Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_014449006.1 LFE_RS04105 3-isopropylmalate dehydratase small subunit
Query= curated2:A1K4A2 (212 letters) >NCBI__GCF_000284315.1:WP_014449006.1 Length = 208 Score = 239 bits (611), Expect = 2e-68 Identities = 116/211 (54%), Positives = 151/211 (71%), Gaps = 8/211 (3%) Query: 1 MKPFTVLDAIVAPLDRANVDTDAIIPKQFLKSIKRSGFGPNLFDEWRYLDVGQPGQDCSN 60 M+ F L +IV P+DRANVDTDAIIPKQFLK+I R+G G +LF +WRYL G Sbjct: 1 MEAFKTLKSIVIPIDRANVDTDAIIPKQFLKTIHRTGLGKSLFYDWRYLSDGVT------ 54 Query: 61 RPKNPDFVLNQARYQGAQVLLARDNFGCGSSREHAPWALEDYGFRVIIAPSFADIFFNNS 120 NPDFV+NQ RY+G ++LL+R+NFG GSSREHAPWAL D+G + IIAPSFADIF+NN Sbjct: 55 --PNPDFVINQTRYKGGRILLSRENFGSGSSREHAPWALLDFGIKAIIAPSFADIFYNNC 112 Query: 121 FKNGLLPIKLDAAELDVLFQQCEATEGYRLKVDLAAQTITRPDGKAIAFDVDPFRKECLL 180 FKNG+LPI++D +D LF++ + T GY+ +++L +Q I PDG+ I F++D F K+CLL Sbjct: 113 FKNGILPIRIDRMIVDGLFKEIDRTPGYQAEINLESQLILLPDGRTIPFEIDAFLKKCLL 172 Query: 181 NGWDDIGLTLRHADKIRDFEAKRRAEHPYYF 211 G DDI LT I +E +RR E P+ F Sbjct: 173 EGLDDISLTFEKKALITSYEDRRRKEAPWLF 203 Lambda K H 0.323 0.141 0.441 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: 168 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: 212 Length of database: 208 Length adjustment: 21 Effective length of query: 191 Effective length of database: 187 Effective search space: 35717 Effective search space used: 35717 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 45 (21.9 bits)
Align candidate WP_014449006.1 LFE_RS04105 (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.3313996.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-83 264.6 0.0 3.1e-83 264.3 0.0 1.1 1 NCBI__GCF_000284315.1:WP_014449006.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000284315.1:WP_014449006.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 264.3 0.0 3.1e-83 3.1e-83 1 185 [. 1 185 [. 1 188 [. 0.98 Alignments for each domain: == domain 1 score: 264.3 bits; conditional E-value: 3.1e-83 TIGR00171 1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasil 73 m+ fk+l+ +v+p+d+anvdtdaiipkqflk+i+rtG+gk lfy+wryl ++G pnp+fv+n+ +y+g il NCBI__GCF_000284315.1:WP_014449006.1 1 MEAFKTLKSIVIPIDRANVDTDAIIPKQFLKTIHRTGLGKSLFYDWRYL-SDGVTPNPDFVINQTRYKGGRIL 72 899*********************************************6.5689******************* PP TIGR00171 74 larenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvd 145 l+renfG Gssrehapwal d+G+k iiapsfadifynn+fkng+lpir+++ +v+ l++ + +g + +++ NCBI__GCF_000284315.1:WP_014449006.1 73 LSRENFGSGSSREHAPWALLDFGIKAIIAPSFADIFYNNCFKNGILPIRIDRMIVDGLFKEIDrTPGYQAEIN 145 **************************************************************9899******* PP TIGR00171 146 leaqkvkdsegkvysfeidefrkhcllnGldeigltlqke 185 le+q + +g+++ feid+f k+cll+Gld+i+lt+ k+ NCBI__GCF_000284315.1:WP_014449006.1 146 LESQLILLPDGRTIPFEIDAFLKKCLLEGLDDISLTFEKK 185 ************************************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (208 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: 10.48 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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