Align Citrate/2-methylcitrate dehydratase; EC 4.2.1.- (characterized)
to candidate WP_007152510.1 MDG893_RS04350 2-methylcitrate dehydratase
Query= SwissProt::P45859 (472 letters) >NCBI__GCF_000170835.1:WP_007152510.1 Length = 494 Score = 617 bits (1590), Expect = 0.0 Identities = 299/482 (62%), Positives = 379/482 (78%), Gaps = 13/482 (2%) Query: 2 PKTDRVIEEITDYVLEKEITSAEAYTTAGHVLLDTLGCGILALRYPECTKLLGPIVPGTT 61 P D V++ I DY L I S EA+ TA + L+DT+GCG+LALR+PECTK LGP+V GT Sbjct: 11 PDYDDVLQAIADYTLGYRIKSKEAWNTARNCLMDTIGCGLLALRFPECTKHLGPLVDGTV 70 Query: 62 VPNGSKVPGTSYVLDPVRAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGILAAADYVSR 121 VP+G++VPGT Y LDPV+AA++IGC++RWLDYNDTWLAAEWGHPSDNLGGILA AD++S+ Sbjct: 71 VPHGARVPGTPYKLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGGILAVADHLSQ 130 Query: 122 VRLSEGKEPLTVRDVLEMMIKAHEIQGVLALENSLNRVGLDHVLFVKVATTAVAAKLLGG 181 R++EGK PLTVRDVLE MI AHEIQGVLALENS NRVGLDHV+ VKVA+TAV AKL+G Sbjct: 131 KRVAEGKAPLTVRDVLEAMIMAHEIQGVLALENSFNRVGLDHVVLVKVASTAVTAKLMGA 190 Query: 182 GREEIKNALSNAWIDNAALRTYRHSPNTGSRKSWAAGDATSRGVHLALMSLKGEMGYPTA 241 R+++ +ALS+AW+D ALRTYRH+PN GSRKSWAAGDATSR V LA ++++GEMG P+ Sbjct: 191 SRDQMLSALSHAWVDGQALRTYRHAPNAGSRKSWAAGDATSRAVRLADIAMRGEMGIPSV 250 Query: 242 LSAPGWGFQDVLF------------NKKEIKLARPLDAYVMENVLFKVSYPAEFHAQTAA 289 L+AP WGF D+LF +K++ L + AYVMEN+LFK+S+PAEFHAQTAA Sbjct: 251 LTAPQWGFYDILFSKTNKDQTLKPEDKRQFTLPQAFGAYVMENILFKISFPAEFHAQTAA 310 Query: 290 ESAVILHPQVKNRIDEIDRVVIRTHESAIRIIDKKGPLHNPADRDHCLQYITAIGLLFGD 349 E+AVILHP+VK+R+DEI+R+VI THESAIRII K+G L N ADRDHCLQY+ A+ L+FG Sbjct: 311 EAAVILHPEVKDRLDEIERIVITTHESAIRIISKQGKLANAADRDHCLQYMAAVPLIFGG 370 Query: 350 ITAQHYEAETAN-DPRIDKLRDKMEVTENKTYTEDYLKPDKRSISNAVQVHFKDGTSTEM 408 +TA+HYE +P ID++RDKMEV E++ YT +YL+ DKRSI+NA+QV F DGTST+ Sbjct: 371 LTAEHYEDSFHEANPLIDQIRDKMEVVEDERYTREYLEADKRSIANAIQVFFTDGTSTDN 430 Query: 409 VECEFPLGHRFRREEAVPKLLEKFSDNLKTHFPDKQHKHIYERCTSYETLQTMRVNEFVD 468 V E+P+GHR RR+E +P L +KF NL T FP ++ + I++ C L+ V+EFV Sbjct: 431 VAVEYPIGHRRRRKEGIPLLEDKFRHNLATRFPGQRCEKIFQLCKDQTELEATPVHEFVG 490 Query: 469 MF 470 MF Sbjct: 491 MF 492 Lambda K H 0.319 0.135 0.402 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: 696 Number of extensions: 21 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: 472 Length of database: 494 Length adjustment: 34 Effective length of query: 438 Effective length of database: 460 Effective search space: 201480 Effective search space used: 201480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
Align candidate WP_007152510.1 MDG893_RS04350 (2-methylcitrate dehydratase)
to HMM TIGR02330 (prpD: 2-methylcitrate dehydratase (EC 4.2.1.79))
