Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_010437196.1 G7G_RS0100350 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >NCBI__GCF_000192475.1:WP_010437196.1 Length = 464 Score = 461 bits (1186), Expect = e-134 Identities = 236/464 (50%), Positives = 308/464 (66%), Gaps = 9/464 (1%) Query: 1 MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60 M++TLY+KL DAH V + + L+Y+D H+++E TSPQAF GL G V +P + Sbjct: 1 MSRTLYDKLVDAHKVCDLPDGDMLIYVDFHIMNEYTSPQAFSGLDQKGLSVWRPEAHLSV 60 Query: 61 MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120 +DH +T+ +D + +++ + L NCK+ + Y L QGI HV+ PEQG+ P Sbjct: 61 VDHVNATRQRDPHDAA--SKLLIDNLEANCKKHNIAFYGLGDRRQGIEHVVVPEQGLVAP 118 Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180 GM I CGDSHT T+GAFGAL FGIGTSEVEHVLATQTL+ R KTM + + G APG TA Sbjct: 119 GMLIACGDSHTTTYGAFGALGFGIGTSEVEHVLATQTLRYKRLKTMLVNIDGDLAPGATA 178 Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240 KDI++ ++ G+ G G+ VEF G AIR M GRMT+CNMA+E+G +A L+ DE Sbjct: 179 KDIIMKVVQVVGAGGANGYAVEFSGSAIRSQEMSGRMTICNMAVELGGRAALIGADEKAL 238 Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300 +K R H+ D W +D GA +DTV + A +I+P V+WGT+P Q + V Sbjct: 239 EKIKARAHS---GTLDFGGLEW---NSDPGAEYDTVFEINAADIAPIVSWGTSPDQSVPV 292 Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360 + ++P P R + +AL YMGLK G +T++ ID FIGSCTNSRIEDLRAAA Sbjct: 293 DGSVPAETEGMTPKAREALNRALGYMGLKAGQAMTDIEIDSAFIGSCTNSRIEDLRAAAS 352 Query: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWR-LPGCSMCLAMNNDRLN 419 I KG+KVA V A+VVPGS + QAE+EG+D++F EAGF+WR GCSMCLAMN+D Sbjct: 353 ILKGKKVAGSVNAIVVPGSTYTRLQAESEGIDRVFKEAGFDWRPESGCSMCLAMNDDIAM 412 Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463 GER AS++NRNFEGRQGRG RTHL+SP M AAAA+ G AD+R Sbjct: 413 DGERIASSTNRNFEGRQGRGARTHLMSPEMVAAAAIHGRIADVR 456 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: 653 Number of extensions: 23 Number of successful extensions: 4 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: 464 Length adjustment: 33 Effective length of query: 433 Effective length of database: 431 Effective search space: 186623 Effective search space used: 186623 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_010437196.1 G7G_RS0100350 (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.1929561.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-177 577.2 0.2 1.3e-177 577.0 0.2 1.0 1 NCBI__GCF_000192475.1:WP_010437196.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000192475.1:WP_010437196.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 577.0 0.2 1.3e-177 1.3e-177 1 466 [] 1 458 [. 1 458 [. 0.98 Alignments for each domain: == domain 1 score: 577.0 bits; conditional E-value: 1.3e-177 TIGR00170 1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve 73 m++tly+kl dah v + ++ l+y+d h++ e tspqaf gl ++g v r++ l+ +dh +t++rd NCBI__GCF_000192475.1:WP_010437196.1 1 MSRTLYDKLVDAHKVCDLPDGDMLIYVDFHIMNEYTSPQAFSGLDQKGLSVWRPEAHLSVVDHVNATRQRD-- 71 79*******************************************************************96.. PP TIGR00170 74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146 ++ +kl + +le n+k+ + +++l + +qgi hvv pe+gl pg+ i cgdsht+t+gafgal fgigt NCBI__GCF_000192475.1:WP_010437196.1 72 PHDAASKLLIDNLEANCKKHNIAFYGLGDRRQGIEHVVVPEQGLVAPGMLIACGDSHTTTYGAFGALGFGIGT 144 67999******************************************************************** PP TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219 sevehvlatqtl+ +r kt+ ++++g la+g takdii+ ++ +g+ g gy vef+g air+ m +rmt+ NCBI__GCF_000192475.1:WP_010437196.1 145 SEVEHVLATQTLRYKRLKTMLVNIDGDLAPGATAKDIIMKVVQVVGAGGANGYAVEFSGSAIRSQEMSGRMTI 217 ************************************************************************* PP TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292 cnma+e+g +a li de ++e +k r ++ + +w +d+ga++d+v ++a di+p v+wgt NCBI__GCF_000192475.1:WP_010437196.1 218 CNMAVELGGRAALIGADEKALEKIKARAHSGT---LDFGGLEWN---SDPGAEYDTVFEINAADIAPIVSWGT 284 ***************************99853...455667895...8************************* PP TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365 +p+q ++v+++vp+ + p ++ ++al y+gl++g+ ++di++d figsctnsriedlraaa+++kgk NCBI__GCF_000192475.1:WP_010437196.1 285 SPDQSVPVDGSVPAETEGMTPKAREALNRALGYMGLKAGQAMTDIEIDSAFIGSCTNSRIEDLRAAASILKGK 357 ************************************************************************* PP TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewr.eagcslclgmnndvldeyercastsnrnfegrq 437 kva +v+ a+vvpgs + qae eg+d++f eagf+wr e+gcs+cl+mn+d+ ++er as++nrnfegrq NCBI__GCF_000192475.1:WP_010437196.1 358 KVAGSVN-AIVVPGSTYTRLQAESEGIDRVFKEAGFDWRpESGCSMCLAMNDDIAMDGERIASSTNRNFEGRQ 429 *******.*******************************889******************************* PP TIGR00170 438 gkgarthlvspamaaaaavagkfvdirel 466 g+garthl+sp m aaaa++g+++d+re+ NCBI__GCF_000192475.1:WP_010437196.1 430 GRGARTHLMSPEMVAAAAIHGRIADVREF 458 ***************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (464 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 32.58 // [ok]
This GapMind analysis is from Jul 26 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