Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_077277800.1 B1C78_RS03700 3-isopropylmalate dehydrogenase
Query= SwissProt::Q56268 (358 letters) >NCBI__GCF_002000365.1:WP_077277800.1 Length = 359 Score = 419 bits (1078), Expect = e-122 Identities = 222/355 (62%), Positives = 267/355 (75%), Gaps = 2/355 (0%) Query: 2 KKIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQL 61 KKI + GDGIGPEIVA A ++L+ + + L E VGGA DA+ PLP +L+L Sbjct: 3 KKILVLPGDGIGPEIVAEATKLLEVLRREHGLVAEFEEAPVGGAGYDAAGHPLPEDTLRL 62 Query: 62 AMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRP 121 A AADAV+LGAVGGPR+D RPE+GLL LR L+L+ANLRPA ++PQL AS L+P Sbjct: 63 AKAADAVLLGAVGGPRYDTLDWELRPERGLLGLRSELNLFANLRPAILYPQLASASALKP 122 Query: 122 ELVRDVDILVVRELTGDIYFGQPRGLEVID-GKRRGFNTMVYDEDEIRRIAHVAFRAAQG 180 E+V +DI+++RELTG YFG+PRG+ D G R GFNT++YDE EI RI F A Sbjct: 123 EIVGGLDIMILRELTGGAYFGKPRGIRTRDDGVREGFNTIIYDEGEIERIVRSGFEIAMK 182 Query: 181 RRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLT 240 R ++LCSVDKANVLE ++LWREV V+ D+PDV LSHMYVDNAAMQL+RAP QFDV++T Sbjct: 183 RGRRLCSVDKANVLEVSQLWREVAIRVSEDFPDVELSHMYVDNAAMQLVRAPKQFDVIVT 242 Query: 241 GNMFGDILSDEASQLTGSIGMLPSASL-GEGRAMYEPIHGSAPDIAGQDKANPLATILSV 299 NMFGDILSD A+ LTGSIGMLPSASL +G+ MYEPIHGSAPDIAGQ ANPLAT+LSV Sbjct: 243 ENMFGDILSDAAAMLTGSIGMLPSASLDADGKGMYEPIHGSAPDIAGQGVANPLATLLSV 302 Query: 300 AMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354 +MMLR+SL+ A RV+AAV RVLDQGLRT DI G+ +GT AMG AVV AL Sbjct: 303 SMMLRYSLDEGALADRVDAAVSRVLDQGLRTPDIWTEGSSKVGTTAMGDAVVAAL 357 Lambda K H 0.320 0.137 0.396 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: 444 Number of extensions: 19 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: 358 Length of database: 359 Length adjustment: 29 Effective length of query: 329 Effective length of database: 330 Effective search space: 108570 Effective search space used: 108570 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_077277800.1 B1C78_RS03700 (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.25625.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-152 491.0 0.0 1e-151 490.8 0.0 1.0 1 lcl|NCBI__GCF_002000365.1:WP_077277800.1 B1C78_RS03700 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002000365.1:WP_077277800.1 B1C78_RS03700 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 490.8 0.0 1e-151 1e-151 1 348 [. 4 352 .. 4 353 .. 0.99 Alignments for each domain: == domain 1 score: 490.8 bits; conditional E-value: 1e-151 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 ki vLpGDgiGpe+vaea+k L++++ +++l efeea +GGa da g+Plpe+tl+ +k+adavLlg lcl|NCBI__GCF_002000365.1:WP_077277800.1 4 KILVLPGDGIGPEIVAEATKLLEVLRREHGLVAEFEEAPVGGAGYDAAGHPLPEDTLRLAKAADAVLLG 72 799****************************************************************** PP TIGR00169 70 avGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiY 138 avGGp++d+l + rPe+gLL lr el+lfanLrPa l+++L ++s+lk+eiv g+D++++reLtgG Y lcl|NCBI__GCF_002000365.1:WP_077277800.1 73 AVGGPRYDTLDWELRPERGLLGLRSELNLFANLRPAILYPQLASASALKPEIVGGLDIMILRELTGGAY 141 ********************************************************************* PP TIGR00169 139 fGepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeia 206 fG+p++++ ++ +++++t Y + eieri+r +fe+a+kr ++++svDkanvLe+s+lWr+++ + lcl|NCBI__GCF_002000365.1:WP_077277800.1 142 FGKPRGIRTRDDgVREGFNTIIYDEGEIERIVRSGFEIAMKRGRRLCSVDKANVLEVSQLWREVAIRVS 210 ******99988879******************************************************* PP TIGR00169 207 keyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfep 275 +++Pdvel+h+y+DnaamqLv++P+q+dv+vt+n+fGDilsD a+++tGs+G+LPsasl +g++++ep lcl|NCBI__GCF_002000365.1:WP_077277800.1 211 EDFPDVELSHMYVDNAAMQLVRAPKQFDVIVTENMFGDILSDAAAMLTGSIGMLPSASLDADGKGMYEP 279 ********************************************************************* PP TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstke 344 +hgsapdiag+g+anp+a++ls++++lrysl+ a++++aav++vl++g rt+d+ +e++ +v+t++ lcl|NCBI__GCF_002000365.1:WP_077277800.1 280 IHGSAPDIAGQGVANPLATLLSVSMMLRYSLDEGALADRVDAAVSRVLDQGLRTPDIWTEGSSKVGTTA 348 ********************************************************************* PP TIGR00169 345 veee 348 +++ lcl|NCBI__GCF_002000365.1:WP_077277800.1 349 MGDA 352 9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (359 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: 9.44 // [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