Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_045580974.1 AL072_RS06770 aconitate hydratase AcnA
Query= SwissProt::P37032 (891 letters) >NCBI__GCF_001305595.1:WP_045580974.1 Length = 896 Score = 1190 bits (3079), Expect = 0.0 Identities = 590/890 (66%), Positives = 704/890 (79%), Gaps = 3/890 (0%) Query: 4 GQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTK 63 GQDSL T+ L+ GK+Y+Y+SLK AE ++RLP+S+KVLLENLLRFEDG TV+ Sbjct: 6 GQDSLKTRRSLSAGGKSYDYFSLKAAEQAGLGDLSRLPFSMKVLLENLLRFEDGRTVSVD 65 Query: 64 DIKAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLS 123 D+KA+A WL +K S EIA+RP RVLMQDFTGVPAV DLAAMR A+ +GG+ KI+PL Sbjct: 66 DVKAVAQWLVDKRSDREIAYRPARVLMQDFTGVPAVCDLAAMREAMAALGGDPAKINPLV 125 Query: 124 PVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICH 183 PVDLVIDHSVMVD F AD+ + N +E ERN ERYEFLRWGQKAF NF+VVPPGTGICH Sbjct: 126 PVDLVIDHSVMVDYFGGADSFQRNVDLEFERNLERYEFLRWGQKAFDNFRVVPPGTGICH 185 Query: 184 QVNLEYLGKTVW-NSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 242 QVN EYL + VW +++ G+ AYPDTLVGTDSHTTM+NGL VLGWGVGGIEAEAAMLGQ Sbjct: 186 QVNTEYLSQVVWTDADPSGRPVAYPDTLVGTDSHTTMVNGLSVLGWGVGGIEAEAAMLGQ 245 Query: 243 PVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADR 302 P+SMLIPEVIGFKL+G++KEG+TATDLVLTVTQMLR+KGVVGKFVEF+GPGL+ + L DR Sbjct: 246 PISMLIPEVIGFKLTGRMKEGMTATDLVLTVTQMLRRKGVVGKFVEFFGPGLDSMTLPDR 305 Query: 303 ATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVF 362 ATI NMAPEYGATCG FP+D ETI+YL TGRD +ALVEAYAKAQGMW + D+ +PVF Sbjct: 306 ATIGNMAPEYGATCGIFPIDAETIRYLTFTGRDPGRVALVEAYAKAQGMWREPDSPDPVF 365 Query: 363 TDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDFQM 422 +D L LD+G+VEPSLAGPKRPQD+V LS+L F + E K + +K VK+ + + Sbjct: 366 SDVLELDMGTVEPSLAGPKRPQDRVALSALAQGFARDMAEAYKADDPKKAVPVKDAGYSL 425 Query: 423 KHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRH 482 + G VVIAAITSCTNTSNP+VL+AAGL+AKKA+EKGL +KPWVK+SLAPGS+VVTDYL Sbjct: 426 EQGAVVIAAITSCTNTSNPAVLVAAGLLAKKAVEKGLAQKPWVKTSLAPGSQVVTDYLAK 485 Query: 483 AGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHP 542 AGLQ YLD+LGFN+VGYGCTTCIGNSGPLP+ I+ V + +LVV +VLSGNRNFEGRV+P Sbjct: 486 AGLQPYLDRLGFNIVGYGCTTCIGNSGPLPEPIAAAVEDGNLVVGAVLSGNRNFEGRVNP 545 Query: 543 QVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEV-AKV 601 RAN+LASPPL VAYAL G DL+ EP+G +G VYLKDIWP+N E+ + A + Sbjct: 546 HTRANYLASPPLCVAYALAGNLNIDLTTEPLGTGTDGQPVYLKDIWPTNREVQDAIDASL 605 Query: 602 SGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIKQ 661 + MFR Y++VFKG WQAI T+ GQTY+W STY++ PPFF L+ +P+ ++ Sbjct: 606 TADMFRSRYSDVFKGPEQWQAIATAEGQTYQWQDASTYVKLPPFFSGLTRTLDPVSDVRG 665 Query: 662 AYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTF 721 A LA+ GDSITTDHISPAGSIK +SPAG YL S V +DFNSYG+RRGNHEVMMRGTF Sbjct: 666 ARALAVLGDSITTDHISPAGSIKRTSPAGEYLLSHQVRLQDFNSYGARRGNHEVMMRGTF 725 Query: 722 ANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWA 781 ANIRIRNE+ PG EGG T++ P+GE + IY AAMRY + LV++AGKEYGTGSSRDWA Sbjct: 726 