Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate BPHYT_RS13280 BPHYT_RS13280 2-isopropylmalate synthase
Query= SwissProt::P42455 (616 letters) >FitnessBrowser__BFirm:BPHYT_RS13280 Length = 572 Score = 600 bits (1547), Expect = e-176 Identities = 311/571 (54%), Positives = 395/571 (69%), Gaps = 33/571 (5%) Query: 37 PVNRYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFEL 96 P +Y F+ ++L DR WP + IT P W + DLRDGNQ+L +PM +RK RMF+ Sbjct: 5 PATKYRSFK----PVTLTDRQWPSRTITHPPIWMSTDLRDGNQSLFEPMDAQRKMRMFKT 60 Query: 97 LVQMGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGA 156 LVQ+GFKEIEV FPSASQTDF+FVRE+IE G IPDDVTI+VL QAR+ LI RTFE+ G Sbjct: 61 LVQIGFKEIEVAFPSASQTDFNFVRELIEGGHIPDDVTIEVLTQARDDLIERTFESLRGV 120 Query: 157 KNVIVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFT 216 IVH YN+T+ R +VF ++K VK+LA +AA +K IA P+T + +QYSPE F+ Sbjct: 121 PRAIVHLYNATAPEFRKIVFNLEKSGVKELAQNAARTMKRIAATMPETQFTFQYSPEVFS 180 Query: 217 GTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSII 276 GTE+E+AKEV DAV +V PTPE+ I+NLP+TVEM TPN+YAD IEWMHRNL RRDS+I Sbjct: 181 GTEIEFAKEVCDAVFDVWQPTPEHKAIVNLPATVEMSTPNIYADQIEWMHRNLARRDSLI 240 Query: 277 LSLHPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLD 336 +S+HPHNDRGT V AAEL MAGADRIEGCLFGNGERTGNV LVTLALN+ TQGVDP LD Sbjct: 241 ISVHPHNDRGTAVAAAELAVMAGADRIEGCLFGNGERTGNVDLVTLALNLYTQGVDPGLD 300 Query: 337 FTDIRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASST 396 F++I ++ T E C QL + RHPY GDLVFTAFSGSHQDA+ KG Sbjct: 301 FSNINEVARTAEECTQLPIHPRHPYVGDLVFTAFSGSHQDAIKKGFAV------------ 348 Query: 397 EVSWEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQ 456 Q D WEVPY+PIDP D+GR Y++VIRVNSQSGKGG+AY+++ +G+ +PR +Q Sbjct: 349 -----QKPDAVWEVPYMPIDPADLGRTYDSVIRVNSQSGKGGIAYLLEQGYGVVLPRRLQ 403 Query: 457 VEFSTVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAE 516 V+FS+ VQ TD G EV S +W++F EY++ TAP+ + + + E +T + Sbjct: 404 VDFSSAVQRFTDDSGQEVTSAQIWELFQQEYVQNTAPIHYVGHSLSERE-GRERIKLTVD 462 Query: 517 LIHNGKDVTVDGRGNGPLAAYANALEKLGIDVEIQEYNQHARTSGDDAEAAAYVLAEVNG 576 + +G + G GNGPL A +A +G+ V IQ Y + A T G DA A A +AE+ G Sbjct: 463 I--HGTRRVLTGEGNGPLDALMHA---IGVPVRIQHYEERALTQGADARAVA--VAEMAG 515 Query: 577 RKV----WGVGIAGSITYASLKAVTSAVNRA 603 V +GVGI ++ AS++AV S VNRA Sbjct: 516 ADVTGSAFGVGIDANLVTASIRAVISGVNRA 546 Lambda K H 0.316 0.133 0.390 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: 924 Number of extensions: 38 Number of successful extensions: 5 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: 616 Length of database: 572 Length adjustment: 37 Effective length of query: 579 Effective length of database: 535 Effective search space: 309765 Effective search space used: 309765 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 (21.6 bits) S2: 53 (25.0 bits)
Align candidate BPHYT_RS13280 BPHYT_RS13280 (2-isopropylmalate synthase)
