Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate Pf1N1B4_15 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 Length = 472 Score = 594 bits (1531), Expect = e-174 Identities = 300/468 (64%), Positives = 363/468 (77%), Gaps = 5/468 (1%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 KTLY+KL+D+H+V + ++ + L+YIDRH++HEVTSPQAF+GLR GR + AT D Sbjct: 4 KTLYDKLWDSHLVKQRDDGSALIYIDRHIIHEVTSPQAFEGLRLAGRKPWRIDANIATPD 63 Query: 63 HNVSTQTK---DINAC-GEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVT 118 HNV T + I+A +++R+Q+Q L NC E+G+ + +N QGIVHV+GPEQG T Sbjct: 64 HNVPTTAERKGGIDAIVDQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGAT 123 Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178 LPGMT+VCGDSHT+THGAFGALA GIGTSEVEHVLATQ L + K M + V+G+ G+ Sbjct: 124 LPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVSVEGQLPFGV 183 Query: 179 TAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDET 238 TAKDIVLA+IGK G+AGG GH +EF G AIRDLS+EGRMT+CNM+IE GA+ GLVA DE Sbjct: 184 TAKDIVLAVIGKIGTAGGNGHAIEFAGSAIRDLSVEGRMTICNMSIEAGARVGLVAADEK 243 Query: 239 TFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVI 298 T YVKGR APKG ++D AV WK L +D A FDT+V L A +I PQV+WGT+P V+ Sbjct: 244 TVAYVKGRPFAPKGAEWDLAVEAWKDLVSDADAKFDTIVELDATQIKPQVSWGTSPEMVL 303 Query: 299 SVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAA 358 +V+ N+PDPA D V+R S E+AL YMGL +T++ +D+VFIGSCTNSRIEDLRAA Sbjct: 304 AVDQNVPDPAKEMDLVKRGSIERALKYMGLTANQAITDIQLDRVFIGSCTNSRIEDLRAA 363 Query: 359 AEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417 A IAKGRKVA + QA+VVPGSG VKAQAE+EGLDKIF+EAGFEWR PGCSMCLAMN DR Sbjct: 364 AVIAKGRKVASTIKQAIVVPGSGLVKAQAESEGLDKIFLEAGFEWREPGCSMCLAMNPDR 423 Query: 418 LNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 L GE CASTSNRNFEGRQG GGRTHLVSPAMAAAAAV G F D+R + Sbjct: 424 LESGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAVNGRFVDVREL 471 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: 744 Number of extensions: 23 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 Pf1N1B4_15 (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.1168449.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-237 773.6 1.8 3.7e-237 773.3 1.8 1.0 1 FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 Domain annotation for each sequence (and alignments): >> FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 773.3 1.8 3.7e-237 3.7e-237 2 466 .] 3 471 .. 2 471 .. 0.99 Alignments for each domain: == domain 1 score: 773.3 bits; conditional E-value: 3.7e-237 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr. 70 ktly+kl+d+h+vk+ ++++ l+yidrh++hevtspqafeglr agrk r+d +at dhn++t++ FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 3 GKTLYDKLWDSHLVKQRDDGSALIYIDRHIIHEVTSPQAFEGLRLAGRKPWRIDANIATPDHNVPTTAEr 72 59***************************************************************98765 PP TIGR00170 71 ...dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgaf 137 i++++++lqv++l+ n++e+g+ f +++++qgivhv+gpe+g tlpg+t+vcgdsht+thgaf FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 73 kggIDAIVDQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAF 142 6753358899************************************************************ PP TIGR00170 138 galafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefagea 207 gala gigtsevehvlatq l+ ++ k++ + veg+l g+takdi+la+igkig+agg g+ +efag a FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 143 GALAHGIGTSEVEHVLATQCLVAKKMKNMLVSVEGQLPFGVTAKDIVLAVIGKIGTAGGNGHAIEFAGSA 212 ********************************************************************** PP TIGR00170 208 irdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvv 277 irdls+e+rmt+cnm+ieaga+ gl+a de t +yvk+r++apkg+e++ av+ wk l +d +akfd+ v FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 213 IRDLSVEGRMTICNMSIEAGARVGLVAADEKTVAYVKGRPFAPKGAEWDLAVEAWKDLVSDADAKFDTIV 282 ********************************************************************** PP TIGR00170 278 tleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsc 347 l+a++i pqv+wgt+p++vl+v+++vpdp++ d v++ s+e+al+y+gl++++ ++di++d+vfigsc FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 283 ELDATQIKPQVSWGTSPEMVLAVDQNVPDPAKEMDLVKRGSIERALKYMGLTANQAITDIQLDRVFIGSC 352 ********************************************************************** PP TIGR00170 348 tnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnnd 417 tnsriedlraaa ++kg+kva+++k+a+vvpgsglvk+qae egldkifleagfewre+gcs+cl+mn+d FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 353 TNSRIEDLRAAAVIAKGRKVASTIKQAIVVPGSGLVKAQAESEGLDKIFLEAGFEWREPGCSMCLAMNPD 422 ********************************************************************** PP TIGR00170 418 vldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466 +l+++e castsnrnfegrqg+g+rthlvspamaaaaav+g+fvd+rel FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 423 RLESGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAVNGRFVDVREL 471 ***********************************************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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 30.44 // [ok]
This GapMind analysis is from Jul 25 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