Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_012973514.1 AZL_RS04740 3-isopropylmalate dehydrogenase
Query= BRENDA::P24404 (370 letters) >NCBI__GCF_000010725.1:WP_012973514.1 Length = 371 Score = 473 bits (1216), Expect = e-138 Identities = 234/366 (63%), Positives = 291/366 (79%), Gaps = 2/366 (0%) Query: 6 LFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDADMEKAL 65 L LPGDGIGPE M +VR++I++M+ F VSEGLVGG+A DAHGV +SDA + +AL Sbjct: 7 LLFLPGDGIGPEVMRQVRRVIDWMDRKRKITFDVSEGLVGGAAIDAHGVPLSDATLAEAL 66 Query: 66 AADAILFGAVGGPKWDG-VPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASSLKPE 124 A DA++ GAVGGPKWD Y RPEAGLL LRK+L LFANLRPA+ + AL AS+LK + Sbjct: 67 AVDAVMLGAVGGPKWDNPTDYTKRPEAGLLALRKELGLFANLRPAVVFDALVDASTLKAD 126 Query: 125 LVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFELARSR 184 ++ GLDILIVRELTGGVYFGEP+ I D+GNG++RG++TQ+Y T EI R+A VAFELAR R Sbjct: 127 VIRGLDILIVRELTGGVYFGEPRGITDIGNGERRGVNTQVYTTSEIRRVARVAFELARKR 186 Query: 185 DNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFDVIVT 244 N++CSMEK NVM+SG+LW Q VT+ H +++DV+L HM AD G MQL++ PKQFDVIVT Sbjct: 187 GNKLCSMEKANVMESGLLWRQEVTKLHQEEFQDVELSHMYADNGAMQLLKNPKQFDVIVT 246 Query: 245 DNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSIANPI 304 DNLFGD+LSD AAM+TGSLGMLPSASLGAPDA G RKA+YEPVHGSAPDIAG+ +ANP Sbjct: 247 DNLFGDILSDEAAMMTGSLGMLPSASLGAPDA-NGNRKALYEPVHGSAPDIAGRDLANPC 305 Query: 305 AMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDAVLAE 364 A + SFAMCLRYSFN+ ++A +E +I NVL G+RT+DIMA G + T+ MGD++L E Sbjct: 306 ATLLSFAMCLRYSFNLDEDAKLIERSIQNVLGGGMRTSDIMAPGMARCSTTVMGDSILRE 365 Query: 365 FKALSA 370 L++ Sbjct: 366 LDKLAS 371 Lambda K H 0.319 0.135 0.387 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: 449 Number of extensions: 14 Number of successful extensions: 3 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: 370 Length of database: 371 Length adjustment: 30 Effective length of query: 340 Effective length of database: 341 Effective search space: 115940 Effective search space used: 115940 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_012973514.1 AZL_RS04740 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))
# 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/TIGR00169.hmm # target sequence database: /tmp/gapView.19170.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00169 [M=349] Accession: TIGR00169 Description: leuB: 3-isopropylmalate dehydrogenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-146 472.1 0.0 5.8e-146 471.9 0.0 1.0 1 lcl|NCBI__GCF_000010725.1:WP_012973514.1 AZL_RS04740 3-isopropylmalate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010725.1:WP_012973514.1 AZL_RS04740 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 471.9 0.0 5.8e-146 5.8e-146 2 348 .. 7 361 .. 6 362 .. 0.98 Alignments for each domain: == domain 1 score: 471.9 bits; conditional E-value: 5.8e-146 TIGR00169 2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 + LpGDgiGpev+ + +v++ ++ + ++ ++ +e l+GGaaida+g Pl+++tl+++ ++dav+lga lcl|NCBI__GCF_000010725.1:WP_012973514.1 7 LLFLPGDGIGPEVMRQVRRVIDWMDRKRKITFDVSEGLVGGAAIDAHGVPLSDATLAEALAVDAVMLGA 75 5689***************************************************************** PP TIGR00169 71 vGGpkWdnlpr.dvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiY 138 vGGpkWdn +rPe gLL+lrkel+lfanLrPa +f++L+++s+lk+++++g+D+++vreLtgG+Y lcl|NCBI__GCF_000010725.1:WP_012973514.1 76 VGGPKWDNPTDyTKRPEAGLLALRKELGLFANLRPAVVFDALVDASTLKADVIRGLDILIVRELTGGVY 144 ********864368******************************************************* PP TIGR00169 139 fGepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeia 206 fGep+++++ ++ e+++++t++Yt++ei+r+arvafelarkr +k++s++kanv+es+ lWr+ v++++ lcl|NCBI__GCF_000010725.1:WP_012973514.1 145 FGEPRGITDIGNgERRGVNTQVYTTSEIRRVARVAFELARKRGNKLCSMEKANVMESGLLWRQEVTKLH 213 *********9999*******************************************************9 PP TIGR00169 207 k.eyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss.....kg 269 + e+ dvel+h+y Dn amqL+k+P+q+dv+vt+nlfGDilsDea+++tGslG+LPsasl+ ++ lcl|NCBI__GCF_000010725.1:WP_012973514.1 214 QeEFQDVELSHMYADNGAMQLLKNPKQFDVIVTDNLFGDILSDEAAMMTGSLGMLPSASLGApdangNR 282 999**********************************************************99999999 PP TIGR00169 270 lalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseatt 338 +al+epvhgsapdiag+++anp+a++ls a+ lrys+nl+e+a+ ie+++++vl g+rt+d++ + + lcl|NCBI__GCF_000010725.1:WP_012973514.1 283 KALYEPVHGSAPDIAGRDLANPCATLLSFAMCLRYSFNLDEDAKLIERSIQNVLGGGMRTSDIMAPGMA 351 9******************************************************************99 PP TIGR00169 339 avstkeveee 348 + st+ ++++ lcl|NCBI__GCF_000010725.1:WP_012973514.1 352 RCSTTVMGDS 361 9999999886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (371 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.82 // [ok]
This GapMind analysis is from Apr 10 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