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_025165804.1 TMS3_RS13490 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8 (869 letters) >NCBI__GCF_000498575.2:WP_025165804.1 Length = 869 Score = 1424 bits (3687), Expect = 0.0 Identities = 710/870 (81%), Positives = 775/870 (89%), Gaps = 4/870 (0%) Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60 MNS RKPLPGT+LD+FD RAAV+AI P AY KLPYTSRVLAE LVRRC+P LTDSL Q Sbjct: 1 MNSQFRKPLPGTRLDFFDTRAAVDAIAPDAYAKLPYTSRVLAEQLVRRCEPDALTDSLKQ 60 Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120 L+ RKRDLDFPW+PARVVCHDILGQTALVDLAGLRDAIA++GGDP+KVNPVVP QLIVDH Sbjct: 61 LIERKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDH 120 Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180 SLAVE GFDPDAF KNRAIEDRRNEDRFHFI+WTK AFKNVDVIP GNGIMHQINLEKM Sbjct: 121 SLAVEAPGFDPDAFTKNRAIEDRRNEDRFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKM 180 Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240 SPVI A GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE VMLG S MRLPDIVGV Sbjct: 181 SPVIQARGGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAETVMLGLPSMMRLPDIVGV 240 Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300 L GKRQPGITATDIVLA+TEFLRKE+VVGA++EF GEGA SLT+GDRATISNM PEYGA Sbjct: 241 RLVGKRQPGITATDIVLAITEFLRKERVVGAWVEFFGEGADSLTIGDRATISNMCPEYGA 300 Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360 TA+MF+ID+QTIDYL+LTGR EQ+ LVE YA+T GLWAD+L AEYERVL+FDLS+VVR Sbjct: 301 TASMFYIDQQTIDYLKLTGREPEQVALVENYAKTTGLWADALVTAEYERVLEFDLSTVVR 360 Query: 361 NMAGPSNPHKRLPTSALAERGIAVD--LDKASAQEAEGLMPDGAVIIAAITSCTNTSNPR 418 NMAGPSNPH+RLPTSAL ERGIA + L +E+EGLMPDGAVIIAAITSCTNTSNPR Sbjct: 361 NMAGPSNPHRRLPTSALHERGIADEGKLAAGKIEESEGLMPDGAVIIAAITSCTNTSNPR 420 Query: 419 NVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACT 478 NV+AA L+A+ ANA GL RKPWVK+S APGSK +LYLE+A LL +LE+LGFGIV +ACT Sbjct: 421 NVVAAGLVAKKANALGLVRKPWVKTSFAPGSKVAKLYLEDAGLLSELEQLGFGIVGYACT 480 Query: 479 TCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 538 TCNGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG Sbjct: 481 TCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 540 Query: 539 TIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASG 598 T+RFDIE+DVLG D+ G PV LKD+WPSDEEIDAIVA SVKPEQF+++Y PMF + Sbjct: 541 TVRFDIEQDVLGIDKAGNPVTLKDLWPSDEEIDAIVAASVKPEQFKQIYIPMFDLGTIQ- 599 Query: 599 ESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNS 658 E+ SPLYDWRP STYIRRPPYWEGALAGERTLK +RPLA+L DNITTDHLSPSNAI+L+S Sbjct: 600 EAESPLYDWRPMSTYIRRPPYWEGALAGERTLKGMRPLAILPDNITTDHLSPSNAILLDS 659 Query: 659 AAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEP 718 AAGEYL +MGLPEEDFNSYATHRGDHLTAQRATFANP L+NEMAVVDGQVKKGSLAR+EP Sbjct: 660 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPQLVNEMAVVDGQVKKGSLARVEP 719 Query: 719 EGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR 778 EGKV+RMWEAIE YM+RKQ LII+AGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR Sbjct: 720 EGKVMRMWEAIEAYMNRKQSLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR 779 Query: 779 TNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTC 838 TNL+GMGVLP+EFKPG RLTLGLDGTETYD+ GE PR LTLV+ RKNGE VPV C Sbjct: 780 TNLVGMGVLPVEFKPGTTRLTLGLDGTETYDIQGELSPRGELTLVIQRKNGEVTRVPVIC 839 Query: 839 RLDSDEEVSIYEAGGVL-HFAQDFLESSRA 867 RLD+ EV++Y AGGVL FAQDFLE + A Sbjct: 840 RLDTAAEVNVYNAGGVLQRFAQDFLEGAVA 869 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: 2229 Number of extensions: 87 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: 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_025165804.1 TMS3_RS13490 (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.2966739.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 1773.1 0.0 0 1772.9 0.0 1.0 1 NCBI__GCF_000498575.2:WP_025165804.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000498575.2:WP_025165804.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1772.9 0.0 0 0 1 858 [] 2 865 .. 2 865 .. 