Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_012170633.1 AZC_RS10900 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >NCBI__GCF_000010525.1:WP_012170633.1 Length = 471 Score = 499 bits (1285), Expect = e-146 Identities = 250/462 (54%), Positives = 318/462 (68%), Gaps = 3/462 (0%) Query: 2 AKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATM 61 A+TL++K++DAHVV + E+ LL+IDRH +HE S AFD + G + +P TF Sbjct: 6 ARTLFDKVWDAHVVVQREDGQSLLWIDRHFLHE-GSFHAFDKVAGRGASLARPDLTFGVE 64 Query: 62 DHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPG 121 DH V T+ + ++ R M++L N V L+D++ P QGIVHV+GPEQG+TLPG Sbjct: 65 DHYVPTRVRQLDLIDPAIRRMMEQLRANTLRHKVRLFDVDDPAQGIVHVVGPEQGLTLPG 124 Query: 122 MTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAK 181 ++IVCGDSHTATHGAFGALAFGIG SEV HVL TQTL Q R K ++I V+G+ APGI AK Sbjct: 125 LSIVCGDSHTATHGAFGALAFGIGASEVAHVLMTQTLWQNRPKRLRIRVEGRLAPGIVAK 184 Query: 182 DIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFN 241 D+ L+II G+ G GH +E+ G +R LSMEGR+TLCN++IE G + G++APD TT + Sbjct: 185 DVALSIIAAIGADGAAGHAIEYAGSVVRGLSMEGRLTLCNLSIEAGGRCGMIAPDATTLD 244 Query: 242 YVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVN 301 YV+GR +AP+G FD A W L +D A FD V L + I+P VTWGT+P + + Sbjct: 245 YVRGRPYAPEGALFDAAAEAWLALGSDADAEFDREVVLDGDAIAPIVTWGTSPEDALPIT 304 Query: 302 DNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEI 361 +PDP D + A A++YM L+PG L+++A+D+VFIGSCTNSRIEDLRAAA + Sbjct: 305 ATVPDPERVDDAAKAAHIRDAVSYMDLRPGQRLSDIAVDRVFIGSCTNSRIEDLRAAAAV 364 Query: 362 AKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421 GR V LV PGS VK QAE EGLD IF AG EW GCSMC+ MN D + G Sbjct: 365 LAGRSAK--VPGLVSPGSALVKRQAEEEGLDAIFRAAGLEWVEAGCSMCVGMNGDLVPAG 422 Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463 ERCAST+NRNF+GRQG G RTHL+SPAM AAAAVTGH D+R Sbjct: 423 ERCASTTNRNFKGRQGPGARTHLMSPAMVAAAAVTGHLTDMR 464 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: 718 Number of extensions: 28 Number of successful extensions: 3 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: 471 Length adjustment: 33 Effective length of query: 433 Effective length of database: 438 Effective search space: 189654 Effective search space used: 189654 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_012170633.1 AZC_RS10900 (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.2386794.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-198 646.3 0.0 1.4e-198 646.1 0.0 1.0 1 NCBI__GCF_000010525.1:WP_012170633.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000010525.1:WP_012170633.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 646.1 0.0 1.4e-198 1.4e-198 2 464 .. 6 464 .. 5 466 .. 0.99 Alignments for each domain: == domain 1 score: 646.1 bits; conditional E-value: 1.4e-198 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdvei 74 a+tl++k++dahvv + e++++ll+idrh++he s af+ + +g + r+d t++ dh ++t++r+++ NCBI__GCF_000010525.1:WP_012170633.1 6 ARTLFDKVWDAHVVVQREDGQSLLWIDRHFLHE-GSFHAFDKVAGRGASLARPDLTFGVEDHYVPTRVRQLDL 77 89*******************************.5899*********************************** PP TIGR00170 75 keekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigts 147 + ++ +++l n+ + v+lfd+++ qgivhvvgpe+gltlpg +ivcgdshtathgafgalafgig+s NCBI__GCF_000010525.1:WP_012170633.1 78 IDPAIRRMMEQLRANTLRHKVRLFDVDDPAQGIVHVVGPEQGLTLPGLSIVCGDSHTATHGAFGALAFGIGAS 150 ************************************************************************* PP TIGR00170 148 evehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvc 220 ev hvl tqtl+q+r+k l+i+veg+la+gi akd+ l ii ig+ g +g+ +e+ag ++r lsme+r+t+c NCBI__GCF_000010525.1:WP_012170633.1 151 EVAHVLMTQTLWQNRPKRLRIRVEGRLAPGIVAKDVALSIIAAIGADGAAGHAIEYAGSVVRGLSMEGRLTLC 223 ************************************************************************* PP TIGR00170 221 nmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtn 293 n++ieag + g+iapd tt++yv++r+yap g+ f+ a + w +l +d +a+fd++v+l+++ i+p vtwgt+ NCBI__GCF_000010525.1:WP_012170633.1 224 NLSIEAGGRCGMIAPDATTLDYVRGRPYAPEGALFDAAAEAWLALGSDADAEFDREVVLDGDAIAPIVTWGTS 296 ************************************************************************* PP TIGR00170 294 pgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkk 366 p+++l+++ +vpdp+ + d + a++ a++y+ l+pg++l di+vd+vfigsctnsriedlraaa+v+ g+ NCBI__GCF_000010525.1:WP_012170633.1 297 PEDALPITATVPDPERVDDAAKAAHIRDAVSYMDLRPGQRLSDIAVDRVFIGSCTNSRIEDLRAAAAVLAGRS 369 ***********************************************************************95 PP TIGR00170 367 vadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgk 439 +v lv pgs lvk+qae+egld if +ag+ew eagcs+c+gmn d ++++ercast+nrnf+grqg NCBI__GCF_000010525.1:WP_012170633.1 370 --AKVP-GLVSPGSALVKRQAEEEGLDAIFRAAGLEWVEAGCSMCVGMNGDLVPAGERCASTTNRNFKGRQGP 439 ..4676.89**************************************************************** PP TIGR00170 440 garthlvspamaaaaavagkfvdir 464 garthl+spam aaaav+g++ d+r NCBI__GCF_000010525.1:WP_012170633.1 440 GARTHLMSPAMVAAAAVTGHLTDMR 464 ***********************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (471 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 27.43 // [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