Align Aconitate hydratase A; 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_086511660.1 BZY95_RS20065 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8 (869 letters) >NCBI__GCF_002151265.1:WP_086511660.1 Length = 869 Score = 1401 bits (3627), Expect = 0.0 Identities = 700/866 (80%), Positives = 764/866 (88%), Gaps = 3/866 (0%) Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60 MN+ RKPLPGT+LDYFD R AVE IQPGAYD LPYTSRVLAE LVRRC+P LTD+L Q Sbjct: 1 MNTQYRKPLPGTELDYFDVREAVEEIQPGAYDTLPYTSRVLAEQLVRRCEPELLTDALKQ 60 Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120 L+ R+RDLDFPW+PARVVCHDILGQTALVDLAGLRDAIA++GGDP+KVNPVVP QLIVDH Sbjct: 61 LIERRRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDH 120 Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180 SLAVECGG DPDAFAKNRAIEDRRNEDRFHFIDWT+ AFKNVDVIP GNGIMHQINLEKM Sbjct: 121 SLAVECGGDDPDAFAKNRAIEDRRNEDRFHFIDWTRTAFKNVDVIPAGNGIMHQINLEKM 180 Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240 SPVI A +GVAYPDTCVGTDSHTPH+D LGVIAIGVGGLEAE VMLGR S MRLPDIVGV Sbjct: 181 SPVIQARDGVAYPDTCVGTDSHTPHIDCLGVIAIGVGGLEAETVMLGRPSMMRLPDIVGV 240 Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300 ELTGKRQ GITATDIVLA+TEFLR+E+VVGAYLEF GEGA SLT+GDRATISNM PEYGA Sbjct: 241 ELTGKRQSGITATDIVLAITEFLRQERVVGAYLEFFGEGADSLTIGDRATISNMTPEYGA 300 Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360 TAAMF+ID+QT+DYL +TGR EQ+ LVE YA+T GLWADSLKN +YERVL FDLS+V R Sbjct: 301 TAAMFYIDQQTLDYLAITGREPEQVALVENYAKTVGLWADSLKNVQYERVLTFDLSTVER 360 Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420 N+AGPSNPH+RLPTSALAERGIAV+L+ A A+E G MPDGAVIIAAITSCTNTSNPRNV Sbjct: 361 NLAGPSNPHRRLPTSALAERGIAVNLELALAEEKAGRMPDGAVIIAAITSCTNTSNPRNV 420 Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480 +AA LLA+ AN GL RKPWVKSS APGSK LYLEEA LLP+LEKLGFGIVA+ACTTC Sbjct: 421 VAAGLLAKKANELGLVRKPWVKSSFAPGSKVARLYLEEAGLLPELEKLGFGIVAYACTTC 480 Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540 NGMSGAL P+IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT+ Sbjct: 481 NGMSGALRPEIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTV 540 Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600 RFDIEKD LG D+ G PV LKD+WPSDEEIDAIV + VKPEQF++VY PMF + ++ Sbjct: 541 RFDIEKDALGYDKAGNPVTLKDLWPSDEEIDAIVGEYVKPEQFKQVYIPMFNLDEVE-QA 599 Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660 SPLYDWRPQSTYIRRPPYWEG +A ER LK +RPLA+L DNITTDHLSPSNAI+L+SAA Sbjct: 600 KSPLYDWRPQSTYIRRPPYWEGNMARERGLKGMRPLAILPDNITTDHLSPSNAILLDSAA 659 Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVD-GQVKKGSLARIEPE 719 GEYLA+MGLPEEDFNSYATHRGDHLTAQRAT ANP L NEM + G+V +GSLARIEPE Sbjct: 660 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATLANPKLFNEMVRDEKGEVIQGSLARIEPE 719 Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779 GKV RMWEAIETYM+R QPLI+IAGADYGQGSSRDWAAKGV LAGVE IVAEGFERIHRT Sbjct: 720 GKVTRMWEAIETYMERGQPLIVIAGADYGQGSSRDWAAKGVALAGVEAIVAEGFERIHRT 779 Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839 NL+GMGV+PL+F+ G R TL LDGTETYDV G+ P ATLTLV++R G VPV CR Sbjct: 780 NLVGMGVMPLQFQEGTTRHTLKLDGTETYDVEGKPAPGATLTLVIHRAGGNSERVPVLCR 839 Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLES 864 LD+ EEVS+Y AGGVL FAQDFLES Sbjct: 840 LDTAEEVSVYSAGGVLQRFAQDFLES 865 Lambda K H 0.318 0.135 0.398 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: 2179 Number of extensions: 80 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: 869 Length of database: 869 Length adjustment: 42 Effective length of query: 827 Effective length of database: 827 Effective search space: 683929 Effective search space used: 683929 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)
Align candidate WP_086511660.1 BZY95_RS20065 (Fe/S-dependent 2-methylisocitrate dehydratase AcnD)
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))
# 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/TIGR02333.hmm # target sequence database: /tmp/gapView.22969.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02333 [M=858] Accession: TIGR02333 Description: 2met_isocit_dHY: 2-methylisocitrate dehydratase, Fe/S-dependent 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 1761.0 0.0 0 1760.9 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086511660.1 BZY95_RS20065 Fe/S-dependent 2-m Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086511660.1 BZY95_RS20065 Fe/S-dependent 2-methylisocitrate dehydratase AcnD # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1760.9 0.0 0 0 1 858 [] 2 864 .. 2 864 .. 