Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.- (characterized)
to candidate WP_035703253.1 BA79_RS13120 methylisocitrate lyase
Query= SwissProt::P54528 (301 letters) >NCBI__GCF_000691145.1:WP_035703253.1 Length = 305 Score = 382 bits (981), Expect = e-111 Identities = 187/298 (62%), Positives = 238/298 (79%) Query: 3 WIVNKQSSQEELAGRFRKLMSAPDILQIPGAHDGMAALLAKEAGFSAIYLSGAAYTASRG 62 WIVN + SQ +LA F++ M + QIPG HDGM+AL A++ GF +YLSGAA+ AS+G Sbjct: 2 WIVNDEVSQADLAAAFKEQMHKSALFQIPGVHDGMSALYARKMGFKGLYLSGAAFCASKG 61 Query: 63 LPDLGIITSAEIAERAKDLVRAADLPLLVDIDTGFGGVLNAARTAREMLEARVAAVQMED 122 LPDLG+I S E+AE+AK+++RA+ LPLLVD+DTG+GGVLNAAR A+EM+E++VAAVQ+ED Sbjct: 62 LPDLGMIHSTEMAEKAKEIIRASQLPLLVDMDTGYGGVLNAARAAKEMVESKVAAVQIED 121 Query: 123 QQLPKKCGHLNGKQLVPIKEMAQKIKAIKQAAPSLIVVARTDARAQEGLDAAIKRSEAYI 182 QQ+PKKCGHLNGK LV +++M KIKAIKQAAP+L+V+ARTDA++ G++ I R+ Y+ Sbjct: 122 QQMPKKCGHLNGKSLVSVEDMMAKIKAIKQAAPTLLVIARTDAKSVNGMEDVIHRANLYL 181 Query: 183 EAGADAIFPEALQAENEFRQFAERIPVPLLANMTEFGKTPYYRADEFEDMGFHMVIYPVT 242 EAGADAIFPEAL +F + I PLLANMTEFGKTPYY ADEF GF MVIYPVT Sbjct: 182 EAGADAIFPEALITAEDFTYASNNIKGPLLANMTEFGKTPYYHADEFSMFGFQMVIYPVT 241 Query: 243 SLRAAAKACERMFGLMKEHGSQKEGLHDMQTRKELYDTISYYDYEALDKTIAKTVLPD 300 SLR AAKA ER+F +KE G+Q+ L DMQTRKELY+TI Y +YE +D+ +AKT+LP+ Sbjct: 242 SLRVAAKAYERLFTEIKEKGTQQGMLEDMQTRKELYETIHYDEYEEMDQHLAKTILPE 299 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: 312 Number of extensions: 8 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: 305 Length adjustment: 27 Effective length of query: 274 Effective length of database: 278 Effective search space: 76172 Effective search space used: 76172 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_035703253.1 BA79_RS13120 (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.674262.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-125 402.8 3.0 4.3e-125 402.6 3.0 1.0 1 NCBI__GCF_000691145.1:WP_035703253.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000691145.1:WP_035703253.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 402.6 3.0 4.3e-125 4.3e-125 3 284 .. 15 294 .. 13 295 .. 0.99 Alignments for each domain: == domain 1 score: 402.6 bits; conditional E-value: 4.3e-125 TIGR02317 3 kalrellkkedilqipGainalvallaekaGfeavYlsGaalaaslglPDlglttleevaeearritrvtklp 75 +a++e ++k+ + qipG++++++al a+k+Gf+++YlsGaa+ as glPDlg++ ++e+ae+a++i r+++lp NCBI__GCF_000691145.1:WP_035703253.1 15 AAFKEQMHKSALFQIPGVHDGMSALYARKMGFKGLYLSGAAFCASKGLPDLGMIHSTEMAEKAKEIIRASQLP 87 689********************************************************************** PP TIGR02317 76 llvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfvl 148 llvD+DtG+G++ln+ar+ ke++e++vaav+ieDq++pkkCGhl+gk+lvs e+m++kika+++a +++ NCBI__GCF_000691145.1:WP_035703253.1 88 LLVDMDTGYGGVLNAARAAKEMVESKVAAVQIEDQQMPKKCGHLNGKSLVSVEDMMAKIKAIKQAAP--TLLV 158 *****************************************************************98..9*** PP TIGR02317 149 iaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadeleel 221 iaRtDa++v+G+++ i+Ra++Y+eaGadaif+eal ++e+f + ++++k pllanmtefGktp++ ade++ NCBI__GCF_000691145.1:WP_035703253.1 159 IARTDAKSVNGMEDVIHRANLYLEAGADAIFPEALITAEDFTYASNNIKGPLLANMTEFGKTPYYHADEFSMF 231 ************************************************************************* PP TIGR02317 222 gykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284 g+++viyPvt+lR+a+ka e++++e+k+kGtq+++l+++qtRkelYe+++y++ye++d++l+k NCBI__GCF_000691145.1:WP_035703253.1 232 GFQMVIYPVTSLRVAAKAYERLFTEIKEKGTQQGMLEDMQTRKELYETIHYDEYEEMDQHLAK 294 ************************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (305 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: 15.78 // [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