Align Citrate/2-methylcitrate dehydratase; EC 4.2.1.- (characterized)
to candidate PP_2338 PP_2338 2-methylcitrate dehydratase
Query= SwissProt::P45859 (472 letters) >FitnessBrowser__Putida:PP_2338 Length = 494 Score = 593 bits (1530), Expect = e-174 Identities = 292/482 (60%), Positives = 371/482 (76%), Gaps = 13/482 (2%) Query: 2 PKTDRVIEEITDYVLEKEITSAEAYTTAGHVLLDTLGCGILALRYPECTKLLGPIVPGTT 61 P DRV++ + DY L + S EA TA + L+DTLGCG+LALR+PECTKLLGP V GT Sbjct: 11 PDYDRVLQTLADYALGYRVDSREALDTARNCLMDTLGCGLLALRFPECTKLLGPQVEGTL 70 Query: 62 VPNGSKVPGTSYVLDPVRAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGILAAADYVSR 121 VPNG++VPGTSY LDPV+AA++IGC +RWLDYNDTWLAAEW HPSDNLGGILA AD++S+ Sbjct: 71 VPNGARVPGTSYRLDPVKAAWDIGCTVRWLDYNDTWLAAEWAHPSDNLGGILAVADHLSQ 130 Query: 122 VRLSEGKEPLTVRDVLEMMIKAHEIQGVLALENSLNRVGLDHVLFVKVATTAVAAKLLGG 181 R++ G++PL +RDVLE M+ AHEIQGVLALEN+ NRVGLDHV+ VKVA+TAV A+L+G Sbjct: 131 KRVAAGEKPLLMRDVLEAMVMAHEIQGVLALENAFNRVGLDHVILVKVASTAVCARLMGA 190 Query: 182 GREEIKNALSNAWIDNAALRTYRHSPNTGSRKSWAAGDATSRGVHLALMSLKGEMGYPTA 241 RE++ +ALS+A++D ALRTYRH+PN GSRKSWAAGDA+SRGV LA ++L+GEMG P Sbjct: 191 NREQMLSALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIALRGEMGVPGV 250 Query: 242 LSAPGWGFQDVLFN------------KKEIKLARPLDAYVMENVLFKVSYPAEFHAQTAA 289 L+A WGF DV F+ + E++L + L +YVMENVLFKVS+PAEFHAQTA Sbjct: 251 LTASQWGFYDVSFSHTNKDLALKPAGQYELRLPQALGSYVMENVLFKVSFPAEFHAQTAC 310 Query: 290 ESAVILHPQVKNRIDEIDRVVIRTHESAIRIIDKKGPLHNPADRDHCLQYITAIGLLFGD 349 E+AV LHP V+NR+ E+DR+VI T ESAIRII K GPL N ADRDHCLQY+ A+ L+FG Sbjct: 311 EAAVTLHPLVRNRLHEVDRIVITTQESAIRIISKSGPLANAADRDHCLQYMVAVPLIFGH 370 Query: 350 ITAQHYE-AETANDPRIDKLRDKMEVTENKTYTEDYLKPDKRSISNAVQVHFKDGTSTEM 408 + A+HYE A AN P ID+LR+KMEV E+ ++ +YL+P KRSI+NA+QV FKDG+STE Sbjct: 371 LVAEHYEDAFHANHPSIDRLREKMEVVEDPRFSREYLEPGKRSIANALQVFFKDGSSTEQ 430 Query: 409 VECEFPLGHRFRREEAVPKLLEKFSDNLKTHFPDKQHKHIYERCTSYETLQTMRVNEFVD 468 V E+P+GHR RR E +P L KF NL T F ++ + ++E C + L+ V+ FVD Sbjct: 431 VVVEYPIGHRRRRGEGIPLLEAKFRANLATRFARQRCQQVFELCKDQQKLEGTAVHRFVD 490 Query: 469 MF 470 +F Sbjct: 491 LF 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: 653 Number of extensions: 20 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 PP_2338 PP_2338 (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.31516.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-265 867.0 0.0 1.7e-265 866.9 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_2338 PP_2338 2-methylcitrate dehydrat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_2338 PP_2338 2-methylcitrate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 866.9 0.0 1.7e-265 1.7e-265 1 468 [] 14 494 .] 14 494 .] 1.00 Alignments for each domain: == domain 1 score: 866.9 bits; conditional E-value: 1.7e-265 TIGR02330 1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyqldpvk 75 d+vl+ +ady+l y++ds+ea+dtar++l+dtlgcgllal++pectkllgp vegtlvpngarvpgtsy+ldpvk lcl|FitnessBrowser__Putida:PP_2338 14 DRVLQTLADYALGYRVDSREALDTARNCLMDTLGCGLLALRFPECTKLLGPQVEGTLVPNGARVPGTSYRLDPVK 88 899************************************************************************ PP TIGR02330 76 aafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikaheiqgvlalen 150 aa++ig+ vrwldyndtwlaaew hpsdnlggilavad+ls+kr+a g++pl +++vleam++aheiqgvlalen lcl|FitnessBrowser__Putida:PP_2338 89 AAWDIGCTVRWLDYNDTWLAAEWAHPSDNLGGILAVADHLSQKRVAAGEKPLLMRDVLEAMVMAHEIQGVLALEN 163 *************************************************************************** PP TIGR02330 151 sfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgsrkswaagdatsrgvrlal 225 +fnrvgldhv+lvkvastav+a+l+ga+re++l+alshafvdgqalrtyrhapn+gsrkswaagda+srgvrla+ lcl|FitnessBrowser__Putida:PP_2338 164 AFNRVGLDHVILVKVASTAVCARLMGANREQMLSALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLAD 238 *************************************************************************** PP TIGR02330 226 ialkgemgypsalsapvwgfedvlfkke............klklareygsyvmenvlfkisfpaefhaqtaveaa 288 ial+gemg+p++l+a++wgf+dv+f+++ +l+l++ +gsyvmenvlfk+sfpaefhaqta+eaa lcl|FitnessBrowser__Putida:PP_2338 239 IALRGEMGVPGVLTASQWGFYDVSFSHTnkdlalkpagqyELRLPQALGSYVMENVLFKVSFPAEFHAQTACEAA 313 ***************************9*********************************************** PP TIGR02330 289 vklheevkerldeierivitthesairiidkkgplanpadrdhclqylvavpllfgdlvaedyeda.vaadprid 362 v+lh+ v++rl+e++rivitt+esairii+k gplan adrdhclqy+vavpl+fg+lvae+yeda +a++p id lcl|FitnessBrowser__Putida:PP_2338 314 VTLHPLVRNRLHEVDRIVITTQESAIRIISKSGPLANAADRDHCLQYMVAVPLIFGHLVAEHYEDAfHANHPSID 388 ******************************************************************99******* PP TIGR02330 363 elreklevvedkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklvdkfkanlatkfs 437 +lrek+evved+r+sreyle+ krsiana++vffkdgs+te+v+veyp+ghrrrr egip+l kf+anlat+f+ lcl|FitnessBrowser__Putida:PP_2338 389 RLREKMEVVEDPRFSREYLEPGKRSIANALQVFFKDGSSTEQVVVEYPIGHRRRRGEGIPLLEAKFRANLATRFA 463 *************************************************************************** PP TIGR02330 438 skkqerilelcldqakleatpvnefldlfvi 468 +++++++elc dq+kle t+v +f+dlfvi lcl|FitnessBrowser__Putida:PP_2338 464 RQRCQQVFELCKDQQKLEGTAVHRFVDLFVI 494 *****************************97 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.87 // [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