# 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/TIGR02330.hmm # target sequence database: /tmp/gapView.2887430.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02330 [M=468] Accession: TIGR02330 Description: prpD: 2-methylcitrate dehydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-267 872.1 0.0 5.2e-267 871.9 0.0 1.0 1 NCBI__GCF_000170835.1:WP_007152510.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000170835.1:WP_007152510.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 871.9 0.0 5.2e-267 5.2e-267 1 468 [] 14 494 .] 14 494 .] 1.00 Alignments for each domain: == domain 1 score: 871.9 bits; conditional E-value: 5.2e-267 TIGR02330 1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyqldp 73 d+vl+ iady l y+i+skea++tar++l+dt+gcgllal++pectk+lgp+v+gt+vp+garvpgt y+ldp NCBI__GCF_000170835.1:WP_007152510.1 14 DDVLQAIADYTLGYRIKSKEAWNTARNCLMDTIGCGLLALRFPECTKHLGPLVDGTVVPHGARVPGTPYKLDP 86 789********************************************************************** PP TIGR02330 74 vkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikaheiqgvl 146 vkaa++ig++vrwldyndtwlaaewghpsdnlggilavad+ls+kr+aegk+pl+v++vleami+aheiqgvl NCBI__GCF_000170835.1:WP_007152510.1 87 VKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGGILAVADHLSQKRVAEGKAPLTVRDVLEAMIMAHEIQGVL 159 ************************************************************************* PP TIGR02330 147 alensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgsrkswaagdatsr 219 alensfnrvgldhv+lvkvastav+akl+ga+r+++l+alsha+vdgqalrtyrhapn+gsrkswaagdatsr NCBI__GCF_000170835.1:WP_007152510.1 160 ALENSFNRVGLDHVVLVKVASTAVTAKLMGASRDQMLSALSHAWVDGQALRTYRHAPNAGSRKSWAAGDATSR 232 ************************************************************************* PP TIGR02330 220 gvrlalialkgemgypsalsapvwgfedvlfkke............klklareygsyvmenvlfkisfpaefh 280 +vrla+ia++gemg+ps+l+ap+wgf+d+lf+k+ +++l++ +g+yvmen+lfkisfpaefh NCBI__GCF_000170835.1:WP_007152510.1 233 AVRLADIAMRGEMGIPSVLTAPQWGFYDILFSKTnkdqtlkpedkrQFTLPQAFGAYVMENILFKISFPAEFH 305 ********************************999************************************** PP TIGR02330 281 aqtaveaavklheevkerldeierivitthesairiidkkgplanpadrdhclqylvavpllfgdlvaedyed 353 aqta+eaav lh+evk+rldeierivitthesairii+k+g lan adrdhclqy++avpl+fg l+ae+yed NCBI__GCF_000170835.1:WP_007152510.1 306 AQTAAEAAVILHPEVKDRLDEIERIVITTHESAIRIISKQGKLANAADRDHCLQYMAAVPLIFGGLTAEHYED 378 ************************************************************************* PP TIGR02330 354 a.vaadpridelreklevvedkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklv 425 + + a+p+id++r+k+evved+ry+reyleadkrsiana++vff+dg++t++v+veyp+ghrrrr+egip+l NCBI__GCF_000170835.1:WP_007152510.1 379 SfHEANPLIDQIRDKMEVVEDERYTREYLEADKRSIANAIQVFFTDGTSTDNVAVEYPIGHRRRRKEGIPLLE 451 *8899******************************************************************** PP TIGR02330 426 dkfkanlatkfsskkqerilelcldqakleatpvnefldlfvi 468 dkf+ nlat+f+ +++e+i++lc dq +leatpv ef+ +fvi NCBI__GCF_000170835.1:WP_007152510.1 452 DKFRHNLATRFPGQRCEKIFQLCKDQTELEATPVHEFVGMFVI 494 ****************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (468 nodes) Target sequences: 1 (494 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 14.41 // [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