Align 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate N515DRAFT_0571 N515DRAFT_0571 3-isopropylmalate/(R)-2-methylmalate dehydratase small subunit
Query= SwissProt::Q1MA52 (202 letters) >FitnessBrowser__Dyella79:N515DRAFT_0571 Length = 194 Score = 174 bits (442), Expect = 7e-49 Identities = 94/192 (48%), Positives = 118/192 (61%), Gaps = 4/192 (2%) Query: 1 MDKFVKLTGVAAPLPVVNVDTDMIIPKDYLKTIKRTGLGTGLFAEARYNEDGSENPDFVL 60 M ++ A L N+DTD IIP +L T +R GLG F + RY DGS+NP F L Sbjct: 1 MKAVTRIHSRTAVLADENIDTDRIIPARFLTTTERAGLGKLCFNDWRYLPDGSDNPAFPL 60 Query: 61 NKPAYRDAKILVAGDNFGCGSSREHAPWALLDFGIRCVISTSFADIFYNNCFKNGILPIK 120 N+P + ILVAG NFGCGSSREHAPWALLDFGI+ V+ + ADIF NN KNG+L I Sbjct: 61 NQPQAKGCAILVAGRNFGCGSSREHAPWALLDFGIQAVLCSEIADIFRNNALKNGLLAIV 120 Query: 121 VSQEDLDKLMDDASRGSNAILTVDLENLEITGPDGGLIKFDLDEFKRHCLLNGLDDIGLT 180 VS + L+D L++D+E I PDGG I F L+ F RHCLLNG+D +G Sbjct: 121 VSDAEHRWLLDH----PGTELSIDVEGQYIALPDGGRIPFQLEPFARHCLLNGVDQLGYL 176 Query: 181 LEKGKAIDSFEK 192 L+ AI +E+ Sbjct: 177 LQHDDAIAHYEQ 188 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: 129 Number of extensions: 2 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: 194 Length adjustment: 20 Effective length of query: 182 Effective length of database: 174 Effective search space: 31668 Effective search space used: 31668 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 N515DRAFT_0571 N515DRAFT_0571 (3-isopropylmalate/(R)-2-methylmalate 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.32102.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-60 190.8 0.0 1.2e-60 190.6 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0571 N515DRAFT_0571 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0571 N515DRAFT_0571 3-isopropylmalate/(R)-2-methylmalate dehydratase small su # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 190.6 0.0 1.2e-60 1.2e-60 1 188 [] 1 183 [. 1 183 [. 0.95 Alignments for each domain: == domain 1 score: 190.6 bits; conditional E-value: 1.2e-60 TIGR00171 1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpq 66 mk + + + +++l n+dtd iip +fl + +r G+gk f++wryl + G ++np f ln+pq lcl|FitnessBrowser__Dyella79:N515DRAFT_0571 1 MKAVTRIHSRTAVLADENIDTDRIIPARFLTTTERAGLGKLCFNDWRYLPD-G-SDNPAFPLNQPQ 64 667777888999************************************854.5.58********** PP TIGR00171 67 yqgasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveell 132 +g il+a+ nfGcGssrehapwal d+G++ ++ adif nn++kngll i +s++e + ll lcl|FitnessBrowser__Dyella79:N515DRAFT_0571 65 AKGCAILVAGRNFGCGSSREHAPWALLDFGIQAVLCSEIADIFRNNALKNGLLAIVVSDAEHRWLL 130 ***********************************************************9987665 PP TIGR00171 133 alvknkglkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188 +g++l++d+e q + +g + f++++f +hcllnG+d++g lq++d+i lcl|FitnessBrowser__Dyella79:N515DRAFT_0571 131 ---DHPGTELSIDVEGQYIALPDGGRIPFQLEPFARHCLLNGVDQLGYLLQHDDAI 183 ...579************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (194 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.18 // [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