0.99 Alignments for each domain: == domain 1 score: 1760.9 bits; conditional E-value: 0 TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldf 69 nt+yrk+lpgt+ldyfd r+ave+i+pgayd+lpytsrvlae+lvrr++pe l+++lkqlier+r+ldf lcl|NCBI__GCF_002151265.1:WP_086511660.1 2 NTQYRKPLPGTELDYFDVREAVEEIQPGAYDTLPYTSRVLAEQLVRRCEPELLTDALKQLIERRRDLDF 70 89******************************************************************* PP TIGR02333 70 pwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknra 138 pwyparvvchdilgqtalvdlaglrdaiaekggdp++vnpvv+tqlivdhslave+gg dpdaf+knra lcl|NCBI__GCF_002151265.1:WP_086511660.1 71 PWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDHSLAVECGGDDPDAFAKNRA 139 ********************************************************************* PP TIGR02333 139 iedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvda 207 iedrrnedrfhfi+wt++afknvdvipagngimhqinlekmspv+q+++gva+pdt+vgtdshtph+d+ lcl|NCBI__GCF_002151265.1:WP_086511660.1 140 IEDRRNEDRFHFIDWTRTAFKNVDVIPAGNGIMHQINLEKMSPVIQARDGVAYPDTCVGTDSHTPHIDC 208 ********************************************************************* PP TIGR02333 208 lgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffg 276 lgviaigvggleaetvmlgr+s+mrlpdivgveltgkrq+gitatdivla+teflr+e+vv+ayleffg lcl|NCBI__GCF_002151265.1:WP_086511660.1 209 LGVIAIGVGGLEAETVMLGRPSMMRLPDIVGVELTGKRQSGITATDIVLAITEFLRQERVVGAYLEFFG 277 ********************************************************************* PP TIGR02333 277 egakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkav 345 ega +lt+gdratisnmtpeygataamf+id+qt+dyl +tgre+eqv+lve yak+ glwadslk+ + lcl|NCBI__GCF_002151265.1:WP_086511660.1 278 EGADSLTIGDRATISNMTPEYGATAAMFYIDQQTLDYLAITGREPEQVALVENYAKTVGLWADSLKNVQ 346 ********************************************************************* PP TIGR02333 346 yervlkfdlssvvrnlagpsnpharlatsdlaakgiakevee....eaeglmpdgaviiaaitsctnts 410 yervl+fdls+v+rnlagpsnph+rl+ts la +gia ++e e g+mpdgaviiaaitsctnts lcl|NCBI__GCF_002151265.1:WP_086511660.1 347 YERVLTFDLSTVERNLAGPSNPHRRLPTSALAERGIAVNLELalaeEKAGRMPDGAVIIAAITSCTNTS 415 *************************************998744444777******************** PP TIGR02333 411 nprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafacttcngms 479 nprnvvaaglla++an+lgl rkpwvkss+apgskv++lyleeagll+eleklgfgiva+acttcngms lcl|NCBI__GCF_002151265.1:WP_086511660.1 416 NPRNVVAAGLLAKKANELGLVRKPWVKSSFAPGSKVARLYLEEAGLLPELEKLGFGIVAYACTTCNGMS 484 ********************************************************************* PP TIGR02333 480 galdpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvda 548 gal p iqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagt+rfdiekd+lg+d+ lcl|NCBI__GCF_002151265.1:WP_086511660.1 485 GALRPEIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTVRFDIEKDALGYDK 553 ********************************************************************* PP TIGR02333 549 dgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdledaqkkvsplydwrpmstyirrppywega 617 g+++ lkd+wpsdeeida+v+++vkpeqf++vyipmf+l++ +++ splydwrp+styirrppyweg lcl|NCBI__GCF_002151265.1:WP_086511660.1 554 AGNPVTLKDLWPSDEEIDAIVGEYVKPEQFKQVYIPMFNLDEVEQAKSPLYDWRPQSTYIRRPPYWEGN 622 ********************************************************************* PP TIGR02333 618 lagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratf 686 +a er lkgmrpla+l+dnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqrat+ lcl|NCBI__GCF_002151265.1:WP_086511660.1 623 MARERGLKGMRPLAILPDNITTDHLSPSNAILLDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATL 691 ********************************************************************* PP TIGR02333 687 anpklfnemvked.gkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgv 754 anpklfnemv+++ g+v qgslariepegkvtrmweaietym+r qpli+iagadygqgssrdwaakgv lcl|NCBI__GCF_002151265.1:WP_086511660.1 692 ANPKLFNEMVRDEkGEVIQGSLARIEPEGKVTRMWEAIETYMERGQPLIVIAGADYGQGSSRDWAAKGV 760 ***********999******************************************************* PP TIGR02333 755 rlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkng 823 lagveaivaegferihrtnlvgmgv+pl+f+ gt r+tl+ldgte+ydv g+ +p+a+ltlv++r+ g lcl|NCBI__GCF_002151265.1:WP_086511660.1 761 ALAGVEAIVAEGFERIHRTNLVGMGVMPLQFQEGTTRHTLKLDGTETYDVEGKPAPGATLTLVIHRAGG 829 ********************************************************************* PP TIGR02333 824 eklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858 ++ vpv crldtaeevsvy aggvlqrfaqdfle lcl|NCBI__GCF_002151265.1:WP_086511660.1 830 NSERVPVLCRLDTAEEVSVYSAGGVLQRFAQDFLE 864 *********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (858 nodes) Target sequences: 1 (869 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 12.29 // [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