Align Citrate/2-methylcitrate dehydratase; EC 4.2.1.- (characterized)
to candidate WP_036833565.1 N784_RS06830 bifunctional 2-methylcitrate dehydratase/aconitate hydratase
Query= SwissProt::P45859 (472 letters) >NCBI__GCF_000775615.1:WP_036833565.1 Length = 480 Score = 690 bits (1781), Expect = 0.0 Identities = 326/467 (69%), Positives = 388/467 (83%) Query: 4 TDRVIEEITDYVLEKEITSAEAYTTAGHVLLDTLGCGILALRYPECTKLLGPIVPGTTVP 63 TD+V+E+I DY + +I S EA+ TA +VL+DT+GCG+LAL+YPECTK LGPIVPGT VP Sbjct: 12 TDQVLEQIADYAINGQIKSEEAWQTARYVLMDTIGCGVLALKYPECTKHLGPIVPGTVVP 71 Query: 64 NGSKVPGTSYVLDPVRAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGILAAADYVSRVR 123 NG VPGTSY LDPV AAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGG+LA ADY+S+ R Sbjct: 72 NGVHVPGTSYKLDPVHAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGVLAVADYISQKR 131 Query: 124 LSEGKEPLTVRDVLEMMIKAHEIQGVLALENSLNRVGLDHVLFVKVATTAVAAKLLGGGR 183 LSEGK P+ + VLE +KAHEIQG+LALENSLNR GLDHVLFVKVATTAV +LGG + Sbjct: 132 LSEGKAPIRMETVLEYTVKAHEIQGILALENSLNRQGLDHVLFVKVATTAVVTAMLGGNK 191 Query: 184 EEIKNALSNAWIDNAALRTYRHSPNTGSRKSWAAGDATSRGVHLALMSLKGEMGYPTALS 243 +++ NA+S AW+DN++LRTYRH+PNTGSRKSWAAGDATSRGV LA+M++ GEMGY TALS Sbjct: 192 QDVVNAVSQAWLDNSSLRTYRHAPNTGSRKSWAAGDATSRGVRLAMMTMFGEMGYKTALS 251 Query: 244 APGWGFQDVLFNKKEIKLARPLDAYVMENVLFKVSYPAEFHAQTAAESAVILHPQVKNRI 303 APGWGFQDVL N +E+ LA+ LD+YVMEN+LFK+ YPAEFHAQTA E+A+ LH +VK+R+ Sbjct: 252 APGWGFQDVLMNGQELTLAQDLDSYVMENILFKIKYPAEFHAQTAVEAAIQLHHEVKDRL 311 Query: 304 DEIDRVVIRTHESAIRIIDKKGPLHNPADRDHCLQYITAIGLLFGDITAQHYEAETANDP 363 +EI +V I THESAIRIIDK GPLHNPADRDHCLQYITAIGL++G++TA HYE TA P Sbjct: 312 EEIHKVTITTHESAIRIIDKTGPLHNPADRDHCLQYITAIGLIYGELTADHYEDATARHP 371 Query: 364 RIDKLRDKMEVTENKTYTEDYLKPDKRSISNAVQVHFKDGTSTEMVECEFPLGHRFRREE 423 +ID+LR+KME ENK Y+ DYL +KRSI+NAVQVHF DGTSTE V+ E+P+GHR RREE Sbjct: 372 QIDRLREKMETVENKQYSADYLDANKRSIANAVQVHFTDGTSTEQVKIEYPIGHRRRREE 431 Query: 424 AVPKLLEKFSDNLKTHFPDKQHKHIYERCTSYETLQTMRVNEFVDMF 470 +P LL KF NLKT FP +Q I C ++ L VNEF+DMF Sbjct: 432 GLPLLLNKFQSNLKTRFPLRQVNQILNLCEDHDVLMRKPVNEFMDMF 478 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: 752 Number of extensions: 18 Number of successful extensions: 1 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: 480 Length adjustment: 33 Effective length of query: 439 Effective length of database: 447 Effective search space: 196233 Effective search space used: 196233 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: 51 (24.3 bits)
Align candidate WP_036833565.1 N784_RS06830 (bifunctional 2-methylcitrate dehydratase/aconitate hydratase)
