Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_010438762.1 G7G_RS0104305 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >NCBI__GCF_000192475.1:WP_010438762.1 Length = 467 Score = 632 bits (1629), Expect = 0.0 Identities = 309/464 (66%), Positives = 377/464 (81%), Gaps = 2/464 (0%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 KTLY+K++DAHV +EA++ T LLYIDRHLVHEVTSPQAF+GLR GR VR P KT A D Sbjct: 4 KTLYDKIWDAHVAHEADDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVRAPEKTIAVPD 63 Query: 63 HNVSTQTKDINAC-GEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPG 121 HNV T +N +RIQ++ L KN K+FG+ Y ++ QGIVH++GPEQG TLPG Sbjct: 64 HNVPTTPDRVNGIENPESRIQVEALDKNAKDFGIHYYPVHDVRQGIVHIVGPEQGWTLPG 123 Query: 122 MTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAK 181 MT+VCGDSHTATHGAFGALA GIGTSEVEHVLATQTL Q ++K MK+E+ GK PG+TAK Sbjct: 124 MTVVCGDSHTATHGAFGALAHGIGTSEVEHVLATQTLIQKKSKNMKVEITGKLQPGVTAK 183 Query: 182 DIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFN 241 DI LA+IG+TG+AGGTG+V+E+CGEAIRDLSMEGRMT+CNMAIE GA+AGL+APDETTF Sbjct: 184 DITLAVIGETGTAGGTGYVIEYCGEAIRDLSMEGRMTVCNMAIEGGARAGLIAPDETTFE 243 Query: 242 YVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVN 301 YVKGR HAPKG ++ A+ +WKTL TDEGA FD V+TL+ E+I+P VTWGT+P V+ + Sbjct: 244 YVKGRPHAPKGAQWEAAMDWWKTLYTDEGARFDKVITLRGEDIAPVVTWGTSPEDVLPIT 303 Query: 302 DNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEI 361 ++P P F + + +A +++ YMGL+ G L++V ID VFIGSCTN RIEDLRAAAEI Sbjct: 304 ASVPHPEDF-EGGKVDAARRSIEYMGLEAGQKLSDVEIDTVFIGSCTNGRIEDLRAAAEI 362 Query: 362 AKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421 KG+K+ G++A+VVPGSG V+AQAE EGL +IF +AGFEWRL GCSMCLAMN D+L PG Sbjct: 363 LKGKKIKDGMRAMVVPGSGLVRAQAEEEGLAEIFKDAGFEWRLAGCSMCLAMNPDQLQPG 422 Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 ERCA+TSNRNFEGRQGRGGRTHL+SPAMAAAAA+TG D+R + Sbjct: 423 ERCAATSNRNFEGRQGRGGRTHLLSPAMAAAAAITGRLTDVREM 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: 805 Number of extensions: 26 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: 467 Length adjustment: 33 Effective length of query: 433 Effective length of database: 434 Effective search space: 187922 Effective search space used: 187922 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_010438762.1 G7G_RS0104305 (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.1609053.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-245 801.4 0.2 1.3e-245 801.1 0.2 1.0 1 NCBI__GCF_000192475.1:WP_010438762.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000192475.1:WP_010438762.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 801.1 0.2 1.3e-245 1.3e-245 2 466 .] 3 466 .. 2 466 .. 0.98 Alignments for each domain: == domain 1 score: 801.1 bits; conditional E-value: 1.3e-245 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve. 73 +ktly+k++dahv +ea+++t llyidrhlvhevtspqafeglr agrkvr ++kt+a dhn++t+ v+ NCBI__GCF_000192475.1:WP_010438762.1 3 PKTLYDKIWDAHVAHEADDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVRAPEKTIAVPDHNVPTTPDRVNg 75 89***************************************************************99877772 PP TIGR00170 74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146 i + ++++qv++l+kn+k+fg++++ +++++qgivh+vgpe+g tlpg+t+vcgdshtathgafgala gigt NCBI__GCF_000192475.1:WP_010438762.1 76 IENPESRIQVEALDKNAKDFGIHYYPVHDVRQGIVHIVGPEQGWTLPGMTVVCGDSHTATHGAFGALAHGIGT 148 56679******************************************************************** PP TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219 sevehvlatqtl+q+++k++k+e+ gkl++g+takdi la+ig +g+aggtgyv+e++geairdlsme+rmtv NCBI__GCF_000192475.1:WP_010438762.1 149 SEVEHVLATQTLIQKKSKNMKVEITGKLQPGVTAKDITLAVIGETGTAGGTGYVIEYCGEAIRDLSMEGRMTV 221 ************************************************************************* PP TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292 cnmaie ga+agliapdettfeyvk+r++apkg+++e a++ wktl tdega+fdkv+tl ++di+p vtwgt NCBI__GCF_000192475.1:WP_010438762.1 222 CNMAIEGGARAGLIAPDETTFEYVKGRPHAPKGAQWEAAMDWWKTLYTDEGARFDKVITLRGEDIAPVVTWGT 294 ************************************************************************* PP TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365 +p++vl+++ +vp+p+++ + a ++++y+gle+g+kl d+++d vfigsctn+riedlraaae++kgk NCBI__GCF_000192475.1:WP_010438762.1 295 SPEDVLPITASVPHPEDFEGG-KVDAARRSIEYMGLEAGQKLSDVEIDTVFIGSCTNGRIEDLRAAAEILKGK 366 ******************764.567789********************************************* PP TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438 k+ d+++ a+vvpgsglv++qae+egl +if +agfewr agcs+cl+mn+d+l+++erca+tsnrnfegrqg NCBI__GCF_000192475.1:WP_010438762.1 367 KIKDGMR-AMVVPGSGLVRAQAEEEGLAEIFKDAGFEWRLAGCSMCLAMNPDQLQPGERCAATSNRNFEGRQG 438 *******.***************************************************************** PP TIGR00170 439 kgarthlvspamaaaaavagkfvdirel 466 +g+rthl+spamaaaaa++g++ d+re+ NCBI__GCF_000192475.1:WP_010438762.1 439 RGGRTHLLSPAMAAAAAITGRLTDVREM 466 **************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (467 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: 30.67 // [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