Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate PP_2334 PP_2334 2-methylisocitrate lyase
Query= reanno::pseudo6_N2E2:Pf6N2E2_6061 (294 letters) >FitnessBrowser__Putida:PP_2334 Length = 296 Score = 525 bits (1353), Expect = e-154 Identities = 267/291 (91%), Positives = 277/291 (95%) Query: 4 STPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGITG 63 STPGQRFRDAVA EHPLQVVG INANHALLAKRAGFKAIYLSGGGVAAGSLG+PDLGITG Sbjct: 5 STPGQRFRDAVAAEHPLQVVGAINANHALLAKRAGFKAIYLSGGGVAAGSLGLPDLGITG 64 Query: 64 LDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAKRC 123 LDDVLTDVRRITDVCDLPLLVDVDTGFG+SAFNVARTV+SM KFGAAAIHIEDQVGAKRC Sbjct: 65 LDDVLTDVRRITDVCDLPLLVDVDTGFGASAFNVARTVRSMSKFGAAAIHIEDQVGAKRC 124 Query: 124 GHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAGAD 183 GHRPNKEIVSQQEMVDRIKAAVDAR+DDSFVIMARTDALAVEGL +ALDRA AC+EAGAD Sbjct: 125 GHRPNKEIVSQQEMVDRIKAAVDARSDDSFVIMARTDALAVEGLNAALDRAQACVEAGAD 184 Query: 184 MIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAFRAM 243 MIFPEAITEL+MYK FA RVKAPILANITEFGATPLYTTE+LA DVSLVLYPLSAFRAM Sbjct: 185 MIFPEAITELQMYKTFADRVKAPILANITEFGATPLYTTEELASVDVSLVLYPLSAFRAM 244 Query: 244 NKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294 NKAAENVYTA+RRDGTQ+NVIDTMQTRMELYD I YH FEQ LDALFA KK Sbjct: 245 NKAAENVYTALRRDGTQKNVIDTMQTRMELYDAIGYHAFEQSLDALFAQKK 295 Lambda K H 0.320 0.134 0.375 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: 354 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: 294 Length of database: 296 Length adjustment: 26 Effective length of query: 268 Effective length of database: 270 Effective search space: 72360 Effective search space used: 72360 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 PP_2334 PP_2334 (2-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.15060.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-136 440.3 1.9 1.6e-136 440.1 1.9 1.0 1 lcl|FitnessBrowser__Putida:PP_2334 PP_2334 2-methylisocitrate lyase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_2334 PP_2334 2-methylisocitrate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 440.1 1.9 1.6e-136 1.6e-136 2 284 .. 8 292 .. 7 293 .. 0.99 Alignments for each domain: == domain 1 score: 440.1 bits; conditional E-value: 1.6e-136 TIGR02317 2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtklp 75 g+++r+++++e++lq++Gaina++alla++aGf+a+YlsG+++aa slglPDlg+t l++v++++rrit+v++lp lcl|FitnessBrowser__Putida:PP_2334 8 GQRFRDAVAAEHPLQVVGAINANHALLAKRAGFKAIYLSGGGVAAgSLGLPDLGITGLDDVLTDVRRITDVCDLP 82 789****************************************999***************************** PP TIGR02317 76 llvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfvli 149 llvD+DtGfG a+nvartv+++ + g+aa+hieDqv +k+CGh+++ke+vs++emv++ikaav+a++d++fv++ lcl|FitnessBrowser__Putida:PP_2334 83 LLVDVDTGFGAsAFNVARTVRSMSKFGAAAIHIEDQVGAKRCGHRPNKEIVSQQEMVDRIKAAVDARSDDSFVIM 157 **********879************************************************************** PP TIGR02317 150 aRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadeleelgyk 224 aRtDa aveGl+aa++Ra+a veaGad+if+ea+++++++++fa++vk+p+lan+tefG tpl+t++el+++ ++ lcl|FitnessBrowser__Putida:PP_2334 158 ARTDALAVEGLNAALDRAQACVEAGADMIFPEAITELQMYKTFADRVKAPILANITEFGATPLYTTEELASVDVS 232 *************************************************************************** PP TIGR02317 225 iviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284 +v+yP++a+Ra++kaae+vy+ l+++Gtqk+++d++qtR elY+ +gy+++e+ ++ lf+ lcl|FitnessBrowser__Putida:PP_2334 233 LVLYPLSAFRAMNKAAENVYTALRRDGTQKNVIDTMQTRMELYDAIGYHAFEQSLDALFA 292 ******************************************************999986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (296 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: 00:00:00.00 # Mc/sec: 11.50 // [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