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.2761316.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-260 849.2 0.1 4.5e-260 849.0 0.1 1.0 1 NCBI__GCF_000775615.1:WP_036833565.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000775615.1:WP_036833565.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 849.0 0.1 4.5e-260 4.5e-260 1 468 [] 13 480 .] 13 480 .] 1.00 Alignments for each domain: == domain 1 score: 849.0 bits; conditional E-value: 4.5e-260 TIGR02330 1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyqldp 73 d+vle+iady+++ +i+s+ea++taryvl+dt+gcg+lal+ypectk+lgp+v+gt+vpng++vpgtsy+ldp NCBI__GCF_000775615.1:WP_036833565.1 13 DQVLEQIADYAINGQIKSEEAWQTARYVLMDTIGCGVLALKYPECTKHLGPIVPGTVVPNGVHVPGTSYKLDP 85 899********************************************************************** PP TIGR02330 74 vkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikaheiqgvl 146 v+aafnig+++rwldyndtwlaaewghpsdnlgg+lavady+s+kr++egk+p+++ vle +kaheiqg+l NCBI__GCF_000775615.1:WP_036833565.1 86 VHAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGVLAVADYISQKRLSEGKAPIRMETVLEYTVKAHEIQGIL 158 ************************************************************************* PP TIGR02330 147 alensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgsrkswaagdatsr 219 alens+nr gldhvl+vkva+tavv+++lg+++++++na+s+a++d+++lrtyrhapntgsrkswaagdatsr NCBI__GCF_000775615.1:WP_036833565.1 159 ALENSLNRQGLDHVLFVKVATTAVVTAMLGGNKQDVVNAVSQAWLDNSSLRTYRHAPNTGSRKSWAAGDATSR 231 ************************************************************************* PP TIGR02330 220 gvrlalialkgemgypsalsapvwgfedvlfkkeklklareygsyvmenvlfkisfpaefhaqtaveaavklh 292 gvrla++++ gemgy +alsap wgf+dvl+++++l+la++++syvmen+lfki +paefhaqtaveaa++lh NCBI__GCF_000775615.1:WP_036833565.1 232 GVRLAMMTMFGEMGYKTALSAPGWGFQDVLMNGQELTLAQDLDSYVMENILFKIKYPAEFHAQTAVEAAIQLH 304 ************************************************************************* PP TIGR02330 293 eevkerldeierivitthesairiidkkgplanpadrdhclqylvavpllfgdlvaedyedavaadpridelr 365 +evk+rl+ei++++itthesairiidk+gpl npadrdhclqy++a++l++g+l+a++yeda a++p+id+lr NCBI__GCF_000775615.1:WP_036833565.1 305 HEVKDRLEEIHKVTITTHESAIRIIDKTGPLHNPADRDHCLQYITAIGLIYGELTADHYEDATARHPQIDRLR 377 ************************************************************************* PP TIGR02330 366 eklevvedkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklvdkfkanlatkfss 438 ek+e ve+k+ys++yl+a+krsianav+v+f+dg++te+v++eyp+ghrrrr+eg+p+l +kf+ nl t+f+ NCBI__GCF_000775615.1:WP_036833565.1 378 EKMETVENKQYSADYLDANKRSIANAVQVHFTDGTSTEQVKIEYPIGHRRRREEGLPLLLNKFQSNLKTRFPL 450 ************************************************************************* PP TIGR02330 439 kkqerilelcldqakleatpvnefldlfvi 468 ++ ++il+lc d++ l + pvnef+d+f i NCBI__GCF_000775615.1:WP_036833565.1 451 RQVNQILNLCEDHDVLMRKPVNEFMDMFTI 480 ***************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (468 nodes) Target sequences: 1 (480 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 28.83 // [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