Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate GFF1850 PS417_09410 isopropylmalate isomerase
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__WCS417:GFF1850 Length = 472 Score = 505 bits (1301), Expect = e-147 Identities = 250/466 (53%), Positives = 327/466 (70%), Gaps = 2/466 (0%) Query: 2 AKTLYEKLFDAHVVYEAENETP-LLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60 A+TLY+K D+H V +++ LLYIDR +++E TSPQAF GLR GR V +PG A Sbjct: 3 ARTLYDKHIDSHTVCPLDDQGHVLLYIDRQVINEYTSPQAFSGLREAGRNVWRPGTALAV 62 Query: 61 MDHNVSTQTKDINACGEMARI-QMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119 +DH T K I A + Q+ L +NC++FG+EL D+ QGI HV+ PEQG L Sbjct: 63 VDHVNPTTPKRIAAMPDAGGARQVSYLAENCRDFGIELLDILDKRQGIEHVIAPEQGFIL 122 Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179 PGM I GDSHT T+GA GA FGIGTSE+EH+LA+QTL R KTM + V G APG+T Sbjct: 123 PGMVIAAGDSHTTTYGALGAFGFGIGTSEIEHLLASQTLVYKRLKTMCVSVDGDLAPGLT 182 Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239 +KD+++A+IGK G++G TG+ +EF G + LS+E RMT+CNMA+E GA+ +APDE Sbjct: 183 SKDVIMALIGKIGASGATGYAIEFRGSTLDALSVEARMTICNMAVEAGARGAFMAPDEKV 242 Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299 F Y+KG+ AP+G+ +D A+A W+ L +D GA FD V L A + P VTWGT+P Q Sbjct: 243 FAYLKGKPRAPQGELWDQALAGWRLLHSDVGAVFDQEVQLDATTLEPMVTWGTSPDQAAP 302 Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359 + +PDP +D + R +AL YMGL+ G+ L+++ I FIGSCTN+RIEDLR AA Sbjct: 303 IGARVPDPQDVSDLILRQDMRRALNYMGLEAGMRLSDIVISHAFIGSCTNARIEDLRDAA 362 Query: 360 EIAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419 + +G+ VA V+A++VPGS V+ QAEAEGL IFI+AGFEWR GCSMCLAMN+D L Sbjct: 363 SVVRGKHVAEHVRAMIVPGSTEVRDQAEAEGLAAIFIDAGFEWRQSGCSMCLAMNDDVLA 422 Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 PG+RCAS++NRNFEGRQG G RTHL+SPAM AAAA+TG DIR++ Sbjct: 423 PGDRCASSTNRNFEGRQGAGARTHLMSPAMVAAAAITGRLTDIRHV 468 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: 692 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 GFF1850 PS417_09410 (isopropylmalate isomerase)
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.16329.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-200 652.6 0.0 1.7e-200 652.4 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF1850 PS417_09410 isopropylmalate isom Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF1850 PS417_09410 isopropylmalate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 652.4 0.0 1.7e-200 1.7e-200 2 466 .] 3 468 .. 2 468 .. 0.98 Alignments for each domain: == domain 1 score: 652.4 bits; conditional E-value: 1.7e-200 TIGR00170 2 aktlyeklfdahvvke.aenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveik 75 a+tly+k d+h v ++++ llyidr ++ e tspqaf glr+agr+v r++++la +dh +t+ + + ++ lcl|FitnessBrowser__WCS417:GFF1850 3 ARTLYDKHIDSHTVCPlDDQGHVLLYIDRQVINEYTSPQAFSGLREAGRNVWRPGTALAVVDHVNPTTPKRIAAM 77 89**********997626677889***************************************999999888776 PP TIGR00170 76 .eekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsev 149 + +qv l +n+++fg++l+d+ +++qgi hv+ pe+g+ lpg+ i gdsht+t+ga+ga+ fgigtse+ lcl|FitnessBrowser__WCS417:GFF1850 78 pDAGGARQVSYLAENCRDFGIELLDILDKRQGIEHVIAPEQGFILPGMVIAAGDSHTTTYGALGAFGFGIGTSEI 152 2666799******************************************************************** PP TIGR00170 150 ehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmai 224 eh+la+qtl+ +r kt+ + v+g la+g+t+kd+i+a+igkig++g tgy +ef g ++++ls+e+rmt+cnma+ lcl|FitnessBrowser__WCS417:GFF1850 153 EHLLASQTLVYKRLKTMCVSVDGDLAPGLTSKDVIMALIGKIGASGATGYAIEFRGSTLDALSVEARMTICNMAV 227 *************************************************************************** PP TIGR00170 225 eagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvls 299 eaga+ ++apde f+y+k+++ ap+g+ +++a+a w+ l++d ga+fd++v+l+a+ + p+vtwgt+p+q+ + lcl|FitnessBrowser__WCS417:GFF1850 228 EAGARGAFMAPDEKVFAYLKGKPRAPQGELWDQALAGWRLLHSDVGAVFDQEVQLDATTLEPMVTWGTSPDQAAP 302 *************************************************************************** PP TIGR00170 300 vneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvkla 374 + vpdp++++d + ++++ +al+y+gle+g++l di + + figsctn+riedlr aa+vv+gk+va+ v+ a lcl|FitnessBrowser__WCS417:GFF1850 303 IGARVPDPQDVSDLILRQDMRRALNYMGLEAGMRLSDIVISHAFIGSCTNARIEDLRDAASVVRGKHVAEHVR-A 376 *************************************************************************.* PP TIGR00170 375 lvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspa 449 ++vpgs v+ qae+egl if++agfewr++gcs+cl+mn+dvl +++rcas++nrnfegrqg+garthl+spa lcl|FitnessBrowser__WCS417:GFF1850 377 MIVPGSTEVRDQAEAEGLAAIFIDAGFEWRQSGCSMCLAMNDDVLAPGDRCASSTNRNFEGRQGAGARTHLMSPA 451 *************************************************************************** PP TIGR00170 450 maaaaavagkfvdirel 466 m aaaa++g++ dir++ lcl|FitnessBrowser__WCS417:GFF1850 452 MVAAAAITGRLTDIRHV 468 ***************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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.94 // [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