Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_013520299.1 ALIDE2_RS19540 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >NCBI__GCF_000204645.1:WP_013520299.1 Length = 469 Score = 472 bits (1215), Expect = e-137 Identities = 242/466 (51%), Positives = 319/466 (68%), Gaps = 6/466 (1%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 +TL++K++DAHVV + LL+IDRHL+H+++ L G PVR PG FAT D Sbjct: 7 RTLFDKVWDAHVVQSLADGWDLLHIDRHLLHDLSGTAGLRQLAERGLPVRNPGLAFATPD 66 Query: 63 HNVST---QTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119 H VS+ +T + A G AR+ Q L ++ G+ ++DL P QGIVHVMGPE G+ Sbjct: 67 HAVSSAPDRTGETFAGG--ARLY-QGLKLLTRQAGIRMFDLGEPGQGIVHVMGPELGIVQ 123 Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179 PGMT+VCGDSHT T+GA GA+AFG+G+SEV HVLA+QTL R +TM++ + G PG+ Sbjct: 124 PGMTLVCGDSHTCTNGALGAIAFGVGSSEVTHVLASQTLVLRRPRTMRVLLDGLPGPGVG 183 Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239 AKD+ LA+IG G+ G G VE+ G A+ + +E RMTLCN++IE+GA+ G+VAPD T Sbjct: 184 AKDLALALIGWLGANAGNGFAVEYAGAAVEAMEVEQRMTLCNLSIELGARIGMVAPDVKT 243 Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299 Y++GR AP+G F A+A+W+TL +D GA ++ + A ++P +TWGT+P ++ Sbjct: 244 EAYLRGRPFAPQGDAFAQALAHWRTLPSDPGARYEQEWHVNAAAVAPTLTWGTSPEHAMA 303 Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359 V+ +PDPA A P +R + + ALAYMGLK G PL ID+VFIGSCTNSR+ DLR AA Sbjct: 304 VDTRVPDPADAASPAQRQAWQAALAYMGLKAGAPLQGTRIDRVFIGSCTNSRLSDLREAA 363 Query: 360 EIAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419 + +GR+VAP VQA VVPGS VK AE EGL + F AGF WR PGCSMC+A N ++ Sbjct: 364 GLLRGRRVAPHVQAWVVPGSENVKRAAEREGLHEAFRAAGFAWREPGCSMCVAANGEQAA 423 Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 PGER STSNRNF GRQG G RTHL SPA A AAA+ G AD R++ Sbjct: 424 PGERVVSTSNRNFVGRQGPGARTHLASPASAVAAALAGAIADPRSL 469 Lambda K H 0.317 0.134 0.396 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: 737 Number of extensions: 27 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: 466 Length of database: 469 Length adjustment: 33 Effective length of query: 433 Effective length of database: 436 Effective search space: 188788 Effective search space used: 188788 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_013520299.1 ALIDE2_RS19540 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large 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/TIGR00170.hmm # target sequence database: /tmp/gapView.26495.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00170 [M=466] Accession: TIGR00170 Description: leuC: 3-isopropylmalate dehydratase, large 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-173 561.8 0.0 5.9e-173 561.7 0.0 1.0 1 lcl|NCBI__GCF_000204645.1:WP_013520299.1 ALIDE2_RS19540 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204645.1:WP_013520299.1 ALIDE2_RS19540 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 561.7 0.0 5.9e-173 5.9e-173 2 465 .. 6 468 .. 5 469 .] 0.98 Alignments for each domain: == domain 1 score: 561.7 bits; conditional E-value: 5.9e-173 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistes. 69 ++tl++k++dahvv+ ++ dll+idrhl+h+++ + l ++g +vr+++ ++at dh++s+ lcl|NCBI__GCF_000204645.1:WP_013520299.1 6 PRTLFDKVWDAHVVQSLADGWDLLHIDRHLLHDLSGTAGLRQLAERGLPVRNPGLAFATPDHAVSSAPd 74 89**************************************************************98761 PP TIGR00170 70 rdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafg 138 r e+ + a+l + l+ +++ g+++fdl + qgivhv+gpe g+ pg+t+vcgdsht+t ga+g lcl|NCBI__GCF_000204645.1:WP_013520299.1 75 RTGETFAGGARL-YQGLKLLTRQAGIRMFDLGEPGQGIVHVMGPELGIVQPGMTLVCGDSHTCTNGALG 142 545555666665.6899999************************************************* PP TIGR00170 139 alafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefagea 207 a+afg+g+sev hvla+qtl+ r++t+++ ++g +g+ akd+ la+ig +g++ g g+ ve+ag a lcl|NCBI__GCF_000204645.1:WP_013520299.1 143 AIAFGVGSSEVTHVLASQTLVLRRPRTMRVLLDGLPGPGVGAKDLALALIGWLGANAGNGFAVEYAGAA 211 ********************************************************************* PP TIGR00170 208 irdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkv 276 ++++ +e+rmt+cn++ie+ga+ g++apd t +y+++r++ap+g+ f +a+a+w+tl +d+ga+++++ lcl|NCBI__GCF_000204645.1:WP_013520299.1 212 VEAMEVEQRMTLCNLSIELGARIGMVAPDVKTEAYLRGRPFAPQGDAFAQALAHWRTLPSDPGARYEQE 280 ********************************************************************* PP TIGR00170 277 vtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfig 345 ++a ++p++twgt+p+++++v+ vpdp++ a p +++ + alay+gl++g +l+ ++d+vfig lcl|NCBI__GCF_000204645.1:WP_013520299.1 281 WHVNAAAVAPTLTWGTSPEHAMAVDTRVPDPADAASPAQRQAWQAALAYMGLKAGAPLQGTRIDRVFIG 349 ********************************************************************* PP TIGR00170 346 sctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgm 414 sctnsr+ dlr+aa +++g++va+ v+ a vvpgs+ vk+ ae+egl + f +agf wre+gcs+c++ lcl|NCBI__GCF_000204645.1:WP_013520299.1 350 SCTNSRLSDLREAAGLLRGRRVAPHVQ-AWVVPGSENVKRAAEREGLHEAFRAAGFAWREPGCSMCVAA 417 ***************************.***************************************** PP TIGR00170 415 nndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465 n ++ ++er stsnrnf grqg garthl spa a aaa+ag ++d r lcl|NCBI__GCF_000204645.1:WP_013520299.1 418 NGEQAAPGERVVSTSNRNFVGRQGPGARTHLASPASAVAAALAGAIADPRS 468 **********************************************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (469 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 10.15 // [ok]
This GapMind analysis is from Apr 10 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