Align 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate AZOBR_RS15560 AZOBR_RS15560 isopropylmalate isomerase
Query= SwissProt::Q1MA52 (202 letters) >FitnessBrowser__azobra:AZOBR_RS15560 Length = 198 Score = 177 bits (449), Expect = 1e-49 Identities = 90/200 (45%), Positives = 123/200 (61%), Gaps = 7/200 (3%) Query: 1 MDKFVKLTGVAAPLPVVNVDTDMIIPKDYLKTIKRTGLGTGLFAEARYNEDGSENPDFVL 60 MD FV LT A PL + N+DTD ++P +LK + G G LF + R P F L Sbjct: 1 MDPFVTLTAPAVPLDIANIDTDQLLPARFLKKPRSAGYGNFLFHDER-------KPGFPL 53 Query: 61 NKPAYRDAKILVAGDNFGCGSSREHAPWALLDFGIRCVISTSFADIFYNNCFKNGILPIK 120 + PAY A++LV+ NFGCGSSRE A +AL+D G RCV++ SF DIF N KNG+L I Sbjct: 54 DDPAYAGARVLVSDRNFGCGSSREGAVYALVDGGFRCVVAPSFGDIFAANAAKNGLLTIT 113 Query: 121 VSQEDLDKLMDDASRGSNAILTVDLENLEITGPDGGLIKFDLDEFKRHCLLNGLDDIGLT 180 + +E + +L A +TVDL ++GPDG + F +D FK+ CL+ GLDD+ LT Sbjct: 114 LPEETVAELRRQLQEAPGAAVTVDLPAQTLSGPDGQPLPFAIDPFKKECLIEGLDDVALT 173 Query: 181 LEKGKAIDSFEKKNAASHPW 200 L AID+F++ +AA+ PW Sbjct: 174 LRHQDAIDAFDRADAAARPW 193 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: 135 Number of extensions: 6 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: 198 Length adjustment: 21 Effective length of query: 181 Effective length of database: 177 Effective search space: 32037 Effective search space used: 32037 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 AZOBR_RS15560 AZOBR_RS15560 (isopropylmalate isomerase)
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.7369.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-57 178.0 0.0 1.2e-56 177.6 0.0 1.1 1 lcl|FitnessBrowser__azobra:AZOBR_RS15560 AZOBR_RS15560 isopropylmalate is Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS15560 AZOBR_RS15560 isopropylmalate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 177.6 0.0 1.2e-56 1.2e-56 1 188 [] 1 180 [. 1 180 [. 0.98 Alignments for each domain: == domain 1 score: 177.6 bits; conditional E-value: 1.2e-56 TIGR00171 1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqg 69 m++f++lt +vpld an+dtd+++p +flkk + G+g++lf++ r p f l+ p y g lcl|FitnessBrowser__azobra:AZOBR_RS15560 1 MDPFVTLTAPAVPLDIANIDTDQLLPARFLKKPRSAGYGNFLFHDERK---------PGFPLDDPAYAG 60 899*****************************************9765.........88********** PP TIGR00171 70 asillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.n 137 a +l++ nfGcGssre a +al d Gf+ ++apsf+dif n+ kngll i l+ee+v el +++ lcl|FitnessBrowser__azobra:AZOBR_RS15560 61 ARVLVSDRNFGCGSSREGAVYALVDGGFRCVVAPSFGDIFAANAAKNGLLTITLPEETVAELRRQLQeA 129 ***************************************************************999979 PP TIGR00171 138 kglkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188 +g +tvdl+aq++ +g+ f id+f+k+cl++Gld+++ltl+++d+i lcl|FitnessBrowser__azobra:AZOBR_RS15560 130 PGAAVTVDLPAQTLSGPDGQPLPFAIDPFKKECLIEGLDDVALTLRHQDAI 180 9************************************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (198 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: 5.03 // [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