Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate WP_043764975.1 U743_RS01510 methylisocitrate lyase
Query= reanno::Cup4G11:RR42_RS11260 (302 letters) >NCBI__GCF_000733765.1:WP_043764975.1 Length = 293 Score = 473 bits (1217), Expect = e-138 Identities = 238/290 (82%), Positives = 264/290 (91%) Query: 8 LARSAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGI 67 + SAGARFR ALA E PLQV+G INANHALLA++AG+RAIYLSGGGVAAGSLGLPDLGI Sbjct: 1 MIESAGARFRAALAAETPLQVIGAINANHALLAQQAGFRAIYLSGGGVAAGSLGLPDLGI 60 Query: 68 SNLDDVLTDVRRITDVCDVPLLVDVDTGFGASAFNVARTTRSLIKFGAGAMHIEDQVGAK 127 S LDDVL DVRRITDVCD PLLVDVDTGFG+S FNVARTT+++IK GAGAMHIEDQVGAK Sbjct: 61 SGLDDVLVDVRRITDVCDTPLLVDVDTGFGSSFFNVARTTKAMIKAGAGAMHIEDQVGAK 120 Query: 128 RCGHRPGKEIVSQGEMADRIKAAVDARTDENFVIMARTDALAVEGLDKAIERAVACVEAG 187 RCGHRPGKEIVS+ EM DRIKAAVDARTD +FVIMARTDALAVEGL+ AI+RA ACVEAG Sbjct: 121 RCGHRPGKEIVSKQEMVDRIKAAVDARTDPDFVIMARTDALAVEGLEAAIDRATACVEAG 180 Query: 188 ADAIFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVLYPLSAFR 247 AD IFPEAMT+LAMY++F +AV VPVLANITEFG+TPLFT +EL A VS+VLYPLSAFR Sbjct: 181 ADMIFPEAMTELAMYKRFAEAVGVPVLANITEFGSTPLFTVDELASADVSLVLYPLSAFR 240 Query: 248 AMNKAAENVYAAIRRDGTQQNVVDTMQTRAELYESIGYHAYEQKLDALFA 297 AMNKAA+NVY A+RRDGTQ+NVVDTMQTRAELYE+I YH YE+KLDALF+ Sbjct: 241 AMNKAAQNVYEAVRRDGTQKNVVDTMQTRAELYEAINYHDYERKLDALFS 290 Lambda K H 0.320 0.134 0.376 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: 331 Number of extensions: 6 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: 302 Length of database: 293 Length adjustment: 26 Effective length of query: 276 Effective length of database: 267 Effective search space: 73692 Effective search space used: 73692 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_043764975.1 U743_RS01510 (methylisocitrate lyase)
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))
# 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/TIGR02317.hmm # target sequence database: /tmp/gapView.525669.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02317 [M=285] Accession: TIGR02317 Description: prpB: methylisocitrate lyase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-133 429.1 2.5 4e-133 428.9 2.5 1.0 1 NCBI__GCF_000733765.1:WP_043764975.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000733765.1:WP_043764975.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 428.9 2.5 4e-133 4e-133 2 284 .. 6 290 .. 5 291 .. 0.99 Alignments for each domain: == domain 1 score: 428.9 bits; conditional E-value: 4e-133 TIGR02317 2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtk 73 g+++r++l++e +lq++Gaina++alla++aGf+a+YlsG+++aa slglPDlg++ l++v+ ++rrit+v++ NCBI__GCF_000733765.1:WP_043764975.1 6 GARFRAALAAETPLQVIGAINANHALLAQQAGFRAIYLSGGGVAAgSLGLPDLGISGLDDVLVDVRRITDVCD 78 689****************************************999*************************** PP TIGR02317 74 lpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkded 145 pllvD+DtGfG+ +nvart k +++ag++a+hieDqv +k+CGh++gke+vsk+emv++ikaav+a++d+d NCBI__GCF_000733765.1:WP_043764975.1 79 TPLLVDVDTGFGSsFFNVARTTKAMIKAGAGAMHIEDQVGAKRCGHRPGKEIVSKQEMVDRIKAAVDARTDPD 151 ************9568********************************************************* PP TIGR02317 146 fvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadel 218 fv++aRtDa aveGl+aai+Ra+a veaGad+if+ea+++++++++fa+av vp+lan+tefG tpl+t+del NCBI__GCF_000733765.1:WP_043764975.1 152 FVIMARTDALAVEGLEAAIDRATACVEAGADMIFPEAMTELAMYKRFAEAVGVPVLANITEFGSTPLFTVDEL 224 ************************************************************************* PP TIGR02317 219 eelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284 +++ +++v+yP++a+Ra++kaa++vye ++++Gtqk+++d++qtR+elYe ++y+dye+k++ lf NCBI__GCF_000733765.1:WP_043764975.1 225 ASADVSLVLYPLSAFRAMNKAAQNVYEAVRRDGTQKNVVDTMQTRAELYEAINYHDYERKLDALFS 290 *************************************************************99985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (293 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: 15.58 // [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