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 AO356_20875 AO356_20875 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8 (869 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20875 Length = 863 Score = 1451 bits (3757), Expect = 0.0 Identities = 732/868 (84%), Positives = 783/868 (90%), Gaps = 7/868 (0%) Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60 MN+ RKPLPGT LDYFD R AV+AI+PGAYD LPYTSRVLAENLVRRCDPATL +SLLQ Sbjct: 1 MNTEFRKPLPGTSLDYFDVRGAVDAIRPGAYDGLPYTSRVLAENLVRRCDPATLRESLLQ 60 Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120 L+ RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA+VNPVVP QLIVDH Sbjct: 61 LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120 Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180 SLAVE GG DP AFAKNRAIEDRRNEDRFHFI+WTK+AFKNVDVIPPGNGIMHQINLEKM Sbjct: 121 SLAVESGGADPQAFAKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180 Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240 SPVI +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+IVGV Sbjct: 181 SPVIQQRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPEIVGV 240 Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300 ELTGK QPGITATD+VLALTEFLRK+KVVGA+LEF GEGAS+LTLGDR TISNMAPEYGA Sbjct: 241 ELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRVTISNMAPEYGA 300 Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360 TAAMF ID+QTIDYL+LTGR D Q++LVETYA+ GLWADSLK A+YER L FDLSSVVR Sbjct: 301 TAAMFHIDQQTIDYLKLTGREDTQVQLVETYAKHVGLWADSLKGAQYERGLTFDLSSVVR 360 Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420 NMAGPSNPH R+ S LA +GI+ D + G MPDGAVIIAAITSCTNTSNPRNV Sbjct: 361 NMAGPSNPHARVAVSELAAKGISGQWD-----DVPGQMPDGAVIIAAITSCTNTSNPRNV 415 Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480 IAA LLARNAN GLARKPWVKSSLAPGSK V LYL+EA L +LEKLGFG+VAFACTTC Sbjct: 416 IAAGLLARNANRLGLARKPWVKSSLAPGSKTVALYLDEAGLTSELEKLGFGVVAFACTTC 475 Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540 NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535 Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600 RFDIEKDVLG DG+ + LKDIWPSDEEIDA+V SVKPEQFR+VY PMFAI +G Sbjct: 536 RFDIEKDVLGV-VDGREIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIQEDTGPK 594 Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660 V+PLYDWRPQSTYIRRPPYWEGALAG R LK +RPLAVL DNITTDHLSPSNAIML+SAA Sbjct: 595 VTPLYDWRPQSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAA 654 Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720 GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM +G+VK+GSLAR+EPEG Sbjct: 655 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVKQGSLARVEPEG 714 Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780 KV+RMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN Sbjct: 715 KVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 774 Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840 L+GMGVLPLEFKPG +R TLG+DG+E YDVIGER PRATLTLV+ RKNGERVEVPVTCRL Sbjct: 775 LVGMGVLPLEFKPGTDRKTLGIDGSEVYDVIGERTPRATLTLVITRKNGERVEVPVTCRL 834 Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRA 867 D+ EEVSIYEAGGVL FAQDFLES+ A Sbjct: 835 DTAEEVSIYEAGGVLQRFAQDFLESAVA 862 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: 2210 Number of extensions: 84 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: 863 Length adjustment: 42 Effective length of query: 827 Effective length of database: 821 Effective search space: 678967 Effective search space used: 678967 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 AO356_20875 AO356_20875 (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.6039.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 1826.9 0.0 0 1826.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 AO356_20875 Fe/S-dependent 2-met Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 AO356_20875 Fe/S-dependent 2-methylisocitrate dehydratase AcnD # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1826.7 0.0 0 0 1 858 [] 2 858 .. 2 858 .. 