Align 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate 3607281 Dshi_0696 3-isopropylmalate dehydratase, small subunit (RefSeq)
Query= SwissProt::Q1MA52 (202 letters) >FitnessBrowser__Dino:3607281 Length = 219 Score = 149 bits (375), Expect = 5e-41 Identities = 87/195 (44%), Positives = 113/195 (57%), Gaps = 2/195 (1%) Query: 8 TGVAAPLPVVNVDTDMIIPKDYLKTIKRTGLGTGLFAEARYNEDGSENPDFVLNKPAYRD 67 TG AA LP+ VDTD +IP ++ T + G G L + R+ + P+F LN+ Sbjct: 10 TGRAAALPMEAVDTDQLIPARFMSTPRAEGYGRYLLHDLRFCDGCVPRPEFALNRVENAG 69 Query: 68 AKILVAGDNFGCGSSREHAPWALLDFGIRCVISTSFADIFYNNCFKNGILPIKVSQEDLD 127 A ILV G NFG GSSRE A +AL+DFGIR V++ SF DIF N NG+ P++V ED Sbjct: 70 ATILVTGRNFGSGSSREAAVYALMDFGIRAVVAPSFGDIFAANAVNNGLCPVQVRPEDGA 129 Query: 128 KLMDDASRGSNAILTVDLENLEITGPDGGLIKFDLDEFKRHCLLNGLDDIGLTLEKGKAI 187 L+ RG+ +TVDLE + GP G + F LD R L+ GLDDI LT G I Sbjct: 130 ALLRGLERGARQ-MTVDLEACALRGP-LGTVGFTLDPVWRRKLIEGLDDIDLTRAYGAEI 187 Query: 188 DSFEKKNAASHPWAA 202 +F +AA+ PWAA Sbjct: 188 AAFRAADAAARPWAA 202 Lambda K H 0.319 0.140 0.419 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: 117 Number of extensions: 3 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: 202 Length of database: 219 Length adjustment: 21 Effective length of query: 181 Effective length of database: 198 Effective search space: 35838 Effective search space used: 35838 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: 45 (21.9 bits)
Align candidate 3607281 Dshi_0696 (3-isopropylmalate dehydratase, 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.32752.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-50 156.3 0.0 5.2e-50 155.9 0.0 1.1 1 lcl|FitnessBrowser__Dino:3607281 Dshi_0696 3-isopropylmalate dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3607281 Dshi_0696 3-isopropylmalate dehydratase, small subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 155.9 0.0 5.2e-50 5.2e-50 4 183 .. 6 182 .. 3 187 .. 0.95 Alignments for each domain: == domain 1 score: 155.9 bits; conditional E-value: 5.2e-50 TIGR00171 4 fkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasillarenfG 80 + ++tG +++l vdtd++ip +f+ + + G+g++l+++ r+ +G p pef ln + ga+il+++ nfG lcl|FitnessBrowser__Dino:3607281 6 WTRHTGRAAALPMEAVDTDQLIPARFMSTPRAEGYGRYLLHDLRFC--DGCVPRPEFALNRVENAGATILVTGRNFG 80 678******************************************5..5888************************* PP TIGR00171 81 cGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvknkglkltvdleaqkvkdsegk 157 Gssre a +al d+G++ ++apsf+dif n+++ngl p+++ e+ ll ++ + ++tvdlea ++ lcl|FitnessBrowser__Dino:3607281 81 SGSSREAAVYALMDFGIRAVVAPSFGDIFAANAVNNGLCPVQVRPEDGAALLRGLERGARQMTVDLEACALRGPL-G 156 **********************************************************************99888.5 PP TIGR00171 158 vysfeidefrkhcllnGldeigltlq 183 ++ f++d+ +++ l++Gld+i lt lcl|FitnessBrowser__Dino:3607281 157 TVGFTLDPVWRRKLIEGLDDIDLTRA 182 779********************965 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (219 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 0.01s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 1.42 // [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