Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_034996465.1 DL88_RS12350 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >NCBI__GCF_000745425.1:WP_034996465.1 Length = 468 Score = 593 bits (1528), Expect = e-174 Identities = 292/462 (63%), Positives = 351/462 (75%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 +TLY+K++D HV+ + T LLYIDRHLVHEVTSPQAF+GLR GR +R P KT A +D Sbjct: 5 RTLYDKIWDDHVIETQADGTSLLYIDRHLVHEVTSPQAFEGLRMAGRKIRAPQKTLAVVD 64 Query: 63 HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122 HNV T + +R+Q+ +L N EFG+E YD QG+VH++GPEQG TLPG Sbjct: 65 HNVPTTDRSQGIEDPESRLQVAQLAANAAEFGIEYYDALDHRQGVVHIIGPEQGFTLPGT 124 Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182 TIVCGDSHT+THGAFGALA GIGTSEVEHVLATQTL Q +AK M+I V G ++AKD Sbjct: 125 TIVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQTLIQAKAKNMRIVVDGVLPDHVSAKD 184 Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242 ++LAIIG+ G+AGGTGHV+E+ GEAIR LSMEGRMT+CNM IE GA+AG++APDE T+ Y Sbjct: 185 LILAIIGEIGTAGGTGHVIEYAGEAIRALSMEGRMTVCNMTIEGGARAGMIAPDEKTYAY 244 Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302 +K R APKG +D A+AYW+TL +DEGA FD + L A + P VTWGT+P V+++ Sbjct: 245 LKDRPKAPKGAAWDAALAYWQTLSSDEGAVFDREIRLDAANLPPTVTWGTSPEDVVAITG 304 Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362 +P P ++AS +AL YMGLK G LT +AID+VFIGSCTN RIEDLRAAA+I Sbjct: 305 LVPSPEDATSEAKKASIARALDYMGLKGGEKLTSIAIDRVFIGSCTNGRIEDLRAAAQIV 364 Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422 +G+ +A V LVVPGSG VK QAEAEGLD IF AGFEWR PGCSMCLAMN D+L+PGE Sbjct: 365 QGKHIAASVNGLVVPGSGLVKEQAEAEGLDVIFKAAGFEWREPGCSMCLAMNPDKLSPGE 424 Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRN 464 RCASTSNRNFEGRQG GRTHLVSPAMAAAA + GHF DIR+ Sbjct: 425 RCASTSNRNFEGRQGFKGRTHLVSPAMAAAAGIAGHFVDIRD 466 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: 745 Number of extensions: 25 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: 468 Length adjustment: 33 Effective length of query: 433 Effective length of database: 435 Effective search space: 188355 Effective search space used: 188355 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_034996465.1 DL88_RS12350 (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.14882.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-243 793.9 0.1 2.5e-243 793.6 0.1 1.0 1 lcl|NCBI__GCF_000745425.1:WP_034996465.1 DL88_RS12350 3-isopropylmalate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745425.1:WP_034996465.1 DL88_RS12350 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 793.6 0.1 2.5e-243 2.5e-243 2 465 .. 4 466 .. 3 467 .. 1.00 Alignments for each domain: == domain 1 score: 793.6 bits; conditional E-value: 2.5e-243 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr 70 ++tly+k++d hv++ + ++t+llyidrhlvhevtspqafeglr agrk+r ++ktla +dhn++t+ r lcl|NCBI__GCF_000745425.1:WP_034996465.1 4 PRTLYDKIWDDHVIETQADGTSLLYIDRHLVHEVTSPQAFEGLRMAGRKIRAPQKTLAVVDHNVPTTDR 72 89******************************************************************* PP TIGR00170 71 dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafga 139 i + +++lqv +l n+ efg++++d +++qg+vh++gpe+g+tlpg+tivcgdsht+thgafga lcl|NCBI__GCF_000745425.1:WP_034996465.1 73 SQGIEDPESRLQVAQLAANAAEFGIEYYDALDHRQGVVHIIGPEQGFTLPGTTIVCGDSHTSTHGAFGA 141 ********************************************************************* PP TIGR00170 140 lafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageai 208 la gigtsevehvlatqtl+qa+ak+++i v+g l + ++akd+ilaiig ig+aggtg+v+e+ageai lcl|NCBI__GCF_000745425.1:WP_034996465.1 142 LAHGIGTSEVEHVLATQTLIQAKAKNMRIVVDGVLPDHVSAKDLILAIIGEIGTAGGTGHVIEYAGEAI 210 ********************************************************************* PP TIGR00170 209 rdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvv 277 r+lsme+rmtvcnm+ie ga+ag+iapde t++y+kdr+ apkg+ ++ a+ayw+tl +dega+fd+++ lcl|NCBI__GCF_000745425.1:WP_034996465.1 211 RALSMEGRMTVCNMTIEGGARAGMIAPDEKTYAYLKDRPKAPKGAAWDAALAYWQTLSSDEGAVFDREI 279 ********************************************************************* PP TIGR00170 278 tleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigs 346 l+a ++ p+vtwgt+p++v+++++ vp+p++ + + +kas+ +al+y+gl+ g kl++i++d+vfigs lcl|NCBI__GCF_000745425.1:WP_034996465.1 280 RLDAANLPPTVTWGTSPEDVVAITGLVPSPEDATSEAKKASIARALDYMGLKGGEKLTSIAIDRVFIGS 348 ********************************************************************* PP TIGR00170 347 ctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmn 415 ctn+riedlraaa++v+gk++a +v+ lvvpgsglvk+qae+egld if +agfewre+gcs+cl+mn lcl|NCBI__GCF_000745425.1:WP_034996465.1 349 CTNGRIEDLRAAAQIVQGKHIAASVN-GLVVPGSGLVKEQAEAEGLDVIFKAAGFEWREPGCSMCLAMN 416 **************************.9***************************************** PP TIGR00170 416 ndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465 +d+l+++ercastsnrnfegrqg ++rthlvspamaaaa++ag+fvdir+ lcl|NCBI__GCF_000745425.1:WP_034996465.1 417 PDKLSPGERCASTSNRNFEGRQGFKGRTHLVSPAMAAAAGIAGHFVDIRD 466 *************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (468 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: 9.03 // [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