ANIRIRNELLPGVEGGETKHYPSGERLPIYTAAMRYADEGVPLVVVAGKEYGTGSSRDWA 785 Query: 782 AKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIE-ISDK 840 AKGT LLG+KAVI ESFERIHRSNL+GMGILPLQFK+G TR LKLDGSE I I Sbjct: 786 AKGTRLLGIKAVIAESFERIHRSNLVGMGILPLQFKDGLTRADLKLDGSETFDIAGIEQD 845 Query: 841 LTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKIS 890 L P V +T+ R DG +E L RIDT DE+EYY+NGG+L +VLR ++ Sbjct: 846 LRPRKDVALTLTRADGTVEHHTLLLRIDTLDEVEYYRNGGVLNFVLRNLA 895 Lambda K H 0.316 0.134 0.393 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: 2095 Number of extensions: 86 Number of successful extensions: 4 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: 891 Length of database: 896 Length adjustment: 43 Effective length of query: 848 Effective length of database: 853 Effective search space: 723344 Effective search space used: 723344 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: 56 (26.2 bits)
Align candidate WP_045580974.1 AL072_RS06770 (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.1465066.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 1377.4 0.0 0 1377.2 0.0 1.0 1 NCBI__GCF_001305595.1:WP_045580974.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001305595.1:WP_045580974.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1377.2 0.0 0 0 1 875 [. 21 894 .. 21 895 .. 0.98 Alignments for each domain: == domain 1 score: 1377.2 bits; conditional E-value: 0 TIGR01341 1 kkvyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlq 72 k++ y+slka+e++ l+++s+lp s+++lle++lr dg++++ +dv+a+++w ++ +d+eia++parv++q NCBI__GCF_001305595.1:WP_045580974.1 21 KSYDYFSLKAAEQAgLGDLSRLPFSMKVLLENLLRFEDGRTVSVDDVKAVAQWLVDKRSDREIAYRPARVLMQ 93 5789********98789******************************************************** PP TIGR01341 73 dftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkw 145 dftGvpav dlaa+rea+++lg+dp+kinplvpvdlvidhsv vd++g ++++ nv+lefern ery+fl+w NCBI__GCF_001305595.1:WP_045580974.1 94 DFTGVPAVCDLAAMREAMAALGGDPAKINPLVPVDLVIDHSVMVDYFGGADSFQRNVDLEFERNLERYEFLRW 166 ************************************************************************* PP TIGR01341 146 akkafknlkvvppgtGivhqvnleylakvvfea.ekdgellaypdslvGtdshttminGlGvlGwGvGGieae 217 ++kaf n++vvppgtGi+hqvn eyl++vv++ + g+ +aypd+lvGtdshttm+nGl vlGwGvGGieae NCBI__GCF_001305595.1:WP_045580974.1 167 GQKAFDNFRVVPPGTGICHQVNTEYLSQVVWTDaDPSGRPVAYPDTLVGTDSHTTMVNGLSVLGWGVGGIEAE 239 ******************************9751568************************************ PP TIGR01341 218 aallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianma 290 aa+lGqp+s+ +peviG+kltG+++eG+tatdlvltvt++lr+kgvvgkfveffG+gl++++l+drati nma NCBI__GCF_001305595.1:WP_045580974.1 240 AAMLGQPISMLIPEVIGFKLTGRMKEGMTATDLVLTVTQMLRRKGVVGKFVEFFGPGLDSMTLPDRATIGNMA 312 ************************************************************************* PP TIGR01341 291 peyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkr 362 peyGat+++fpid++t+ yl tgrd +v lve+y+kaq+++++ ds +p+++dv+eld+ +ve+s+aGpkr