to HMM TIGR00970 (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/TIGR00970.hmm # target sequence database: /tmp/gapView.13162.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00970 [M=564] Accession: TIGR00970 Description: leuA_yeast: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-237 773.2 0.0 9.4e-237 772.9 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS13280 BPHYT_RS13280 2-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS13280 BPHYT_RS13280 2-isopropylmalate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 772.9 0.0 9.4e-237 9.4e-237 1 562 [. 5 546 .. 5 548 .. 0.96 Alignments for each domain: == domain 1 score: 772.9 bits; conditional E-value: 9.4e-237 TIGR00970 1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfp 70 p+ ky+ fk++ l++r+wp + it+ p w+s+dlrdGnq+l +pm+++rk r+fk lv+iGfkeiev+fp lcl|FitnessBrowser__BFirm:BPHYT_RS13280 5 PATKYRSFKPVTLTDRQWPSRTITHPPIWMSTDLRDGNQSLFEPMDAQRKMRMFKTLVQIGFKEIEVAFP 74 889******************************************************************* PP TIGR00970 71 sasqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasr 140 sasqtdf+fvre+ie g ipddvti+vltq+r++li+rt+e+l+G ++aivhlynat++ fr++vf+ ++ lcl|FitnessBrowser__BFirm:BPHYT_RS13280 75 SASQTDFNFVRELIEGGHIPDDVTIEVLTQARDDLIERTFESLRGVPRAIVHLYNATAPEFRKIVFNLEK 144 ********************************************************************** PP TIGR00970 141 eevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnlp 210 v +la ++ +r + + aa +et+++f+yspe fs+te efa+evc+av +v++pt+e+ i nlp lcl|FitnessBrowser__BFirm:BPHYT_RS13280 145 SGVKELAQNA---ARTMKRIAATMPETQFTFQYSPEVFSGTEIEFAKEVCDAVFDVWQPTPEHKAIVNLP 211 **********...788888899************************************************ PP TIGR00970 211 atvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertGnv 280 atve++tpn+yad+ie++ +n+a r+++i+s+hphndrGtavaaael ++aGadrieGclfGnGertGnv lcl|FitnessBrowser__BFirm:BPHYT_RS13280 212 ATVEMSTPNIYADQIEWMHRNLARRDSLIISVHPHNDRGTAVAAAELAVMAGADRIEGCLFGNGERTGNV 281 ********************************************************************** PP TIGR00970 281 dlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGldaldk 350 dlvtlalnlytqGv+p ldfs+++e+ r+ e+c ++p+h+rhpy Gdlv+tafsGshqdaikkG+ +++ lcl|FitnessBrowser__BFirm:BPHYT_RS13280 282 DLVTLALNLYTQGVDPGLDFSNINEVARTAEECTQLPIHPRHPYVGDLVFTAFSGSHQDAIKKGFAVQKP 351 *****************************************************************99864 PP TIGR00970 351 kkaaadtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiads 420 d++w+vpy+p+dp d+gr+y++virvnsqsGkGG+ay+l + +G+ lprrlq++fss+v+ ++d lcl|FitnessBrowser__BFirm:BPHYT_RS13280 352 -----DAVWEVPYMPIDPADLGRTYDSVIRVNSQSGKGGIAYLLEQGYGVVLPRRLQVDFSSAVQRFTDD 416 .....679************************************************************** PP TIGR00970 421 kGkelsskeisdlfkeeyllnveqlerislvdyaveddGteskvitavvkikgekkdieGsGnGplsalv 490 G+e++s +i++lf++ey n+ +++ v +++++ +++ i+ +v+i+g+++ + G GnGpl al+ lcl|FitnessBrowser__BFirm:BPHYT_RS13280 417 SGQEVTSAQIWELFQQEYVQNTAPIH---YVGHSLSERE-GRERIKLTVDIHGTRRVLTGEGNGPLDALM 482 ******************99766655...5555555544.5889**********************9999 PP TIGR00970 491 daladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsaslravlsavn 560 +a+ v v + +y e al+ G da+a + e++ + +GvGi++++ +as+rav+s+vn lcl|FitnessBrowser__BFirm:BPHYT_RS13280 483 HAIG----VPVRIQHYEERALTQGADARAVAVAEMAGADV----TGSAFGVGIDANLVTASIRAVISGVN 544 9974....7789*****************99888765544....5899********************** PP TIGR00970 561 ra 562 ra lcl|FitnessBrowser__BFirm:BPHYT_RS13280 545 RA 546 98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (564 nodes) Target sequences: 1 (572 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: 10.77 // [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