Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_014450629.1 LFE_RS12730 3-isopropylmalate dehydrogenase
Query= SwissProt::Q56268 (358 letters) >NCBI__GCF_000284315.1:WP_014450629.1 Length = 367 Score = 399 bits (1024), Expect = e-116 Identities = 201/354 (56%), Positives = 264/354 (74%), Gaps = 5/354 (1%) Query: 3 KIAIFAGDGIGPEIVAAARQVLDAVDQA-----AHLGLRCTEGLVGGAALDASDDPLPAA 57 +I + GDGIGPE+ R+++ ++++ + EGL+GGAA DA+ PLP Sbjct: 8 QILLLPGDGIGPEVTVPVRELVSEINRSESGSQGKFQIELLEGLIGGAATDATGKPLPKE 67 Query: 58 SLQLAMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDAS 117 +L++A + DAV+L AVGGP++D P RPE+ LL +R+ L +ANLRPA++FP+L+DAS Sbjct: 68 TLEMADSCDAVLLAAVGGPKYDLLPYELRPERALLGIREHLGAFANLRPARLFPELVDAS 127 Query: 118 PLRPELVRDVDILVVRELTGDIYFGQPRGLEVIDGKRRGFNTMVYDEDEIRRIAHVAFRA 177 L+PE++ D+D++VVRELTG IYFG+PRG+ +G RRG NT Y E EI R+A VAF Sbjct: 128 TLKPEVISDLDLMVVRELTGGIYFGKPRGIVEENGIRRGINTETYTEPEIERVARVAFDL 187 Query: 178 AQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDV 237 A+ R ++ SVDKANVLE++ LWREVV V +DYPDV L HMYVDNAAMQL+R P QFDV Sbjct: 188 ARKRSHRVTSVDKANVLESSVLWREVVIRVHKDYPDVTLDHMYVDNAAMQLVRKPKQFDV 247 Query: 238 LLTGNMFGDILSDEASQLTGSIGMLPSASLGEGRAMYEPIHGSAPDIAGQDKANPLATIL 297 ++TGN+FGDILSDEASQLTGSIGML SAS+G +YEPIHGSAPDIAG++ ANP+A IL Sbjct: 248 IVTGNLFGDILSDEASQLTGSIGMLASASIGGKTGLYEPIHGSAPDIAGKNIANPMAMIL 307 Query: 298 SVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVV 351 S+A++LR+SLN E AQR+E +V VL QG RTADIA V+GT+ MG ++ Sbjct: 308 SLALLLRYSLNREDLAQRIERSVSSVLAQGFRTADIAQVKGQVLGTREMGEKII 361 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: 381 Number of extensions: 9 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: 358 Length of database: 367 Length adjustment: 29 Effective length of query: 329 Effective length of database: 338 Effective search space: 111202 Effective search space used: 111202 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_014450629.1 LFE_RS12730 (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.2702041.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-148 479.4 0.0 3.6e-148 479.2 0.0 1.0 1 NCBI__GCF_000284315.1:WP_014450629.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000284315.1:WP_014450629.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 479.2 0.0 3.6e-148 3.6e-148 2 349 .] 9 360 .. 8 360 .. 0.96 Alignments for each domain: == domain 1 score: 479.2 bits; conditional E-value: 3.6e-148 TIGR00169 2 iavLpGDgiGpevvaealkvLkavee.....rfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 i +LpGDgiGpev+ + + +++ + ++++e e liGGaa datg+Plp+etl+ +++ davLl+ NCBI__GCF_000284315.1:WP_014450629.1 9 ILLLPGDGIGPEVTVPVRELVSEINRsesgsQGKFQIELLEGLIGGAATDATGKPLPKETLEMADSCDAVLLA 81 899**********9999998888875312234467888889******************************** PP TIGR00169 70 avGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGep 142 avGGpk+d lp + rPe++LL +r++l+ fanLrPa+lf++L+++s+lk+e+++++Dl+vvreLtgGiYfG+p NCBI__GCF_000284315.1:WP_014450629.1 82 AVGGPKYDLLPYELRPERALLGIREHLGAFANLRPARLFPELVDASTLKPEVISDLDLMVVRELTGGIYFGKP 154 ************************************************************************* PP TIGR00169 143 kereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvele 215 +++ e++ +++++te+Yt++eier+arvaf larkr ++vtsvDkanvLess lWr++v ++k+yPdv+l+ NCBI__GCF_000284315.1:WP_014450629.1 155 RGIVEENGIRRGINTETYTEPEIERVARVAFDLARKRSHRVTSVDKANVLESSVLWREVVIRVHKDYPDVTLD 227 *****888***************************************************************** PP TIGR00169 216 hlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgi 288 h+y+DnaamqLv++P+q+dv+vt+nlfGDilsDeas +tGs+G+L sas++ +++l+ep+hgsapdiagk+i NCBI__GCF_000284315.1:WP_014450629.1 228 HMYVDNAAMQLVRKPKQFDVIVTGNLFGDILSDEASQLTGSIGMLASASIG-GKTGLYEPIHGSAPDIAGKNI 299 ***************************************************.6789***************** PP TIGR00169 289 anpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveeel 349 anp+a+ils+alllrysln e+ a++ie++v+ vl++g rt+d+a+ +++ +t+e++e++ NCBI__GCF_000284315.1:WP_014450629.1 300 ANPMAMILSLALLLRYSLNREDLAQRIERSVSSVLAQGFRTADIAQVKGQVLGTREMGEKI 360 *********************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (367 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: 26.18 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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