1.00 Alignments for each domain: == domain 1 score: 1826.7 bits; conditional E-value: 0 TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlier 63 nt++rk+lpgt+ldyfd r av+ai+pgayd lpytsrvlaenlvrr+dp+tl +sl qlier lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 2 NTEFRKPLPGTSLDYFDVRGAVDAIRPGAYDGLPYTSRVLAENLVRRCDPATLRESLLQLIER 64 899************************************************************ PP TIGR02333 64 kreldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyg 126 kr+ldfpw+parvvchdilgqtalvdlaglrdaia +ggdpaqvnpvv+tqlivdhslave g lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 65 KRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDHSLAVESG 127 *************************************************************** PP TIGR02333 127 gfdpdafeknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegv 189 g dp+af+knraiedrrnedrfhfinwtkkafknvdvip+gngimhqinlekmspv+q ++gv lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 128 GADPQAFAKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKMSPVIQQRDGV 190 *************************************************************** PP TIGR02333 190 afpdtlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitat 252 afpdt+vgtdshtphvdalgviaigvggleae+vmlgras+mrlp+ivgveltgk qpgitat lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 191 AFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPEIVGVELTGKLQPGITAT 253 *************************************************************** PP TIGR02333 253 divlalteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylk 315 d+vlalteflrk+kvv+a+leffgega altlgdr tisnm+peygataamf id+qtidylk lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 254 DMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRVTISNMAPEYGATAAMFHIDQQTIDYLK 316 *************************************************************** PP TIGR02333 316 ltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaa 378 ltgre+ qv+lvetyak glwadslk a+yer l+fdlssvvrn+agpsnphar+a s+laa lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 317 LTGREDTQVQLVETYAKHVGLWADSLKGAQYERGLTFDLSSVVRNMAGPSNPHARVAVSELAA 379 *************************************************************** PP TIGR02333 379 kgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvkssla 441 kgi++++++++ g+mpdgaviiaaitsctntsnprnv+aagllarnan+lgl rkpwvkssla lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 380 KGISGQWDDVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANRLGLARKPWVKSSLA 441 ***********.*************************************************** PP TIGR02333 442 pgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgn 504 pgsk+v lyl+eagl +eleklgfg+vafacttcngmsgaldpviqqeiidrdlyatavlsgn lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 442 PGSKTVALYLDEAGLTSELEKLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGN 504 *************************************************************** PP TIGR02333 505 rnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeida 567 rnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgv +dg+eirlkdiwpsdeeida lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 505 RNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGV-VDGREIRLKDIWPSDEEIDA 566 ******************************************.******************** PP TIGR02333 568 vvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrp 629 vv+a+vkpeqfr+vyipmf+++ d++ kv+plydwrp+styirrppywegalag r lkgmrp lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 567 VVKASVKPEQFRQVYIPMFAIQeDTGPKVTPLYDWRPQSTYIRRPPYWEGALAGARPLKGMRP 629 *********************989*************************************** PP TIGR02333 630 lavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklf 692 lavl+dnittdhlspsnai+ldsaageylakmglpeedfnsyathrgdhltaqratfanpklf lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 630 LAVLPDNITTDHLSPSNAIMLDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLF 692 *************************************************************** PP TIGR02333 693 nemvkedgkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvr 755 nemv+e+gkvkqgslar+epegkv+rmweaietym+rkqpliiiagadygqgssrdwaakgvr lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 693 NEMVQENGKVKQGSLARVEPEGKVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVR 755 *************************************************************** PP TIGR02333 756 lagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvv 818 lagveai aegferihrtnlvgmgvlplefkpgt+rktl++dg+evydv+ge+tpra+ltlv+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 756 LAGVEAIAAEGFERIHRTNLVGMGVLPLEFKPGTDRKTLGIDGSEVYDVIGERTPRATLTLVI 818 *************************************************************** PP TIGR02333 819 trkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858 trknge++evpvtcrldtaeevs+yeaggvlqrfaqdfle lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 819 TRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 858 **************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (858 nodes) Target sequences: 1 (863 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 0.01s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 12.91 // [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