Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate 203317 SO4236 2-isopropylmalate synthase (NCBI ptt file)
Query= SwissProt::P15875 (523 letters) >FitnessBrowser__MR1:203317 Length = 522 Score = 685 bits (1767), Expect = 0.0 Identities = 348/518 (67%), Positives = 414/518 (79%), Gaps = 1/518 (0%) Query: 1 MSQQVIIFDTTLRDGEQALQASLSAKEKLQIALALERMGVDVMEVGFPVSSPGDFESVQT 60 MS +VIIFDTTLRDGEQAL ASLS KEKLQIA+ALER+GVDVMEVGFPVSSPGDFESVQT Sbjct: 1 MSNRVIIFDTTLRDGEQALAASLSVKEKLQIAMALERLGVDVMEVGFPVSSPGDFESVQT 60 Query: 61 IARTIKNSRVCALARCVEKDIDVAAQALKVADAFRIHTFIATSPMHIATKLRSTLDEVIE 120 IARTIKNSRVCAL+R +EKDID AAQAL VA+ FRIHTFI+TS +H+ +KL+ + ++V+E Sbjct: 61 IARTIKNSRVCALSRALEKDIDAAAQALSVAEQFRIHTFISTSTIHVESKLKRSFEQVLE 120 Query: 121 RAVYMVKRARNYTDDVEFSCEDAGRTPVDDLARVVEAAINAGARTINIPDTVGYTMPFEF 180 AV VK AR +TDDVEFSCEDAGRTP+D+L R+VEAAI+AGARTINIPDTVGYT+P EF Sbjct: 121 MAVGAVKYARRFTDDVEFSCEDAGRTPIDNLCRMVEAAIHAGARTINIPDTVGYTVPSEF 180 Query: 181 AGIISGLYERVPNIDKAIISVHTHDDLGIAVGNSLAAVHAGARQVEGAMNGIGERAGNCA 240 II L+ RVPNID+AIISVH HDDLG++V NS+ AV GARQ+E MNGIGERAGNC+ Sbjct: 181 GSIIQTLFNRVPNIDQAIISVHCHDDLGLSVANSITAVQHGARQIECTMNGIGERAGNCS 240 Query: 241 LEEVIMAIKVRKDIMNVHTNINHHEIWRTSQTVSQICNMPIPANKAIVGSGAFAHSSGIH 300 LEE+ M + RK+++ T IN EI RTS VSQ+CNMPI +NKAIVG+ AF HSSGIH Sbjct: 241 LEEIAMILATRKNLLGFETGINAKEIHRTSNLVSQLCNMPIQSNKAIVGANAFTHSSGIH 300 Query: 301 QDGVLKNRENYEIMTPESIGLNQIQLNLTSRSGRAAVKHRMEEMGYKDTDYNMDHLYDAF 360 QDG+LK + YEIMTPESIGLN+ LN+TSRSGR +KHRMEEMGY DYN+D LY+ F Sbjct: 301 QDGMLKAQNTYEIMTPESIGLNRNNLNMTSRSGRHVIKHRMEEMGYSSQDYNLDALYEQF 360 Query: 361 LKLADKKGQVFDYDLEALAFINKQQEEPEHFRLDYFSVQSGSSD-IATASVKLACGEEIK 419 L LADKKGQVFDYDLEALAFI Q E ++L VQS S++ +ATA+V++ G EIK Sbjct: 361 LHLADKKGQVFDYDLEALAFIEAQAAEDNFYQLRQLVVQSDSTEGVATATVRIEVGGEIK 420 Query: 420 AEAANGNGPVDAIYQAINRITGYDVELVKYDLNAKGQGKDALGQVDIVVNHHGRRFHGVG 479 EAA GNGPVDA Y AI R T ++++ Y L AKG G+DALGQVDI +H + FHGVG Sbjct: 421 TEAATGNGPVDAAYNAIARATDRRIDIISYKLGAKGVGQDALGQVDITAVYHEQNFHGVG 480 Query: 480 LATDIVESSAKAMVHVLNNIWRAAEVEKELQRKAQNKE 517 LATD+VE+SA+A+VHV+N RA +V Q +N+E Sbjct: 481 LATDVVEASARALVHVMNLTCRADKVADYKQNMHKNRE 518 Lambda K H 0.317 0.132 0.372 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: 752 Number of extensions: 23 Number of successful extensions: 2 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: 523 Length of database: 522 Length adjustment: 35 Effective length of query: 488 Effective length of database: 487 Effective search space: 237656 Effective search space used: 237656 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: 52 (24.6 bits)
Align candidate 203317 SO4236 (2-isopropylmalate synthase (NCBI ptt file))
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))
