Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate 5211053 Shew_3469 isopropylmalate isomerase small subunit (RefSeq)
Query= SwissProt::P04787 (201 letters) >FitnessBrowser__PV4:5211053 Length = 201 Score = 256 bits (655), Expect = 1e-73 Identities = 124/198 (62%), Positives = 155/198 (78%), Gaps = 1/198 (0%) Query: 3 EKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPEFV 62 + FT HTGL V +D+AN+DTD IIPKQFL KVTR GFG HLF+DWR+LD+ G QPNPEF Sbjct: 2 QPFTTHTGLAVIIDSANIDTDQIIPKQFLSKVTRDGFGVHLFHDWRYLDDAGDQPNPEFS 61 Query: 63 LNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPV 122 LN P YQGASILLA+ENFGCGSSREHAPWAL D+G +V+IAPSFADIFYGN+ NN LLPV Sbjct: 62 LNRPRYQGASILLAKENFGCGSSREHAPWALADFGLRVIIAPSFADIFYGNAINNGLLPV 121 Query: 123 TLSDAQVDELFALVKANPGIKFEVDLEAQVVKA-GDKTYSFKIDDFRRHCMLNGLDSIGL 181 L++A+V +L V+A G + VDL+AQ V + ++SF+I RH +LNGLD+IG+ Sbjct: 122 RLTEAEVVQLMREVEAEEGAQVSVDLQAQTVTSPSGASFSFEIAPSARHNLLNGLDAIGI 181 Query: 182 TLQHEDAIAAYENKQPAF 199 +L + +AIAAYE + P + Sbjct: 182 SLGYGEAIAAYETEIPGW 199 Lambda K H 0.321 0.138 0.416 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: 178 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: 201 Length adjustment: 21 Effective length of query: 180 Effective length of database: 180 Effective search space: 32400 Effective search space used: 32400 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 5211053 Shew_3469 (isopropylmalate isomerase small subunit (RefSeq))
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.19157.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-88 279.9 0.0 5.6e-88 279.8 0.0 1.0 1 lcl|FitnessBrowser__PV4:5211053 Shew_3469 isopropylmalate isomer Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5211053 Shew_3469 isopropylmalate isomerase small subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 279.8 0.0 5.6e-88 5.6e-88 1 187 [. 1 188 [. 1 189 [. 0.98 Alignments for each domain: == domain 1 score: 279.8 bits; conditional E-value: 5.6e-88 TIGR00171 1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasillaren 78 m++f ++tGl+v +d an+dtd+iipkqfl k++r Gfg hlf++wryld+ G++pnpef ln p+yqgasilla+en lcl|FitnessBrowser__PV4:5211053 1 MQPFTTHTGLAVIIDSANIDTDQIIPKQFLSKVTRDGFGVHLFHDWRYLDDAGDQPNPEFSLNRPRYQGASILLAKEN 78 89**************************************************************************** PP TIGR00171 79 fGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvdleaqkvkdse 155 fGcGssrehapwal+d+G++viiapsfadify+n+++ngllp+rl+e+ev +l+ v+ ++g +++vdl+aq+v++ lcl|FitnessBrowser__PV4:5211053 79 FGCGSSREHAPWALADFGLRVIIAPSFADIFYGNAINNGLLPVRLTEAEVVQLMREVEaEEGAQVSVDLQAQTVTSPS 156 *********************************************************9999***************** PP TIGR00171 156 gkvysfeidefrkhcllnGldeigltlqkede 187 g sfei + +h llnGld ig++l ++ lcl|FitnessBrowser__PV4:5211053 157 GASFSFEIAPSARHNLLNGLDAIGISLGYGEA 188 **************************987766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (201 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: 7.68 // [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