Align Probable 2-methylisocitrate lyase 2; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate WP_101586816.1 BJEO58_RS00620 methylisocitrate lyase
Query= SwissProt::Q8NSL2 (307 letters) >NCBI__GCF_900169175.1:WP_101586816.1 Length = 301 Score = 333 bits (855), Expect = 2e-96 Identities = 172/304 (56%), Positives = 211/304 (69%), Gaps = 3/304 (0%) Query: 1 MAGLFSSAVAPTERRKALRAALAAPEIARMPGAFSPLAARAIQEAGFEGVYVSGAVVAAD 60 M G +A A RR RA L + E+ + PGA +PL A I++ GFEGVY+SG +A Sbjct: 1 MLGATKTAAA---RRADFRALLDSGEVVQFPGAINPLNAMLIEQTGFEGVYISGGAFSAA 57 Query: 61 LALPDIGLTTLTEVAHRSRQIARVTDLPVLVDADTGFGEPMSAARTVSELEDAGVAGCHL 120 LPDIGLTTLTEV R IARVT+LP +DADTG+GE M+ ARTV E EDAG++G HL Sbjct: 58 QGLPDIGLTTLTEVVDHGRSIARVTNLPTFIDADTGWGEAMNVARTVQEFEDAGLSGIHL 117 Query: 121 EDQVNPKRCGHLDGKEVVGTDIMVRRIAAAVNERRDEQFVICARTDAAGVEGIDSAIERA 180 EDQVNPKRCGHLDGKEVV T MV+RI+AA RRDE F++CARTD+ EG+D+AI+RA Sbjct: 118 EDQVNPKRCGHLDGKEVVTTAEMVKRISAAAKGRRDENFILCARTDSRAGEGLDAAIDRA 177 Query: 181 KAYADAGADMIFTEALYSPADFEKFRAAVDIPLLANMTEFGKTELLPAQLLEDIGYNAVI 240 +AY AGADMIF EA+ +FE F AVD P+LANMTEFGK+EL + L D G VI Sbjct: 178 RAYVAAGADMIFPEAMRDLGEFETFANAVDAPILANMTEFGKSELFTTKQLADAGVRVVI 237 Query: 241 YPVTLLRIAMGQVEQALGDIANTGIQTDWVDRMQHRSRLYELLRYNEYNAFDQQVFTYSA 300 YPVT LR+AMG + L I + G Q VDRMQ R+ LYE + Y YN+FD VF +S Sbjct: 238 YPVTTLRLAMGAITDGLQAIRSEGTQASVVDRMQTRADLYETVDYEAYNSFDSAVFNFSQ 297 Query: 301 DSYK 304 + ++ Sbjct: 298 EGHQ 301 Lambda K H 0.320 0.134 0.382 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: 296 Number of extensions: 11 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: 307 Length of database: 301 Length adjustment: 27 Effective length of query: 280 Effective length of database: 274 Effective search space: 76720 Effective search space used: 76720 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_101586816.1 BJEO58_RS00620 (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.2899125.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-129 415.9 0.5 4.2e-129 415.7 0.5 1.0 1 NCBI__GCF_900169175.1:WP_101586816.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900169175.1:WP_101586816.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.7 0.5 4.2e-129 4.2e-129 2 284 .. 12 294 .. 11 295 .. 0.99 Alignments for each domain: == domain 1 score: 415.7 bits; conditional E-value: 4.2e-129 TIGR02317 2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaaslglPDlglttleevaeearritrvtkl 74 ++ +r+ll++++++q pGain+l a+l+e++Gfe+vY+sG+a++a glPD+glttl+ev+ + r+i+rvt+l NCBI__GCF_900169175.1:WP_101586816.1 12 RADFRALLDSGEVVQFPGAINPLNAMLIEQTGFEGVYISGGAFSAAQGLPDIGLTTLTEVVDHGRSIARVTNL 84 678********************************************************************** PP TIGR02317 75 pllvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfv 147 p+++DaDtG+Gea+nvartv+e+e+ag++++h+eDqv+pk+CGhldgke+v++ emvk+i aa+k+++de+f+ NCBI__GCF_900169175.1:WP_101586816.1 85 PTFIDADTGWGEAMNVARTVQEFEDAGLSGIHLEDQVNPKRCGHLDGKEVVTTAEMVKRISAAAKGRRDENFI 157 ************************************************************************* PP TIGR02317 148 liaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadelee 220 l+aRtD+ra eGldaai+Ra+aYv aGad+if+ea++++ ef++fa+av++p+lanmtefGk+ l+t+++l++ NCBI__GCF_900169175.1:WP_101586816.1 158 LCARTDSRAGEGLDAAIDRARAYVAAGADMIFPEAMRDLGEFETFANAVDAPILANMTEFGKSELFTTKQLAD 230 ************************************************************************* PP TIGR02317 221 lgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284 +g+++viyPvt+lR+a++a+++ ++ ++ +Gtq +++d++qtR++lYe+++ye+y+++d+ +f+ NCBI__GCF_900169175.1:WP_101586816.1 231 AGVRVVIYPVTTLRLAMGAITDGLQAIRSEGTQASVVDRMQTRADLYETVDYEAYNSFDSAVFN 294 ************************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (301 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: 15.46 // [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