0.99 Alignments for each domain: == domain 1 score: 1772.9 bits; conditional E-value: 0 TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyp 73 n+++rk+lpgt ld+fd+raav+ai+p ay+klpytsrvlae+lvrr++p+ l++slkqlierkr+ldfpwyp NCBI__GCF_000498575.2:WP_025165804.1 2 NSQFRKPLPGTRLDFFDTRAAVDAIAPDAYAKLPYTSRVLAEQLVRRCEPDALTDSLKQLIERKRDLDFPWYP 74 899********************************************************************** PP TIGR02333 74 arvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrned 146 arvvchdilgqtalvdlaglrdaiaekggdp++vnpvv+tqlivdhslave gfdpdaf+knraiedrrned NCBI__GCF_000498575.2:WP_025165804.1 75 ARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDHSLAVEAPGFDPDAFTKNRAIEDRRNED 147 ************************************************************************* PP TIGR02333 147 rfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggle 219 rfhfi+wtk+afknvdvipagngimhqinlekmspv+q++ gvafpdt+vgtdshtphvdalgviaigvggle NCBI__GCF_000498575.2:WP_025165804.1 148 RFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKMSPVIQARGGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLE 220 ************************************************************************* PP TIGR02333 220 aetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisn 292 aetvmlg +s+mrlpdivgv+l gkrqpgitatdivla+teflrke+vv+a++effgega +lt+gdratisn NCBI__GCF_000498575.2:WP_025165804.1 221 AETVMLGLPSMMRLPDIVGVRLVGKRQPGITATDIVLAITEFLRKERVVGAWVEFFGEGADSLTIGDRATISN 293 ************************************************************************* PP TIGR02333 293 mtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagps 365 m+peygata+mf+id+qtidylkltgre+eqv+lve yak++glwad+l +a+yervl+fdls+vvrn+agps NCBI__GCF_000498575.2:WP_025165804.1 294 MCPEYGATASMFYIDQQTIDYLKLTGREPEQVALVENYAKTTGLWADALVTAEYERVLEFDLSTVVRNMAGPS 366 ************************************************************************* PP TIGR02333 366 npharlatsdlaakgiakevee......eaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkr 432 nph+rl+ts l +gia e + e+eglmpdgaviiaaitsctntsnprnvvaagl+a++an+lgl r NCBI__GCF_000498575.2:WP_025165804.1 367 NPHRRLPTSALHERGIADEGKLaagkieESEGLMPDGAVIIAAITSCTNTSNPRNVVAAGLVAKKANALGLVR 439 ****************987654444555999****************************************** PP TIGR02333 433 kpwvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnr 505 kpwvk+s+apgskv+klyle+agll+ele+lgfgiv++acttcngmsgaldpviqqeiidrdlyatavlsgnr NCBI__GCF_000498575.2:WP_025165804.1 440 KPWVKTSFAPGSKVAKLYLEDAGLLSELEQLGFGIVGYACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNR 512 ************************************************************************* PP TIGR02333 506 nfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqf 578 nfdgrihpyakqaflaspplvvayaiagt+rfdie+dvlg+d+ g+++ lkd+wpsdeeida+vaa+vkpeqf NCBI__GCF_000498575.2:WP_025165804.1 513 NFDGRIHPYAKQAFLASPPLVVAYAIAGTVRFDIEQDVLGIDKAGNPVTLKDLWPSDEEIDAIVAASVKPEQF 585 ************************************************************************* PP TIGR02333 579 rkvyipmfdledaqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailld 651 +++yipmfdl++ q++ splydwrpmstyirrppywegalagertlkgmrpla+l+dnittdhlspsnailld NCBI__GCF_000498575.2:WP_025165804.1 586 KQIYIPMFDLGTIQEAESPLYDWRPMSTYIRRPPYWEGALAGERTLKGMRPLAILPDNITTDHLSPSNAILLD 658 ************************************************************************* PP TIGR02333 652 saageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmweaie 724 saageyl+kmglpeedfnsyathrgdhltaqratfanp+l+nem+ +dg+vk+gslar+epegkv+rmweaie NCBI__GCF_000498575.2:WP_025165804.1 659 SAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPQLVNEMAVVDGQVKKGSLARVEPEGKVMRMWEAIE 731 ************************************************************************* PP TIGR02333 725 tymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlald 797 +ymnrkq lii+agadygqgssrdwaakgvrlagve ivaegferihrtnlvgmgvlp+efkpgt r tl+ld NCBI__GCF_000498575.2:WP_025165804.1 732 AYMNRKQSLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTNLVGMGVLPVEFKPGTTRLTLGLD 804 ************************************************************************* PP TIGR02333 798 gtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858 gte+yd+ ge +pr +ltlv++rknge vpv crldta ev+vy+aggvlqrfaqdfle NCBI__GCF_000498575.2:WP_025165804.1 805 GTETYDIQGELSPRGELTLVIQRKNGEVTRVPVICRLDTAAEVNVYNAGGVLQRFAQDFLE 865 ***********************************************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 27.75 // [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