NCBI__GCF_001305595.1:WP_045580974.1 313 PEYGATCGIFPIDAETIRYLTFTGRDPGRVALVEAYAKAQGMWREpDSPDPVFSDVLELDMGTVEPSLAGPKR 385 *********************************************9*************************** PP TIGR01341 363 pqdrvalkevkaafksslesnagekglalrkeakekklegkeaelkdgavviaaitsctntsnpsvllgagll 435 pqdrval+++ + f++ + + + +k+a+ k + ++l++gavviaaitsctntsnp+vl++agll NCBI__GCF_001305595.1:WP_045580974.1 386 PQDRVALSALAQGFARDMAEAYKADD---PKKAVPVK--DAGYSLEQGAVVIAAITSCTNTSNPAVLVAAGLL 453 **************999887666655...55555544..899******************************* PP TIGR01341 436 akkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikend 508 akkave Gl kp+vktslapGs+vvtdyla++gl+pyl++lGfn+vGyGcttciGnsGpl+e ++ a+ +++ NCBI__GCF_001305595.1:WP_045580974.1 454 AKKAVEKGLAQKPWVKTSLAPGSQVVTDYLAKAGLQPYLDRLGFNIVGYGCTTCIGNSGPLPEPIAAAVEDGN 526 ************************************************************************* PP TIGR01341 509 levsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiae 581 l+v avlsGnrnfegr++p ++anylasppl vayalaG+++idl++ep+gt++dG++vylkdiwp+++e+++ NCBI__GCF_001305595.1:WP_045580974.1 527 LVVGAVLSGNRNFEGRVNPHTRANYLASPPLCVAYALAGNLNIDLTTEPLGTGTDGQPVYLKDIWPTNREVQD 599 ************************************************************************* PP TIGR01341 582 lvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillll 654 +++ +++ ++f+ +y+ v++g e+w+ + ++++++y+w++ sty+++ppff++l+ + + v+d++gar l++l NCBI__GCF_001305595.1:WP_045580974.1 600 AIDASLTADMFRSRYSDVFKGPEQWQAIATAEGQTYQWQDASTYVKLPPFFSGLTRTLDPVSDVRGARALAVL 672 ************************************************************************* PP TIGR01341 655 GdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvy 727 GdsittdhispaGsik+ spa++yl + v +dfnsyG+rrGnhevm+rGtfaniri+n+l++g eGg t++ NCBI__GCF_001305595.1:WP_045580974.1 673 GDSITTDHISPAGSIKRTSPAGEYLLSHQVRLQDFNSYGARRGNHEVMMRGTFANIRIRNELLPGVEGGETKH 745 ************************************************************************* PP TIGR01341 728 lpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlpl 800 +p +e + +y aam+y +egvplvv+aGkeyG+Gssrdwaakgt+llG+kaviaesferihrsnlvgmG+lpl NCBI__GCF_001305595.1:WP_045580974.1 746 YPSGERLPIYTAAMRYADEGVPLVVVAGKEYGTGSSRDWAAKGTRLLGIKAVIAESFERIHRSNLVGMGILPL 818 ************************************************************************* PP TIGR01341 801 efkqgedaetlgltgeetidvddi.eelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvl 872 +fk+g ++ l l+g+et d+ +i ++l+p+k+v ++l+++dg +e + lridt e++y+++gG+l++vl NCBI__GCF_001305595.1:WP_045580974.1 819 QFKDGLTRADLKLDGSETFDIAGIeQDLRPRKDVALTLTRADGTVEHHTLLLRIDTLDEVEYYRNGGVLNFVL 891 ***********************8358********************************************** PP TIGR01341 873 rkl 875 r+l NCBI__GCF_001305595.1:WP_045580974.1 892 RNL 894 *96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (876 nodes) Target sequences: 1 (896 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 32.22 // [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