Align 3-isopropylmalate dehydratase subunit LeuD (EC 4.2.1.33) (characterized)
to candidate RR42_RS01535 RR42_RS01535 3-isopropylmalate dehydratase
Query= ecocyc::LEUD-MONOMER (201 letters) >FitnessBrowser__Cup4G11:RR42_RS01535 Length = 215 Score = 164 bits (414), Expect = 1e-45 Identities = 89/182 (48%), Positives = 108/182 (59%), Gaps = 2/182 (1%) Query: 11 LVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPDFVLNFPQYQG 70 L PL N+DTD I+PKQFL+ + + G LF D RF D +G P P F LN +YQG Sbjct: 12 LGAPLPIGNLDTDQIMPKQFLRIIDKAGLDRGLFYDMRF-DAQGV-PRPAFALNQARYQG 69 Query: 71 ASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPVKLSDAEVD 130 A +L+A NFGCGSSREHA W L YG + VIAPSF +IFY N+ NN+LL V L AEVD Sbjct: 70 AGVLVAGPNFGCGSSREHAVWGLQQYGIRAVIAPSFGEIFYSNAINNRLLLVMLPQAEVD 129 Query: 131 ELFALVKANPGIHFDVDLEAQEVKAGEKTYRFTIDAFRRHCMMNGLDSIGLTLQHDDAIA 190 L A V + ++DL A V AG + FT+ R GLD IG TL IA Sbjct: 130 ALMAAVSGSAPARIEIDLAAMSVSAGALRFAFTLAERHRTMFRQGLDMIGATLAQSSQIA 189 Query: 191 AY 192 A+ Sbjct: 190 AF 191 Lambda K H 0.322 0.138 0.421 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: 128 Number of extensions: 4 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: 201 Length of database: 215 Length adjustment: 21 Effective length of query: 180 Effective length of database: 194 Effective search space: 34920 Effective search space used: 34920 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 (21.9 bits) S2: 45 (21.9 bits)
Align candidate RR42_RS01535 RR42_RS01535 (3-isopropylmalate dehydratase)
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))
# 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/TIGR00171.hmm # target sequence database: /tmp/gapView.11566.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00171 [M=188] Accession: TIGR00171 Description: leuD: 3-isopropylmalate dehydratase, small subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-59 185.7 0.0 4.7e-59 185.5 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS01535 RR42_RS01535 3-isopropylmalate d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS01535 RR42_RS01535 3-isopropylmalate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 185.5 0.0 4.7e-59 4.7e-59 10 188 .] 12 188 .. 6 188 .. 0.96 Alignments for each domain: == domain 1 score: 185.5 bits; conditional E-value: 4.7e-59 TIGR00171 10 lvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasillaren 78 l +pl n+dtd+i+pkqfl+ i++ G+++ lfy+ r+ d++G p p f ln+ +yqga +l+a+ n lcl|FitnessBrowser__Cup4G11:RR42_RS01535 12 LGAPLPIGNLDTDQIMPKQFLRIIDKAGLDRGLFYDMRF-DAQG-VPRPAFALNQARYQGAGVLVAGPN 78 67899999*******************************.****.9*********************** PP TIGR00171 79 fGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvdl 146 fGcGssreha w l++yG++ +iapsf++ify+n+++n+ll + l+++ev+ l+a v+ ++++dl lcl|FitnessBrowser__Cup4G11:RR42_RS01535 79 FGCGSSREHAVWGLQQYGIRAVIAPSFGEIFYSNAINNRLLLVMLPQAEVDALMAAVSgSAPARIEIDL 147 **********************************************************88889****** PP TIGR00171 147 eaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188 a+ v ++ f++ e ++ ++ Gld ig tl + +i lcl|FitnessBrowser__Cup4G11:RR42_RS01535 148 AAMSVSAGA-LRFAFTLAERHRTMFRQGLDMIGATLAQSSQI 188 *******99.99************************987765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (215 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.57 // [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