Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate Ac3H11_1525 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1525 Length = 473 Score = 572 bits (1473), Expect = e-167 Identities = 295/470 (62%), Positives = 346/470 (73%), Gaps = 7/470 (1%) Query: 1 MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60 M +TLY+K++D HVV+ E+ T +LYIDRHLVHEVTSPQAF+GLR GR V + T Sbjct: 1 MGRTLYDKIWDEHVVHTEEDGTSILYIDRHLVHEVTSPQAFEGLREAGRKVWRMSSIVGT 60 Query: 61 MDHNVSTQTKDINACG---EMARIQMQELIKNCKEFG-VELYDLNHPYQGIVHVMGPEQG 116 DHN T + G +++ Q+ L N + H QGIVHV+GPE G Sbjct: 61 ADHNTPTTGWEHGYDGITDPISKEQITTLNDNMATISPAAFFPFMHKRQGIVHVIGPENG 120 Query: 117 VTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAP 176 TLPGMT+VCGDSHT+THGAFGALA GIGTSEVEHV+ATQTL +AK M ++V G A Sbjct: 121 ATLPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVMATQTLLAKKAKNMLVQVDGTLAK 180 Query: 177 GITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPD 236 G+T KD+VLAIIGK G+AGGTG+ +EF G R +SMEGRMT+CNMAIE GA+AGLVA D Sbjct: 181 GVTPKDVVLAIIGKIGTAGGTGYTIEFAGSVFRAMSMEGRMTVCNMAIEGGARAGLVAVD 240 Query: 237 ETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQ 296 + T YVKGR +P G ++D AVAYWKTL +D A FDTVV L A EI PQVTWGT+P Sbjct: 241 DKTIEYVKGRPLSPTGVEWDQAVAYWKTLHSDADAQFDTVVKLDAAEIQPQVTWGTSPEM 300 Query: 297 VISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLR 356 V+ ++ +PDP D +R + E+AL YM L+PG P+ ++ IDKVFIGSCTNSRIED+R Sbjct: 301 VLGIDARVPDPDKEKDANKRGAIERALTYMDLQPGKPINDITIDKVFIGSCTNSRIEDMR 360 Query: 357 AAAEIAK--GRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAM 413 AA + K GRKVA V+ ALVVPGSG VK QAE EGLD+IF AGFEWR PGCSMCLAM Sbjct: 361 EAAAVVKNLGRKVASNVKLALVVPGSGLVKEQAEREGLDQIFKAAGFEWREPGCSMCLAM 420 Query: 414 NNDRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463 N DRL PGERCASTSNRNFEGRQG GGRTHLVSPAMAAAAAV GHF DIR Sbjct: 421 NADRLEPGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAVHGHFVDIR 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: 729 Number of extensions: 18 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: 473 Length adjustment: 33 Effective length of query: 433 Effective length of database: 440 Effective search space: 190520 Effective search space used: 190520 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 Ac3H11_1525 (3-isopropylmalate dehydratase large subunit (EC 4.2.1.33))
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.23971.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-236 769.3 1.6 6.8e-236 769.2 1.6 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 3-isopropylmalate dehydratase la Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 769.2 1.6 6.8e-236 6.8e-236 1 466 [] 1 472 [. 1 472 [. 0.98 Alignments for each domain: == domain 1 score: 769.2 bits; conditional E-value: 6.8e-236 TIGR00170 1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatld 62 m +tly+k++d+hvv+ +e++t++lyidrhlvhevtspqafeglr+agrkv r+++ ++t d lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 1 MGRTLYDKIWDEHVVHTEEDGTSILYIDRHLVHEVTSPQAFEGLREAGRKVWRMSSIVGTAD 62 789*********************************************************** PP TIGR00170 63 hnistesr...dveikeekaklqvkeleknvkefg.vklfdlssaeqgivhvvgpeegltlp 120 hn +t+ i++ +k q+++l+ n+ + +f + +++qgivhv+gpe+g tlp lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 63 HNTPTTGWehgYDGITDPISKEQITTLNDNMATISpAAFFPFMHKRQGIVHVIGPENGATLP 124 *****9873333468999************9988637899********************** PP TIGR00170 121 gktivcgdshtathgafgalafgigtsevehvlatqtlkqaraktlkievegklakgitakd 182 g+t+vcgdsht+thgafgala gigtsevehv+atqtl ++ak++ ++v+g+lakg+t kd lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 125 GMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVMATQTLLAKKAKNMLVQVDGTLAKGVTPKD 186 ************************************************************** PP TIGR00170 183 iilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagakagliapdettfeyvk 244 ++laiigkig+aggtgy +efag ++r++sme+rmtvcnmaie ga+agl+a d+ t+eyvk lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 187 VVLAIIGKIGTAGGTGYTIEFAGSVFRAMSMEGRMTVCNMAIEGGARAGLVAVDDKTIEYVK 248 ************************************************************** PP TIGR00170 245 drkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpd 306 +r+++p g e+++avaywktl++d +a+fd+vv+l+a +i pqvtwgt+p++vl ++ vpd lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 249 GRPLSPTGVEWDQAVAYWKTLHSDADAQFDTVVKLDAAEIQPQVTWGTSPEMVLGIDARVPD 310 ************************************************************** PP TIGR00170 307 pksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvk..gkk 366 p++ d ++ +e+al+y+ l+pg++++di +dkvfigsctnsried+r+aa+vvk g+k lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 311 PDKEKDANKRGAIERALTYMDLQPGKPINDITIDKVFIGSCTNSRIEDMREAAAVVKnlGRK 372 ********************************************************9889** PP TIGR00170 367 vadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercast 428 va+nvklalvvpgsglvk+qae+egld+if +agfewre+gcs+cl+mn d+l+++ercast lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 373 VASNVKLALVVPGSGLVKEQAEREGLDQIFKAAGFEWREPGCSMCLAMNADRLEPGERCAST 434 ************************************************************** PP TIGR00170 429 snrnfegrqgkgarthlvspamaaaaavagkfvdirel 466 snrnfegrqg+g+rthlvspamaaaaav+g+fvdir++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 435 SNRNFEGRQGAGGRTHLVSPAMAAAAAVHGHFVDIRQF 472 ************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (473 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: 00:00:00.01 # Mc/sec: 12.37 // [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