Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_012172581.1 AZC_RS20820 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >NCBI__GCF_000010525.1:WP_012172581.1 Length = 474 Score = 595 bits (1535), Expect = e-175 Identities = 295/461 (63%), Positives = 353/461 (76%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 KTLY+K+FD HVV E+ T LLYIDRHLVHEVTSPQAF+GLR GR VR P KT A +D Sbjct: 9 KTLYDKIFDDHVVSRQEDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVRAPSKTLAVVD 68 Query: 63 HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122 HNV T + + Q++ L +N +EFG+E Y+ QGIVHV+GPEQG TLPG Sbjct: 69 HNVPTTDRSHGIDDPESATQVETLAENTREFGIEYYNERDIRQGIVHVIGPEQGFTLPGT 128 Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182 TIVCGDSHT+THGAFGALA GIGTSEVEHVLATQTL Q ++K M++ V G G+ AKD Sbjct: 129 TIVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQTLIQKKSKNMRVTVDGTLPEGVGAKD 188 Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242 + LAIIG G+AGGTG+V+E+ G+ +R LSMEGRMT+CNM+IE GA+AG+VAPDE F Y Sbjct: 189 VTLAIIGSIGTAGGTGYVIEYAGDVMRQLSMEGRMTVCNMSIEGGARAGMVAPDEKAFAY 248 Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302 +K R APKG D+D AVAYW+TL++DEGA FD V L + P V+WGT+P V+SV Sbjct: 249 LKDRPRAPKGADWDKAVAYWETLRSDEGAYFDAEVRLDGANLPPIVSWGTSPEDVVSVEG 308 Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362 +PDP + D V R + ++ALAYMGL G ++++AID+VFIGSCTN RIED+R AA+I Sbjct: 309 LVPDPEAIEDAVRRDAKKRALAYMGLTAGTKISDIAIDRVFIGSCTNGRIEDMRQAAQIV 368 Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422 G V V+A+VVPGSG VKAQAEAEGLDKIF+ AGFEWR PGCSMCLAMN DRL+P E Sbjct: 369 AGHTVNANVKAMVVPGSGLVKAQAEAEGLDKIFLAAGFEWREPGCSMCLAMNADRLSPEE 428 Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463 RCASTSNRNFEGRQG GRTHLVSPAMAAAAA+ G F D+R Sbjct: 429 RCASTSNRNFEGRQGFKGRTHLVSPAMAAAAAIAGRFVDVR 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: 759 Number of extensions: 28 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: 466 Length of database: 474 Length adjustment: 33 Effective length of query: 433 Effective length of database: 441 Effective search space: 190953 Effective search space used: 190953 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_012172581.1 AZC_RS20820 (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.1932382.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-245 799.7 0.3 4.2e-245 799.5 0.3 1.0 1 NCBI__GCF_000010525.1:WP_012172581.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000010525.1:WP_012172581.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 799.5 0.3 4.2e-245 4.2e-245 2 465 .. 8 470 .. 7 471 .. 1.00 Alignments for each domain: == domain 1 score: 799.5 bits; conditional E-value: 4.2e-245 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdvei 74 +ktly+k+fd hvv ++e++t llyidrhlvhevtspqafeglr agrkvr ++ktla +dhn++t+ r i NCBI__GCF_000010525.1:WP_012172581.1 8 PKTLYDKIFDDHVVSRQEDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVRAPSKTLAVVDHNVPTTDRSHGI 80 8************************************************************************ PP TIGR00170 75 keekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigts 147 + ++ qv++l +n++efg+++++ ++ +qgivhv+gpe+g+tlpg+tivcgdsht+thgafgala gigts NCBI__GCF_000010525.1:WP_012172581.1 81 DDPESATQVETLAENTREFGIEYYNERDIRQGIVHVIGPEQGFTLPGTTIVCGDSHTSTHGAFGALAHGIGTS 153 ************************************************************************* PP TIGR00170 148 evehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvc 220 evehvlatqtl+q+++k+++++v+g+l +g+ akd+ laiig ig+aggtgyv+e+ag+++r+lsme+rmtvc NCBI__GCF_000010525.1:WP_012172581.1 154 EVEHVLATQTLIQKKSKNMRVTVDGTLPEGVGAKDVTLAIIGSIGTAGGTGYVIEYAGDVMRQLSMEGRMTVC 226 ************************************************************************* PP TIGR00170 221 nmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtn 293 nm+ie ga+ag++apde +f+y+kdr+ apkg++++kavayw tl++dega fd +v l++ ++ p v+wgt+ NCBI__GCF_000010525.1:WP_012172581.1 227 NMSIEGGARAGMVAPDEKAFAYLKDRPRAPKGADWDKAVAYWETLRSDEGAYFDAEVRLDGANLPPIVSWGTS 299 ************************************************************************* PP TIGR00170 294 pgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkk 366 p++v+sv++ vpdp+ + d v++ ++alay+gl++gtk+ di++d+vfigsctn+ried+r+aa++v g+ NCBI__GCF_000010525.1:WP_012172581.1 300 PEDVVSVEGLVPDPEAIEDAVRRDAKKRALAYMGLTAGTKISDIAIDRVFIGSCTNGRIEDMRQAAQIVAGHT 372 ************************************************************************* PP TIGR00170 367 vadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgk 439 v nvk a+vvpgsglvk+qae+egldkifl+agfewre+gcs+cl+mn d+l++ ercastsnrnfegrqg NCBI__GCF_000010525.1:WP_012172581.1 373 VNANVK-AMVVPGSGLVKAQAEAEGLDKIFLAAGFEWREPGCSMCLAMNADRLSPEERCASTSNRNFEGRQGF 444 ******.****************************************************************** PP TIGR00170 440 garthlvspamaaaaavagkfvdire 465 ++rthlvspamaaaaa+ag+fvd+r NCBI__GCF_000010525.1:WP_012172581.1 445 KGRTHLVSPAMAAAAAIAGRFVDVRT 470 ************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (474 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 16.74 // [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