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 GFF4113 PS417_21070 aconitate hydratase
Query= SwissProt::Q937N8 (869 letters) >FitnessBrowser__WCS417:GFF4113 Length = 864 Score = 1441 bits (3729), Expect = 0.0 Identities = 730/870 (83%), Positives = 779/870 (89%), Gaps = 7/870 (0%) Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60 MN+ RKPLPG++LDYFDARAAV+AI PGAY LPYTSRVLAENLVRRCDPATL SL Q Sbjct: 1 MNTEFRKPLPGSRLDYFDARAAVDAISPGAYATLPYTSRVLAENLVRRCDPATLNASLSQ 60 Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120 L+ RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA+VNPVVP QLIVDH Sbjct: 61 LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120 Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180 SLAVE GGFDPDAF KNRAIEDRRNEDRFHFI+WTK+AFKNVDVIPPGNGIMHQINLEKM Sbjct: 121 SLAVEAGGFDPDAFEKNRAIEDRRNEDRFHFIEWTKKAFKNVDVIPPGNGIMHQINLEKM 180 Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240 SPVI +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+ VGV Sbjct: 181 SPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGV 240 Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300 ELTGK PGITATD+VLALTEFLRK+KVVGA+LEF GEGAS+LTLGDRATISNMAPEYGA Sbjct: 241 ELTGKLLPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGA 300 Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360 TAAMF+ID+QTI YL+LTGR DEQ+ LVE YAR GLWAD LK A+YER L FDLSSVVR Sbjct: 301 TAAMFYIDQQTIAYLKLTGREDEQVTLVEQYARHTGLWADDLKGAQYERGLTFDLSSVVR 360 Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420 NMAGPSNPH R+ TS LA +GI+ D E G MPDGAVIIAAITSCTNTSNPRNV Sbjct: 361 NMAGPSNPHARVATSDLASKGISGQWD-----EVPGQMPDGAVIIAAITSCTNTSNPRNV 415 Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480 IAA LLARNAN GL RKPWVKSSLAPGSK V +YLEEA L +LEKLGFG+VAFACTTC Sbjct: 416 IAAGLLARNANKLGLTRKPWVKSSLAPGSKTVAMYLEEAGLGHELEKLGFGVVAFACTTC 475 Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540 NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535 Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600 RFDIEKDVLG D +GK + L+DIWPSDEEIDA+V SVKPEQFR VY PMFAI +G Sbjct: 536 RFDIEKDVLGLDANGKEIRLQDIWPSDEEIDAVVKASVKPEQFRAVYIPMFAIHEDTGPK 595 Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660 V+PLYDWRPQSTYIRRPPYWEGALAG R LK +RPLAVL DNITTDHLSPSNAIML+SAA Sbjct: 596 VAPLYDWRPQSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAA 655 Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720 GEYLA+MGLPE DFNSYATHRGDHLTAQRATFANP L NEM V +G+VK+GSLARIEPEG Sbjct: 656 GEYLAKMGLPEVDFNSYATHRGDHLTAQRATFANPKLFNEMVVENGKVKQGSLARIEPEG 715 Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780 +V RMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN Sbjct: 716 QVTRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 775 Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840 L+GMGVLPLEF PG +R TL +DG+ETYDV+G R PRA LTLV+NRKNGERVEVPVTCRL Sbjct: 776 LVGMGVLPLEFLPGTDRHTLKIDGSETYDVVGARTPRAQLTLVINRKNGERVEVPVTCRL 835 Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRATA 869 D+ EEVSIYEAGGVL FAQDFLES+ ATA Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESA-ATA 864 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: 2182 Number of extensions: 84 Number of successful extensions: 3 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: 864 Length adjustment: 42 Effective length of query: 827 Effective length of database: 822 Effective search space: 679794 Effective search space used: 679794 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 GFF4113 PS417_21070 (aconitate hydratase)
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.28011.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 1821.2 0.0 0 1821.1 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF4113 PS417_21070 aconitate hydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF4113 PS417_21070 aconitate hydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1821.1 0.0 0 0 1 858 [] 2 859 .. 2 859 .. 