Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate GFF1877 HP15_1834 protein containing 3-isopropylmalate dehydratase, large subunit region domain
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__Marino:GFF1877 Length = 472 Score = 597 bits (1540), Expect = e-175 Identities = 295/467 (63%), Positives = 358/467 (76%), Gaps = 4/467 (0%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 KTLY+KL+D H+V + ++ + L+YIDR L+HEVTSPQAF+GLR GR + AT D Sbjct: 4 KTLYDKLWDDHLVKQRDDGSALIYIDRQLLHEVTSPQAFEGLRLAGRKPWRIDANIATPD 63 Query: 63 HNVSTQTKDINACG---EMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119 HNV T +D G ++RIQ++ L KNC EFG+ + + QGIVHV+GPEQG TL Sbjct: 64 HNVPTTDRDRGVEGIVDPVSRIQVETLDKNCDEFGILEFKIKDQRQGIVHVIGPEQGATL 123 Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179 PGM+IVCGDSHT+THGAFG LA GIGTSEVEHVLATQ L Q + K M ++V GK PG+T Sbjct: 124 PGMSIVCGDSHTSTHGAFGCLAHGIGTSEVEHVLATQCLVQQKMKNMLVKVNGKLGPGVT 183 Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239 KD+VLAIIGK G+AGGTGH +EF GEAIR LSMEGRMT+CNM+IE GA+ G+VA D+TT Sbjct: 184 GKDVVLAIIGKIGTAGGTGHAIEFGGEAIRGLSMEGRMTICNMSIEAGARVGMVAVDDTT 243 Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299 YV+ R PKG+ +D AV YW+TL +D A FD +V L+ EI PQV+WGT+P V Sbjct: 244 IEYVRNRPFGPKGEQWDAAVEYWRTLHSDSDAVFDKIVELEGSEIQPQVSWGTSPEMVAG 303 Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359 ++ +PDP ADP++R +AL YMGL+P + +T++ +D+VFIGSCTNSRIEDLR AA Sbjct: 304 IDGKVPDPEQEADPIKREGIVRALKYMGLQPNMAITDIKLDRVFIGSCTNSRIEDLREAA 363 Query: 360 EIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRL 418 + KGRKV+P + QA+VVPGSG VKAQAE EGLDKIFIEAG EWR PGCSMCLAMN D+L Sbjct: 364 AVVKGRKVSPILKQAMVVPGSGLVKAQAEQEGLDKIFIEAGLEWRDPGCSMCLAMNADKL 423 Query: 419 NPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 GE CASTSNRNFEGRQG GGRTHLVSPAMAAAAAVTGHF D+R + Sbjct: 424 GQGEHCASTSNRNFEGRQGFGGRTHLVSPAMAAAAAVTGHFVDVREL 470 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: 24 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: 472 Length adjustment: 33 Effective length of query: 433 Effective length of database: 439 Effective search space: 190087 Effective search space used: 190087 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 GFF1877 HP15_1834 (protein containing 3-isopropylmalate dehydratase, large subunit region domain)
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.2963.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-239 781.3 0.4 1.7e-239 781.0 0.4 1.0 1 lcl|FitnessBrowser__Marino:GFF1877 HP15_1834 protein containing 3-i Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1877 HP15_1834 protein containing 3-isopropylmalate dehydratase, large subunit region # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 781.0 0.4 1.7e-239 1.7e-239 2 466 .] 3 470 .. 2 470 .. 0.99 Alignments for each domain: == domain 1 score: 781.0 bits; conditional E-value: 1.7e-239 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve... 73 ktly+kl+d h+vk+ ++++ l+yidr l+hevtspqafeglr agrk r+d +at dhn++t+ rd lcl|FitnessBrowser__Marino:GFF1877 3 GKTLYDKLWDDHLVKQRDDGSALIYIDRQLLHEVTSPQAFEGLRLAGRKPWRIDANIATPDHNVPTTDRDRGveg 77 59*******************************************************************854113 PP TIGR00170 74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtse 148 i++ ++++qv++l+kn++efg+ f +++++qgivhv+gpe+g tlpg++ivcgdsht+thgafg+la gigtse lcl|FitnessBrowser__Marino:GFF1877 78 IVDPVSRIQVETLDKNCDEFGILEFKIKDQRQGIVHVIGPEQGATLPGMSIVCGDSHTSTHGAFGCLAHGIGTSE 152 7899*********************************************************************** PP TIGR00170 149 vehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnma 223 vehvlatq l+q++ k++ ++v+gkl +g+t kd++laiigkig+aggtg+ +ef geair lsme+rmt+cnm+ lcl|FitnessBrowser__Marino:GFF1877 153 VEHVLATQCLVQQKMKNMLVKVNGKLGPGVTGKDVVLAIIGKIGTAGGTGHAIEFGGEAIRGLSMEGRMTICNMS 227 *************************************************************************** PP TIGR00170 224 ieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvl 298 ieaga+ g++a d+tt+eyv++r++ pkg++++ av+yw+tl++d +a+fdk v le+++i pqv+wgt+p++v lcl|FitnessBrowser__Marino:GFF1877 228 IEAGARVGMVAVDDTTIEYVRNRPFGPKGEQWDAAVEYWRTLHSDSDAVFDKIVELEGSEIQPQVSWGTSPEMVA 302 *************************************************************************** PP TIGR00170 299 svneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvkl 373 ++++vpdp++ adp++++++ +al+y+gl+p++ ++dik+d+vfigsctnsriedlr+aa+vvkg+kv++ +k+ lcl|FitnessBrowser__Marino:GFF1877 303 GIDGKVPDPEQEADPIKREGIVRALKYMGLQPNMAITDIKLDRVFIGSCTNSRIEDLREAAAVVKGRKVSPILKQ 377 *************************************************************************** PP TIGR00170 374 alvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvsp 448 a+vvpgsglvk+qae+egldkif+eag+ewr++gcs+cl+mn d+l+++e castsnrnfegrqg g+rthlvsp lcl|FitnessBrowser__Marino:GFF1877 378 AMVVPGSGLVKAQAEQEGLDKIFIEAGLEWRDPGCSMCLAMNADKLGQGEHCASTSNRNFEGRQGFGGRTHLVSP 452 *************************************************************************** PP TIGR00170 449 amaaaaavagkfvdirel 466 amaaaaav+g+fvd+rel lcl|FitnessBrowser__Marino:GFF1877 453 AMAAAAAVTGHFVDVREL 470 ****************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (472 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: 00:00:00.02 # Mc/sec: 9.41 // [ok]
This GapMind analysis is from Apr 09 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