Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate N515DRAFT_0031 N515DRAFT_0031 2-methylcitrate dehydratase (EC 4.2.1.79)
Query= BRENDA::P74840 (483 letters) >FitnessBrowser__Dyella79:N515DRAFT_0031 Length = 483 Score = 581 bits (1498), Expect = e-170 Identities = 295/486 (60%), Positives = 363/486 (74%), Gaps = 6/486 (1%) Query: 1 MSTQELNI--RPDFDREIVDIVDYVMNYEITSKVAYDTAHYCLLDTLGCGLEALEYPACK 58 MST +L RPD D +VDI DYV++Y I S AYDTA Y LLD+L + A+++P C Sbjct: 1 MSTHDLRSARRPDPDPPMVDIADYVVDYRIDSAEAYDTARYMLLDSLASAMLAMKFPECV 60 Query: 59 KLLGPIVPGTVVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLG 118 K LGP+VPG V+P GARVPGT +LDP QAAF IG IRWLDFNDTWLAAEWGHPSDNLG Sbjct: 61 KHLGPLVPGAVLPGGARVPGTSHELDPAQAAFAIGTQIRWLDFNDTWLAAEWGHPSDNLG 120 Query: 119 GILATADWLSRNAVAAGKAPLTMKQVLSGMIKAHEIQGCIALENAFNRVGLDHVLLVKVA 178 ILA AD+L R AV G +++ VL IKAHEIQGC AL N+FNRVG DHV+LV++A Sbjct: 121 AILALADYLGRKAVREGGRASSLRDVLGWAIKAHEIQGCYALRNSFNRVGQDHVILVRLA 180 Query: 179 STAVVAEMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALM 238 STAV MLG +++I+ AVS +W+D +LR+YRHAPNTG RKSWAAGDA RAV A+ Sbjct: 181 STAVATAMLGGGKEQIVTAVSHSWIDNGALRSYRHAPNTGPRKSWAAGDACRRAVIHAIN 240 Query: 239 A-KTGEMGYPSALTAKTWGFYDVSFKGETFRFQRPYGSYVMENVLFKISFPAEFHSQTAV 297 A G +GYPSAL+A TWG+YDV+F+G+ F F+RP+GSYVMENVLFK+S+PAEFH+QTAV Sbjct: 241 AVDRGVVGYPSALSAATWGYYDVAFEGKAFEFERPFGSYVMENVLFKLSYPAEFHAQTAV 300 Query: 298 EAAMTLYEQMQAAGKTAADIEKVTIRTHEACLRIIDKKGPLNNPADRDHCIQYMVAVPLL 357 E AM L+ Q+ AG+ A+I++V I T EA RIIDK GPL N ADRDHCIQYMVAVPLL Sbjct: 301 ECAMRLHGQV--AGR-IAEIDQVVIETQEAGARIIDKTGPLANYADRDHCIQYMVAVPLL 357 Query: 358 FGRLTAADYEDEVAQDKRIDALREKIVCYEDPAFTADYHDPEKRAIGNAITVEFTDGSRF 417 FGRLTA DY DEVA D RIDALRE++ E+P FT DY DP++R IGN++ V F DGS Sbjct: 358 FGRLTADDYGDEVAADPRIDALRERMAVSENPRFTRDYFDPDRRYIGNSVQVFFKDGSHT 417 Query: 418 GEVVVEYPIGHARRRADGIPKLIEKFKINLARQFPTRQQQRILDVSLDRARLEQMPVNEY 477 +V ++YPIGH RRRA+GIP L+ KF+ + P + + IL + D A L+ MPV E+ Sbjct: 418 DKVSIDYPIGHRRRRAEGIPVLLGKFEAAIRGHLPAHRVKAILQATSDPAGLDSMPVQEF 477 Query: 478 LDLYVI 483 L+L+ + Sbjct: 478 LELFTL 483 Lambda K H 0.321 0.136 0.408 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: 710 Number of extensions: 25 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: 483 Length of database: 483 Length adjustment: 34 Effective length of query: 449 Effective length of database: 449 Effective search space: 201601 Effective search space used: 201601 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 (21.9 bits) S2: 52 (24.6 bits)
Align candidate N515DRAFT_0031 N515DRAFT_0031 (2-methylcitrate dehydratase (EC 4.2.1.79))
