Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.- (characterized)
to candidate WP_036833563.1 N784_RS06825 methylisocitrate lyase
Query= SwissProt::P54528 (301 letters) >NCBI__GCF_000775615.1:WP_036833563.1 Length = 306 Score = 391 bits (1005), Expect = e-114 Identities = 194/300 (64%), Positives = 241/300 (80%) Query: 1 MSWIVNKQSSQEELAGRFRKLMSAPDILQIPGAHDGMAALLAKEAGFSAIYLSGAAYTAS 60 M+WIV + +Q E A L+ ILQIPG HDGMAA +AK+ GF AIYLSGAAYTAS Sbjct: 1 MTWIVENRKTQVERAKELHNLIKEETILQIPGTHDGMAARIAKDVGFQAIYLSGAAYTAS 60 Query: 61 RGLPDLGIITSAEIAERAKDLVRAADLPLLVDIDTGFGGVLNAARTAREMLEARVAAVQM 120 LPDLG+I S E+A +A++L++A+DLPL+VDIDTG+GGVLN ARTA+EM+EA VAAVQ+ Sbjct: 61 HALPDLGMIYSNEMAAKARELIQASDLPLIVDIDTGYGGVLNVARTAKEMVEAGVAAVQI 120 Query: 121 EDQQLPKKCGHLNGKQLVPIKEMAQKIKAIKQAAPSLIVVARTDARAQEGLDAAIKRSEA 180 EDQ LPKKCGHLNGK+L+ +EM QKI+ IK A+PSL+VVARTDA+A EG++ AI R+ Sbjct: 121 EDQHLPKKCGHLNGKKLISTEEMMQKIQTIKAASPSLLVVARTDAKATEGIEQAITRANQ 180 Query: 181 YIEAGADAIFPEALQAENEFRQFAERIPVPLLANMTEFGKTPYYRADEFEDMGFHMVIYP 240 Y++AGADAIFPEAL +E +FR+ +E I PLLANMTEFGKTPYY A++F G +MVIYP Sbjct: 181 YLQAGADAIFPEALTSEADFRRASEAIQGPLLANMTEFGKTPYYTAEQFASFGMNMVIYP 240 Query: 241 VTSLRAAAKACERMFGLMKEHGSQKEGLHDMQTRKELYDTISYYDYEALDKTIAKTVLPD 300 VTSLR AAKA ER+F + + G+Q L DMQTR++LY+TI YYDYE LDKTIAKT+LP+ Sbjct: 241 VTSLRVAAKAYERIFTTILKQGTQSNMLEDMQTREQLYETIHYYDYEKLDKTIAKTILPE 300 Lambda K H 0.318 0.133 0.370 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: 318 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: 301 Length of database: 306 Length adjustment: 27 Effective length of query: 274 Effective length of database: 279 Effective search space: 76446 Effective search space used: 76446 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_036833563.1 N784_RS06825 (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.3393905.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-126 407.6 4.8 1.5e-126 407.4 4.8 1.0 1 NCBI__GCF_000775615.1:WP_036833563.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000775615.1:WP_036833563.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 407.4 4.8 1.5e-126 1.5e-126 2 284 .. 15 295 .. 14 296 .. 0.99 Alignments for each domain: == domain 1 score: 407.4 bits; conditional E-value: 1.5e-126 TIGR02317 2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaaslglPDlglttleevaeearritrvtkl 74 +k+l++l+k+e ilqipG++++++a a+++Gf+a+YlsGaa++as +lPDlg++ ++e+a++ar++ ++++l NCBI__GCF_000775615.1:WP_036833563.1 15 AKELHNLIKEETILQIPGTHDGMAARIAKDVGFQAIYLSGAAYTASHALPDLGMIYSNEMAAKARELIQASDL 87 57899******************************************************************** PP TIGR02317 75 pllvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfv 147 pl+vD+DtG+G++lnvart ke++eagvaav+ieDq pkkCGhl+gk+l+s+eem++ki+ ++ a +++ NCBI__GCF_000775615.1:WP_036833563.1 88 PLIVDIDTGYGGVLNVARTAKEMVEAGVAAVQIEDQHLPKKCGHLNGKKLISTEEMMQKIQTIKAASP--SLL 158 *************************************************************9998887..9** PP TIGR02317 148 liaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadelee 220 ++aRtDa+a+eG+++ai Ra+ Y++aGadaif+eal+se++fr+ ++a++ pllanmtefGktp++ta+++++ NCBI__GCF_000775615.1:WP_036833563.1 159 VVARTDAKATEGIEQAITRANQYLQAGADAIFPEALTSEADFRRASEAIQGPLLANMTEFGKTPYYTAEQFAS 231 ************************************************************************* PP TIGR02317 221 lgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284 g+++viyPvt+lR+a+ka e++++++ k+Gtq ++l+++qtR++lYe+++y+dyek dk+++k NCBI__GCF_000775615.1:WP_036833563.1 232 FGMNMVIYPVTSLRVAAKAYERIFTTILKQGTQSNMLEDMQTREQLYETIHYYDYEKLDKTIAK 295 *************************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (306 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: 25.56 // [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