# 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.aa/TIGR00973.hmm # target sequence database: /tmp/gapView.6569.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00973 [M=494] Accession: TIGR00973 Description: leuA_bact: 2-isopropylmalate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-240 784.5 10.3 1.9e-240 784.4 10.3 1.0 1 lcl|FitnessBrowser__MR1:203317 SO4236 2-isopropylmalate synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:203317 SO4236 2-isopropylmalate synthase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 784.4 10.3 1.9e-240 1.9e-240 1 494 [] 4 498 .. 4 498 .. 0.99 Alignments for each domain: == domain 1 score: 784.4 bits; conditional E-value: 1.9e-240 TIGR00973 1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravekdid 79 rv+ifdttlrdGeqa+ asl+v+eklqia alerlgvd++e+Gfpvss+gdfe+vq+iar++kn+rv++l+ra+ekdid lcl|FitnessBrowser__MR1:203317 4 RVIIFDTTLRDGEQALAASLSVKEKLQIAMALERLGVDVMEVGFPVSSPGDFESVQTIARTIKNSRVCALSRALEKDID 82 79***************************************************************************** PP TIGR00973 80 aaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvveaaiea 158 aaa+al +ae++rihtfi+ts ih+e klk+++++vle++v avkya+ f+ddvefs+edagrt++++l+r+veaai+a lcl|FitnessBrowser__MR1:203317 83 AAAQALSVAEQFRIHTFISTSTIHVESKLKRSFEQVLEMAVGAVKYARRFTDDVEFSCEDAGRTPIDNLCRMVEAAIHA 161 ******************************************************************************* PP TIGR00973 159 GattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinGiGeraGnaa 237 Ga tiniPdtvGy++P+e+g++i++l ++vPnid+ai+svhchddlGl+vans++av++Garq+ect+nGiGeraGn++ lcl|FitnessBrowser__MR1:203317 162 GARTINIPDTVGYTVPSEFGSIIQTLFNRVPNIDQAIISVHCHDDLGLSVANSITAVQHGARQIECTMNGIGERAGNCS 240 ******************************************************************************* PP TIGR00973 238 leevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknketyeilspesi 316 lee++m+l +rk++l+ etgin kei+rts+lvs+l++m++q+nkaivG+naf h+sGihqdG+lk ++tyei++pesi lcl|FitnessBrowser__MR1:203317 241 LEEIAMILATRKNLLGFETGINAKEIHRTSNLVSQLCNMPIQSNKAIVGANAFTHSSGIHQDGMLKAQNTYEIMTPESI 319 ******************************************************************************* PP TIGR00973 317 GlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqv 395 Gl++++l++++rsGr+ +k+r+ee+G+ ++++ld l+e+f++ladkk++vfd+dleal+++e + e++ ++l +l v lcl|FitnessBrowser__MR1:203317 320 GLNRNNLNMTSRSGRHVIKHRMEEMGYSSQDYNLDALYEQFLHLADKKGQVFDYDLEALAFIEAQAAEDNFYQLRQLVV 398 ******************************************************************************* PP TIGR00973 396 qsge.esvptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkys 473 qs + e v+tatv+++v ge k++aatGnGpvda y+ai ++++ ++++ y++ akg g+dalg+v++++ +++++++ lcl|FitnessBrowser__MR1:203317 399 QSDStEGVATATVRIEVGGEIKTEAATGNGPVDAAYNAIARATDRRIDIISYKLGAKGVGQDALGQVDITAVYHEQNFH 477 9965167************************************************************************ PP TIGR00973 474 Grgvatdiveasakayvnaln 494 G+g+atd+veasa+a+v+++n lcl|FitnessBrowser__MR1:203317 478 GVGLATDVVEASARALVHVMN 498 *******************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (494 nodes) Target sequences: 1 (522 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 12.76 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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