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.27537.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-227 740.1 0.0 5.5e-227 739.9 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 N515DRAFT_0031 2-methylcitrate d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 N515DRAFT_0031 2-methylcitrate dehydratase (EC 4.2.1.79) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 739.9 0.0 5.5e-227 5.5e-227 4 467 .. 18 482 .. 15 483 .] 0.99 Alignments for each domain: == domain 1 score: 739.9 bits; conditional E-value: 5.5e-227 TIGR02330 4 lediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsy 69 ++diadyv++y+ids+eaydtary+lld+l +la+++pec k+lgp+v+g + p garvpgts+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 18 MVDIADYVVDYRIDSAEAYDTARYMLLDSLASAMLAMKFPECVKHLGPLVPGAVLPGGARVPGTSH 83 789*************************************************************** PP TIGR02330 70 qldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevlea 135 +ldp +aaf ig+ +rwld+ndtwlaaewghpsdnlg+ila adyl rk++ eg ++++vl lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 84 ELDPAQAAFAIGTQIRWLDFNDTWLAAEWGHPSDNLGAILALADYLGRKAVREGGRASSLRDVLGW 149 ****************************************************************** PP TIGR02330 136 mikaheiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrh 201 ikaheiqg+ al nsfnrvg dhv+lv++astav++++lg+ +e+i++a+sh+++d++alr+yrh lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 150 AIKAHEIQGCYALRNSFNRVGQDHVILVRLASTAVATAMLGGGKEQIVTAVSHSWIDNGALRSYRH 215 ****************************************************************** PP TIGR02330 202 apntgsrkswaagdatsrgvrlalial.kgemgypsalsapvwgfedvlfkkeklklareygsyvm 266 apntg rkswaagda+ r+v a+ a+ +g +gypsalsa++wg++dv f+++ ++++r++gsyvm lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 216 APNTGPRKSWAAGDACRRAVIHAINAVdRGVVGYPSALSAATWGYYDVAFEGKAFEFERPFGSYVM 281 ********************999998648************************************* PP TIGR02330 267 envlfkisfpaefhaqtaveaavklheevkerldeierivitthesairiidkkgplanpadrdhc 332 envlfk+s+paefhaqtave+a++lh +v r++ei+++vi t+e++ riidk+gplan adrdhc lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 282 ENVLFKLSYPAEFHAQTAVECAMRLHGQVAGRIAEIDQVVIETQEAGARIIDKTGPLANYADRDHC 347 ****************************************************************** PP TIGR02330 333 lqylvavpllfgdlvaedyedavaadpridelreklevvedkrysreyleadkrsianavevffkd 398 +qy+vavpllfg+l+a+dy d+vaadprid+lre++ v e++r++r+y+++d+r i n+v+vffkd lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 348 IQYMVAVPLLFGRLTADDYGDEVAADPRIDALRERMAVSENPRFTRDYFDPDRRYIGNSVQVFFKD 413 ****************************************************************** PP TIGR02330 399 gskteeveveyplghrrrrdegipklvdkfkanlatkfsskkqerilelcldqakleatpvnefld 464 gs+t++v+++yp+ghrrrr+egip+l kf+a++ ++++++ + il+ ++d a l+++pv+efl+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 414 GSHTDKVSIDYPIGHRRRRAEGIPVLLGKFEAAIRGHLPAHRVKAILQATSDPAGLDSMPVQEFLE 479 ****************************************************************** PP TIGR02330 465 lfv 467 lf lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 480 LFT 482 *97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (468 nodes) Target sequences: 1 (483 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.10 // [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