Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate 7026692 Shewana3_3825 2-methylisocitrate lyase (RefSeq)
Query= SwissProt::Q8EJW1 (292 letters) >FitnessBrowser__ANA3:7026692 Length = 292 Score = 566 bits (1458), Expect = e-166 Identities = 289/292 (98%), Positives = 290/292 (99%) Query: 1 MTQSAGLRFRQALANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANASYGLPDLGM 60 MTQSAGLRFRQALANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANASYGLPDLGM Sbjct: 1 MTQSAGLRFRQALANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANASYGLPDLGM 60 Query: 61 TSMNDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEKIGVAAVHMEDQVSQKR 120 TSMNDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEK GVAAVHMEDQVSQKR Sbjct: 61 TSMNDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEKAGVAAVHMEDQVSQKR 120 Query: 121 CGHRPNKAVVSTEEMVDRIKAAVDARTDPNFVIMARTDAVAVEGLEAGIERAKAYIAAGA 180 CGHRPNKAVVSTEEMVDRIKAAVDARTDPNFVIMARTDAVAVEGLEAGIERAKAYIAAGA Sbjct: 121 CGHRPNKAVVSTEEMVDRIKAAVDARTDPNFVIMARTDAVAVEGLEAGIERAKAYIAAGA 180 Query: 181 DMIFAEALTELDQYRHFKAQVKAPILANMTEFGQTQLFNKEELAQAGADMVLYPLGTFRA 240 DMIFAEALTELDQYRHFKAQV APILANMTEFGQTQLFNKEELA+AGADMVLYPLGTFRA Sbjct: 181 DMIFAEALTELDQYRHFKAQVNAPILANMTEFGQTQLFNKEELAEAGADMVLYPLGTFRA 240 Query: 241 ANQAALKVMQALMNDGHQRNVLDTMQTRADLYKYLGYHAFEDKLDQLFSQDK 292 ANQAALKVMQALMNDGHQRNVLDTMQTRADLYKYLGYHAFEDKLDQLFSQDK Sbjct: 241 ANQAALKVMQALMNDGHQRNVLDTMQTRADLYKYLGYHAFEDKLDQLFSQDK 292 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: 462 Number of extensions: 12 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: 292 Length adjustment: 26 Effective length of query: 266 Effective length of database: 266 Effective search space: 70756 Effective search space used: 70756 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 7026692 Shewana3_3825 (2-methylisocitrate lyase (RefSeq))
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.23304.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-132 425.5 4.1 5.1e-132 425.3 4.1 1.0 1 lcl|FitnessBrowser__ANA3:7026692 Shewana3_3825 2-methylisocitrate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7026692 Shewana3_3825 2-methylisocitrate lyase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.3 4.1 5.1e-132 5.1e-132 2 284 .. 6 289 .. 5 290 .. 0.99 Alignments for each domain: == domain 1 score: 425.3 bits; conditional E-value: 5.1e-132 TIGR02317 2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtklpll 77 g ++r++l+++++lqi+G+ na+ al+ae++Gf+a+YlsGa++a+ s glPDlg+t++++v+ +a rit++t+lpll lcl|FitnessBrowser__ANA3:7026692 6 GLRFRQALANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANaSYGLPDLGMTSMNDVLIDAGRITSATQLPLL 82 579*****************************************989****************************** PP TIGR02317 78 vDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfvliaRtDa 154 vD+DtG+G+a+n+art+ke+e+agvaavh+eDqv +k+CGh+++k++vs+eemv++ikaav+a++d++fv++aRtDa lcl|FitnessBrowser__ANA3:7026692 83 VDIDTGWGGAFNIARTIKEFEKAGVAAVHMEDQVSQKRCGHRPNKAVVSTEEMVDRIKAAVDARTDPNFVIMARTDA 159 ***************************************************************************** PP TIGR02317 155 raveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadeleelgykiviyPvt 231 aveGl+a ieRakaY+ aGad+if+eal++++++r+f+++v++p+lanmtefG+t+l++ +el+e+g ++v+yP+ lcl|FitnessBrowser__ANA3:7026692 160 VAVEGLEAGIERAKAYIAAGADMIFAEALTELDQYRHFKAQVNAPILANMTEFGQTQLFNKEELAEAGADMVLYPLG 236 ***************************************************************************** PP TIGR02317 232 alRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284 ++Raa++aa kv++ l+++G q+++ld++qtR++lY+ lgy+++e+k+++lf lcl|FitnessBrowser__ANA3:7026692 237 TFRAANQAALKVMQALMNDGHQRNVLDTMQTRADLYKYLGYHAFEDKLDQLFS 289 **************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (292 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: 9.74 // [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