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 PfGW456L13_4116 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)
Query= SwissProt::Q937N8 (869 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 Length = 864 Score = 1444 bits (3738), Expect = 0.0 Identities = 726/866 (83%), Positives = 781/866 (90%), Gaps = 7/866 (0%) Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60 MN+ RKPLPG+ LDYFD RAAVEAIQPGAYD LPYTSRVLAENLVRRCDPATLT+SL Q Sbjct: 1 MNTQFRKPLPGSHLDYFDVRAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQ 60 Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120 + RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA+VNPVVP QLIVDH Sbjct: 61 FIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120 Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180 SLAVE GGFDP+AF KNRAIEDRRNEDRFHFI+WTK+AFKNVDVIPPGNGIMHQINLEKM Sbjct: 121 SLAVERGGFDPEAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180 Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240 SPVI +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+ VGV Sbjct: 181 SPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGV 240 Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300 ELTGK QPGITATD+VLALTEFLRK+KVVGA+LEF GEGA++LTLGDRATISNMAPEYGA Sbjct: 241 ELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFFGEGAAALTLGDRATISNMAPEYGA 300 Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360 TAAMF+ID+QTIDYL+LTGR DEQ++LVE YA+ GLWADSLK A+YER L FDLSSVVR Sbjct: 301 TAAMFYIDQQTIDYLKLTGREDEQVQLVENYAKQVGLWADSLKGAQYERGLTFDLSSVVR 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 IAAGLLARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAGLTDELEQLGFGVVAFACTTC 475 Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540 NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535 Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600 RFDIEKDVLG DGK + LKDIWPSDEEIDA+V SVKPEQFR+VY PMFAI +G Sbjct: 536 RFDIEKDVLGV-VDGKEIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIHEDTGPK 594 Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660 V+PLY+WR STYIRRPPYWEGALAG R LK +RPLAVL DNITTDHLSPSNAIML+SAA Sbjct: 595 VAPLYEWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAA 654 Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720 GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM + +G+VK+GSLAR+EPEG Sbjct: 655 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVLENGKVKQGSLARVEPEG 714 Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780 KV+RMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN Sbjct: 715 KVMRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 774 Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840 L+GMGVLPLEFKPG NR TL +DG+ETYDVIG+R PRA LTLV++RKNGERV+VPVTCRL Sbjct: 775 LVGMGVLPLEFKPGTNRHTLAIDGSETYDVIGDRTPRAELTLVIHRKNGERVDVPVTCRL 834 Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESS 865 D+ EEVSIYEAGGVL FAQDFLE S Sbjct: 835 DTAEEVSIYEAGGVLQRFAQDFLEES 860 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: 2219 Number of extensions: 87 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: 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 PfGW456L13_4116 (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.2543.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 1834.3 0.0 0 1834.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 2-methylcitrate dehydratase FeS Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 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 ! 1834.1 0.0 0 0 1 858 [] 2 858 .. 2 858 .. 1.00 Alignments for each domain: == domain 1 score: 1834.1 bits; conditional E-value: 0 TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetlea 55 nt++rk+lpg++ldyfd raaveai+pgayd+lpytsrvlaenlvrr+dp+tl++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 2 NTQFRKPLPGSHLDYFDVRAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPATLTE 56 89***************************************************** PP TIGR02333 56 slkqlierkreldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpv 110 slkq+ierkr+ldfpw+parvvchdilgqtalvdlaglrdaia +ggdpaqvnpv lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 57 SLKQFIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPV 111 ******************************************************* PP TIGR02333 111 vetqlivdhslaveyggfdpdafeknraiedrrnedrfhfinwtkkafknvdvip 165 v+tqlivdhslave ggfdp+afeknraiedrrnedrfhfinwtkkafknvdvip lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 112 VPTQLIVDHSLAVERGGFDPEAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIP 166 ******************************************************* PP TIGR02333 166 agngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvgglea 220 +gngimhqinlekmspv+qv++gvafpdt+vgtdshtphvdalgviaigvgglea lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 167 PGNGIMHQINLEKMSPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEA 221 ******************************************************* PP TIGR02333 221 etvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleff 275 e+vmlgras+mrlp+ vgveltgk qpgitatd+vlalteflrk+kvv+a+leff lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 222 ESVMLGRASWMRLPESVGVELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFF 276 ******************************************************* PP TIGR02333 276 gegakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvety 330 gega altlgdratisnm+peygataamf+id+qtidylkltgre+eqv+lve y lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 277 GEGAAALTLGDRATISNMAPEYGATAAMFYIDQQTIDYLKLTGREDEQVQLVENY 331 ******************************************************* PP TIGR02333 331 akaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakev 385 ak glwadslk a+yer l+fdlssvvrn+agpsnphar+a sdlaakgi++++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 332 AKQVGLWADSLKGAQYERGLTFDLSSVVRNMAGPSNPHARVAVSDLAAKGISGQW 386 ******************************************************* PP TIGR02333 386 eeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvkssl 440 ++++ g+mpdgaviiaaitsctntsnprnv+aagllarnanklgl+rkpwvkssl lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 387 DDVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANKLGLTRKPWVKSSL 440 ****.************************************************** PP TIGR02333 441 apgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdl 495 apgsk+v lyl+eagl +ele+lgfg+vafacttcngmsgaldpviqqeiidrdl lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 441 APGSKTVALYLDEAGLTDELEQLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDL 495 ******************************************************* PP TIGR02333 496 yatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadg 550 yatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgv +dg lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 496 YATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGV-VDG 549 ***************************************************.*** PP TIGR02333 551 keirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpm 604 keirlkdiwpsdeeidavv+a+vkpeqfr+vyipmf+++ d++ kv+ply+wr m lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 550 KEIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIHeDTGPKVAPLYEWREM 604 **************************************989************** PP TIGR02333 605 styirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaageyla 659 styirrppywegalag r lkgmrplavl+dnittdhlspsnai+ldsaageyla lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 605 STYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAAGEYLA 659 ******************************************************* PP TIGR02333 660 kmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepeg 714 kmglpeedfnsyathrgdhltaqratfanpklfnemv e+gkvkqgslar+epeg lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 660 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVLENGKVKQGSLARVEPEG 714 ******************************************************* PP TIGR02333 715 kvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegfer 769 kv+rmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveai aegfer lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 715 KVMRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFER 769 ******************************************************* PP TIGR02333 770 ihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrknge 824 ihrtnlvgmgvlplefkpgtnr+tla+dg+e+ydv+g++tpra+ltlv++rknge lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 770 IHRTNLVGMGVLPLEFKPGTNRHTLAIDGSETYDVIGDRTPRAELTLVIHRKNGE 824 ******************************************************* PP TIGR02333 825 klevpvtcrldtaeevsvyeaggvlqrfaqdfle 858 +++vpvtcrldtaeevs+yeaggvlqrfaqdfle lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 825 RVDVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 858 ********************************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: 10.99 // [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