1.00 Alignments for each domain: == domain 1 score: 1821.1 bits; conditional E-value: 0 TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwypar 75 nt++rk+lpg+ ldyfdaraav+ai pgay++lpytsrvlaenlvrr+dp+tl+asl+qlierkr+ldfpw+par lcl|FitnessBrowser__WCS417:GFF4113 2 NTEFRKPLPGSRLDYFDARAAVDAISPGAYATLPYTSRVLAENLVRRCDPATLNASLSQLIERKRDLDFPWFPAR 76 899************************************************************************ PP TIGR02333 76 vvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhf 150 vvchdilgqtalvdlaglrdaia +ggdpaqvnpvv+tqlivdhslave ggfdpdafeknraiedrrnedrfhf lcl|FitnessBrowser__WCS417:GFF4113 77 VVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDHSLAVEAGGFDPDAFEKNRAIEDRRNEDRFHF 151 *************************************************************************** PP TIGR02333 151 inwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvml 225 i+wtkkafknvdvip+gngimhqinlekmspv+qv++gvafpdt+vgtdshtphvdalgviaigvggleae+vml lcl|FitnessBrowser__WCS417:GFF4113 152 IEWTKKAFKNVDVIPPGNGIMHQINLEKMSPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVML 226 *************************************************************************** PP TIGR02333 226 graslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygat 300 gras+mrlp+ vgveltgk pgitatd+vlalteflrk+kvv+a+leffgega altlgdratisnm+peygat lcl|FitnessBrowser__WCS417:GFF4113 227 GRASWMRLPESVGVELTGKLLPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGAT 301 *************************************************************************** PP TIGR02333 301 aamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsd 375 aamf+id+qti ylkltgre+eqv lve ya+ +glwad+lk a+yer l+fdlssvvrn+agpsnphar+atsd lcl|FitnessBrowser__WCS417:GFF4113 302 AAMFYIDQQTIAYLKLTGREDEQVTLVEQYARHTGLWADDLKGAQYERGLTFDLSSVVRNMAGPSNPHARVATSD 376 *************************************************************************** PP TIGR02333 376 laakgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvkly 450 la+kgi+++++e++ g+mpdgaviiaaitsctntsnprnv+aagllarnanklgl+rkpwvksslapgsk+v +y lcl|FitnessBrowser__WCS417:GFF4113 377 LASKGISGQWDEVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANKLGLTRKPWVKSSLAPGSKTVAMY 450 **************.************************************************************ PP TIGR02333 451 leeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasppl 525 leeagl +eleklgfg+vafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasppl lcl|FitnessBrowser__WCS417:GFF4113 451 LEEAGLGHELEKLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPL 525 *************************************************************************** PP TIGR02333 526 vvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsply 599 vvayaiagtirfdiekdvlg+da+gkeirl+diwpsdeeidavv+a+vkpeqfr vyipmf+++ d++ kv+ply lcl|FitnessBrowser__WCS417:GFF4113 526 VVAYAIAGTIRFDIEKDVLGLDANGKEIRLQDIWPSDEEIDAVVKASVKPEQFRAVYIPMFAIHeDTGPKVAPLY 600 ***************************************************************989********* PP TIGR02333 600 dwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyath 674 dwrp+styirrppywegalag r lkgmrplavl+dnittdhlspsnai+ldsaageylakmglpe dfnsyath lcl|FitnessBrowser__WCS417:GFF4113 601 DWRPQSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAAGEYLAKMGLPEVDFNSYATH 675 *************************************************************************** PP TIGR02333 675 rgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdw 749 rgdhltaqratfanpklfnemv e+gkvkqgslariepeg+vtrmweaietym+rkqpliiiagadygqgssrdw lcl|FitnessBrowser__WCS417:GFF4113 676 RGDHLTAQRATFANPKLFNEMVVENGKVKQGSLARIEPEGQVTRMWEAIETYMERKQPLIIIAGADYGQGSSRDW 750 *************************************************************************** PP TIGR02333 750 aakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrknge 824 aakgvrlagveai aegferihrtnlvgmgvlplef pgt+r+tl++dg+e+ydvvg++tpra+ltlv++rknge lcl|FitnessBrowser__WCS417:GFF4113 751 AAKGVRLAGVEAIAAEGFERIHRTNLVGMGVLPLEFLPGTDRHTLKIDGSETYDVVGARTPRAQLTLVINRKNGE 825 *************************************************************************** PP TIGR02333 825 klevpvtcrldtaeevsvyeaggvlqrfaqdfle 858 ++evpvtcrldtaeevs+yeaggvlqrfaqdfle lcl|FitnessBrowser__WCS417:GFF4113 826 RVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 859 ********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (858 nodes) Target sequences: 1 (864 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: 12.30 // [ok]
This GapMind analysis is from Sep 17 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