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 Pf6N2E2_6063 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)
Query= SwissProt::Q937N8 (869 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 Length = 863 Score = 1452 bits (3758), Expect = 0.0 Identities = 730/868 (84%), Positives = 785/868 (90%), Gaps = 7/868 (0%) Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60 MN+ RKPLPGT LDYFD R AV+AI+PGAYD LPYTSRVLAENLVRRCDPATL +SLLQ Sbjct: 1 MNTEFRKPLPGTSLDYFDVREAVDAIRPGAYDGLPYTSRVLAENLVRRCDPATLRESLLQ 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 SLAVESGGSDPQAFAKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180 Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240 SPVI +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+I+GV Sbjct: 181 SPVIQQRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPEIIGV 240 Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300 ELTGK QPGITATD+VLALTEFLRK+KVVGA+LEF GEGAS+LTLGDRATISNMAPEYGA Sbjct: 241 ELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGA 300 Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360 TAAMF+ID+QTIDYL+LTGR D+Q++LVETYA+ AGLWAD LK A+YER L FDLSSVVR Sbjct: 301 TAAMFYIDQQTIDYLKLTGREDDQVRLVETYAKQAGLWADKLKGAQYERGLTFDLSSVVR 360 Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420 NMAGPSNPH R+ S LA +GI+ D + G MPDGAVIIAAITSCTNTSNPRNV Sbjct: 361 NMAGPSNPHARVAVSDLAAKGISGQWD-----DVPGQMPDGAVIIAAITSCTNTSNPRNV 415 Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480 IAA LLARNAN GL RKPWVKSSLAPGSK V LYL+EA L +LE+LGFG+VAFACTTC Sbjct: 416 IAAGLLARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAGLTKELEQLGFGVVAFACTTC 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 LVGMGVLPLEFKPGTDRKTLGIDGSEIYDVIGERTPRATLTLVITRKNGERVEVPVTCRL 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: 82 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 Pf6N2E2_6063 (2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79))
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.32683.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 1836.2 0.0 0 1836.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 2-methylcitrate dehydratase FeS Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1836.1 0.0 0 0 1 858 [] 2 858 .. 2 858 .. 1.00 Alignments for each domain: == domain 1 score: 1836.1 bits; conditional E-value: 0 TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierk 64 nt++rk+lpgt+ldyfd r+av+ai+pgayd lpytsrvlaenlvrr+dp+tl +sl qlierk lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 2 NTEFRKPLPGTSLDYFDVREAVDAIRPGAYDGLPYTSRVLAENLVRRCDPATLRESLLQLIERK 65 899************************************************************* PP TIGR02333 65 reldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggf 128 r+ldfpw+parvvchdilgqtalvdlaglrdaia +ggdpaqvnpvv+tqlivdhslave gg lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 66 RDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDHSLAVESGGS 129 **************************************************************** PP TIGR02333 129 dpdafeknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafp 192 dp+af+knraiedrrnedrfhfinwtkkafknvdvip+gngimhqinlekmspv+q ++gvafp lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 130 DPQAFAKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKMSPVIQQRDGVAFP 193 **************************************************************** PP TIGR02333 193 dtlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivl 256 dt+vgtdshtphvdalgviaigvggleae+vmlgras+mrlp+i+gveltgk qpgitatd+vl lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 194 DTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPEIIGVELTGKLQPGITATDMVL 257 **************************************************************** PP TIGR02333 257 alteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkltgre 320 alteflrk+kvv+a+leffgega altlgdratisnm+peygataamf+id+qtidylkltgre lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 258 ALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGATAAMFYIDQQTIDYLKLTGRE 321 **************************************************************** PP TIGR02333 321 eeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiake 384 ++qv+lvetyak aglwad+lk a+yer l+fdlssvvrn+agpsnphar+a sdlaakgi+++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 322 DDQVRLVETYAKQAGLWADKLKGAQYERGLTFDLSSVVRNMAGPSNPHARVAVSDLAAKGISGQ 385 **************************************************************** PP TIGR02333 385 veeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvk 448 +++++ g+mpdgaviiaaitsctntsnprnv+aagllarnanklgl+rkpwvksslapgsk+v lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 386 WDDVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANKLGLTRKPWVKSSLAPGSKTVA 448 *****.********************************************************** PP TIGR02333 449 lyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrih 512 lyl+eagl kele+lgfg+vafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrih lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 449 LYLDEAGLTKELEQLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIH 512 **************************************************************** PP TIGR02333 513 pyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpe 576 pyakqaflaspplvvayaiagtirfdiekdvlgv +dg+eirlkdiwpsdeeidavv+a+vkpe lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 513 PYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGV-VDGREIRLKDIWPSDEEIDAVVKASVKPE 575 **********************************.***************************** PP TIGR02333 577 qfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnitt 639 qfr+vyipmf+++ d++ kv+plydwrp+styirrppywegalag r lkgmrplavl+dnitt lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 576 QFRQVYIPMFAIQeDTGPKVTPLYDWRPQSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITT 639 ************989************************************************* PP TIGR02333 640 dhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvk 703 dhlspsnai+ldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemv+e+gkvk lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 640 DHLSPSNAIMLDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVK 703 **************************************************************** PP TIGR02333 704 qgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegf 767 qgslar+epegkv+rmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveai aegf lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 704 QGSLARVEPEGKVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGF 767 **************************************************************** PP TIGR02333 768 erihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvt 831 erihrtnlvgmgvlplefkpgt+rktl++dg+e+ydv+ge+tpra+ltlv+trknge++evpvt lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 768 ERIHRTNLVGMGVLPLEFKPGTDRKTLGIDGSEIYDVIGERTPRATLTLVITRKNGERVEVPVT 831 **************************************************************** PP TIGR02333 832 crldtaeevsvyeaggvlqrfaqdfle 858 crldtaeevs+yeaggvlqrfaqdfle lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 832 CRLDTAEEVSIYEAGGVLQRFAQDFLE 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.08 # Mc/sec: 9.08 // [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