwaakgt+llG+k+viaesferihrsnlv+m NCBI__GCF_000775615.1:WP_036833329.1 748 GYTTFWPTDEVMPIYDAAMKYQEQGTGLLVIAGNDYGMGSSRDWAAKGTNLLGIKTVIAESFERIHRSNLVMM 820 ************************************************************************* PP TIGR01341 796 GvlplefkqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveavlridtevelayvkkgGil 868 Gvlpl+fk+g++a++lgl+g+et d++ e++kp++ v v +++e g+k+ +++ +r+d+ ve++y+++gGil NCBI__GCF_000775615.1:WP_036833329.1 821 GVLPLQFKDGDSADSLGLSGKETFDIKIDETVKPRDLVDVIAIDEAGNKTEFQVIARFDSGVEIDYYRHGGIL 893 ***********************99997799****************************************** PP TIGR01341 869 qyvlrkll 876 q vlr++l NCBI__GCF_000775615.1:WP_036833329.1 894 QKVLRDKL 901 ****9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (876 nodes) Target sequences: 1 (904 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 25.69 // [ok]
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