Align 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate BPHYT_RS13515 BPHYT_RS13515 3-isopropylmalate dehydratase small subunit
Query= SwissProt::Q1MA52 (202 letters) >FitnessBrowser__BFirm:BPHYT_RS13515 Length = 203 Score = 174 bits (441), Expect = 1e-48 Identities = 84/200 (42%), Positives = 124/200 (62%) Query: 3 KFVKLTGVAAPLPVVNVDTDMIIPKDYLKTIKRTGLGTGLFAEARYNEDGSENPDFVLNK 62 + ++ G AAPLP+ N+DTD I+PK +L+ I + GL GL + R++ G D VLN+ Sbjct: 2 RLTEIHGTAAPLPIENLDTDQIMPKQFLRIIGKAGLKDGLLYDLRFDAQGEPRSDCVLNQ 61 Query: 63 PAYRDAKILVAGDNFGCGSSREHAPWALLDFGIRCVISTSFADIFYNNCFKNGILPIKVS 122 P YRDA+IL+ G NFGCGSSREHA W L G VI+ SFA+IFY+N N +L +++ Sbjct: 62 PEYRDARILIGGSNFGCGSSREHAVWGLQQGGFEAVIAPSFAEIFYSNAMNNRLLLVQLE 121 Query: 123 QEDLDKLMDDASRGSNAILTVDLENLEITGPDGGLIKFDLDEFKRHCLLNGLDDIGLTLE 182 ++++D L+ DA+ A L +D+E +T G + F L + ++ G+D I LTL Sbjct: 122 RDEIDVLLHDAATQPAAPLHIDIERQTVTSATGRVFAFPLGARHKQMVVEGMDTIDLTLA 181 Query: 183 KGKAIDSFEKKNAASHPWAA 202 I++FE+ + A H WAA Sbjct: 182 SLHDIEAFERDHFARHSWAA 201 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: 125 Number of extensions: 4 Number of successful extensions: 1 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: 203 Length adjustment: 21 Effective length of query: 181 Effective length of database: 182 Effective search space: 32942 Effective search space used: 32942 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 BPHYT_RS13515 BPHYT_RS13515 (3-isopropylmalate dehydratase small subunit)
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.11063.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-60 190.1 0.0 2e-60 189.9 0.0 1.1 1 lcl|FitnessBrowser__BFirm:BPHYT_RS13515 BPHYT_RS13515 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS13515 BPHYT_RS13515 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 189.9 0.0 2e-60 2e-60 4 184 .. 3 182 .. 1 186 [. 0.97 Alignments for each domain: == domain 1 score: 189.9 bits; conditional E-value: 2e-60 TIGR00171 4 fkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasil 73 + + +G ++pl n+dtd+i+pkqfl+ i + G++ l+y+ r+ d++G ep ++ vln+p+y++a il lcl|FitnessBrowser__BFirm:BPHYT_RS13515 3 LTEIHGTAAPLPIENLDTDQIMPKQFLRIIGKAGLKDGLLYDLRF-DAQG-EPRSDCVLNQPEYRDARIL 70 56789****************************************.****.9****************** PP TIGR00171 74 larenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkl 142 + + nfGcGssreha w l++ Gf +iapsfa+ify+n+++n+ll ++l+++e++ ll+ + ++ l lcl|FitnessBrowser__BFirm:BPHYT_RS13515 71 IGGSNFGCGSSREHAVWGLQQGGFEAVIAPSFAEIFYSNAMNNRLLLVQLERDEIDVLLHDAAtQPAAPL 140 ***********************************************************9998688999* PP TIGR00171 143 tvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqk 184 ++d+e q+v+++ g+v f + + +k+++++G+d i ltl lcl|FitnessBrowser__BFirm:BPHYT_RS13515 141 HIDIERQTVTSATGRVFAFPLGARHKQMVVEGMDTIDLTLAS 182 ***************************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (203 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: 6.17 // [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