Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate GFF1975 HP15_1932 methylisocitrate lyase 2
Query= SwissProt::Q8EJW1 (292 letters) >FitnessBrowser__Marino:GFF1975 Length = 295 Score = 401 bits (1030), Expect = e-116 Identities = 202/289 (69%), Positives = 236/289 (81%) Query: 4 SAGLRFRQALANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANASYGLPDLGMTSM 63 S G RFR+AL +++PLQIVGT NAY A+MAE+ G QA+YLSG GVANASYGLPDLGMTSM Sbjct: 6 SPGARFRKALKDNQPLQIVGTINAYAAMMAEKVGHQAIYLSGGGVANASYGLPDLGMTSM 65 Query: 64 NDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEKIGVAAVHMEDQVSQKRCGH 123 N+V+ D RIT+AT +PLLVDIDTGWGGAFNIARTI+E E+ G AAVH+EDQV+QKRCGH Sbjct: 66 NEVVEDVRRITAATDVPLLVDIDTGWGGAFNIARTIREMERAGAAAVHIEDQVAQKRCGH 125 Query: 124 RPNKAVVSTEEMVDRIKAAVDARTDPNFVIMARTDAVAVEGLEAGIERAKAYIAAGADMI 183 RPNK +VS EEMVDRIKAAVDAR D +F IMARTDA EGLEA IERAKA I AGAD I Sbjct: 126 RPNKEIVSQEEMVDRIKAAVDAREDKDFFIMARTDAFQKEGLEAAIERAKACIEAGADGI 185 Query: 184 FAEALTELDQYRHFKAQVKAPILANMTEFGQTQLFNKEELAQAGADMVLYPLGTFRAANQ 243 FAEA+TEL+ Y+ F + PILAN+TEFG T L+N++ELA+AGADMVLYPL FRA N+ Sbjct: 186 FAEAVTELEHYKAFSEALDVPILANITEFGATPLYNRKELAEAGADMVLYPLSAFRAMNK 245 Query: 244 AALKVMQALMNDGHQRNVLDTMQTRADLYKYLGYHAFEDKLDQLFSQDK 292 AAL V Q ++ G Q++V+D MQTR +LY +L YH FE KLDQLF Q K Sbjct: 246 AALTVYQNILEKGDQKDVVDMMQTRMELYDFLNYHDFEQKLDQLFQQSK 294 Lambda K H 0.319 0.132 0.369 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: 302 Number of extensions: 9 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: 292 Length of database: 295 Length adjustment: 26 Effective length of query: 266 Effective length of database: 269 Effective search space: 71554 Effective search space used: 71554 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 GFF1975 HP15_1932 (methylisocitrate lyase 2)
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.28292.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 4.3 4e-133 428.9 4.3 1.0 1 lcl|FitnessBrowser__Marino:GFF1975 HP15_1932 methylisocitrate lyase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1975 HP15_1932 methylisocitrate lyase 2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 428.9 4.3 4e-133 4e-133 2 284 .. 8 291 .. 7 292 .. 0.99 Alignments for each domain: == domain 1 score: 428.9 bits; conditional E-value: 4e-133 TIGR02317 2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtklp 75 g+++r++lk +++lqi+G+ina++a++aek+G++a+YlsG+++a+ s glPDlg+t+++ev+e++rrit++t++p lcl|FitnessBrowser__Marino:GFF1975 8 GARFRKALKDNQPLQIVGTINAYAAMMAEKVGHQAIYLSGGGVANaSYGLPDLGMTSMNEVVEDVRRITAATDVP 82 689*****************************************989**************************** PP TIGR02317 76 llvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfvlia 150 llvD+DtG+G+a+n+art++e+e+ag+aavhieDqva+k+CGh+++ke+vs+eemv++ikaav+a++d+df+++a lcl|FitnessBrowser__Marino:GFF1975 83 LLVDIDTGWGGAFNIARTIREMERAGAAAVHIEDQVAQKRCGHRPNKEIVSQEEMVDRIKAAVDAREDKDFFIMA 157 *************************************************************************** PP TIGR02317 151 RtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadeleelgyki 225 RtDa eGl+aaieRaka +eaGad if+ea++++e+++ f++a++vp+lan+tefG tpl++ +el+e+g ++ lcl|FitnessBrowser__Marino:GFF1975 158 RTDAFQKEGLEAAIERAKACIEAGADGIFAEAVTELEHYKAFSEALDVPILANITEFGATPLYNRKELAEAGADM 232 *************************************************************************** PP TIGR02317 226 viyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284 v+yP++a+Ra++kaa +vy+++ +kG qk+++d +qtR elY+ l+y+d+e+k+++lf+ lcl|FitnessBrowser__Marino:GFF1975 233 VLYPLSAFRAMNKAALTVYQNILEKGDQKDVVDMMQTRMELYDFLNYHDFEQKLDQLFQ 291 ********************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (295 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: 10.87 // [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