Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate AO353_20620 AO353_20620 isopropylmalate isomerase
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20620 Length = 472 Score = 590 bits (1520), Expect = e-173 Identities = 298/468 (63%), Positives = 358/468 (76%), 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 HNVSTQTKDINACG----EMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVT 118 HNV T + E++R+Q+Q L NC E+G+ + +N QGIVHV+GPEQG T Sbjct: 64 HNVPTTPERKGGIAAIADEVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGAT 123 Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178 LPGMT+VCGDSHT+THGAFGALA GIGTSEVEHVLATQ L + K M + V+G G+ Sbjct: 124 LPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVRVEGTLPFGV 183 Query: 179 TAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDET 238 TAKDIVLA+IGK G+AGG GH +EF G AIR+LS+EGRMT+CNM+IE GA+ GLVA DE Sbjct: 184 TAKDIVLAVIGKIGTAGGNGHAIEFAGSAIRELSVEGRMTICNMSIEAGARVGLVAADEK 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 TVAYVKGRPFAPKGAEWDLAVEAWKDLVSDADAKFDTIVELDAAQIKPQVSWGTSPEMVL 303 Query: 299 SVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAA 358 +V+ N+PDPA D V+R S +AL YMGL +T++ +D+VFIGSCTNSRIEDLRAA Sbjct: 304 AVDQNVPDPAKEMDLVKRDSIVRALKYMGLTANQAITDIQLDRVFIGSCTNSRIEDLRAA 363 Query: 359 AEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417 A IAKGRKVA + QA+VVPGSG VKAQAEAEGLDKIF+EAGFEWR PGCSMCLAMN DR Sbjct: 364 AVIAKGRKVASTIKQAIVVPGSGLVKAQAEAEGLDKIFLEAGFEWREPGCSMCLAMNPDR 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: 738 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 AO353_20620 AO353_20620 (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.15889.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-237 774.1 1.6 2.7e-237 773.8 1.6 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_20620 AO353_20620 isopropylmalate isom Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_20620 AO353_20620 isopropylmalate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 773.8 1.6 2.7e-237 2.7e-237 2 466 .] 3 471 .. 2 471 .. 0.99 Alignments for each domain: == domain 1 score: 773.8 bits; conditional E-value: 2.7e-237 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnis 66 ktly+kl+d+h+vk+ ++++ l+yidrh++hevtspqafeglr agrk r+d +at dhn++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_20620 3 GKTLYDKLWDSHLVKQRDDGSALIYIDRHIIHEVTSPQAFEGLRLAGRKPWRIDANIATPDHNVP 67 59*************************************************************** PP TIGR00170 67 tesr....dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcg 127 t+ i +e+++lqv++l+ n++e+g+ f +++++qgivhv+gpe+g tlpg+t+vcg lcl|FitnessBrowser__pseudo3_N2E3:AO353_20620 68 TTPErkggIAAIADEVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGATLPGMTVVCG 132 9865466556899**************************************************** PP TIGR00170 128 dshtathgafgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkig 192 dsht+thgafgala gigtsevehvlatq l+ ++ k++ ++veg+l g+takdi+la+igkig lcl|FitnessBrowser__pseudo3_N2E3:AO353_20620 133 DSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVRVEGTLPFGVTAKDIVLAVIGKIG 197 ***************************************************************** PP TIGR00170 193 vaggtgyvvefageairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefek 257 +agg g+ +efag air+ls+e+rmt+cnm+ieaga+ gl+a de t +yvk+r++apkg+e++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_20620 198 TAGGNGHAIEFAGSAIRELSVEGRMTICNMSIEAGARVGLVAADEKTVAYVKGRPFAPKGAEWDL 262 ***************************************************************** PP TIGR00170 258 avaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaeka 322 av+ wk l +d +akfd+ v l+a +i pqv+wgt+p++vl+v+++vpdp++ d v++ s+ +a lcl|FitnessBrowser__pseudo3_N2E3:AO353_20620 263 AVEAWKDLVSDADAKFDTIVELDAAQIKPQVSWGTSPEMVLAVDQNVPDPAKEMDLVKRDSIVRA 327 ***************************************************************** PP TIGR00170 323 laylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqa 387 l+y+gl++++ ++di++d+vfigsctnsriedlraaa ++kg+kva+++k+a+vvpgsglvk+qa lcl|FitnessBrowser__pseudo3_N2E3:AO353_20620 328 LKYMGLTANQAITDIQLDRVFIGSCTNSRIEDLRAAAVIAKGRKVASTIKQAIVVPGSGLVKAQA 392 ***************************************************************** PP TIGR00170 388 ekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaa 452 e+egldkifleagfewre+gcs+cl+mn+d+l+++e castsnrnfegrqg+g+rthlvspamaa lcl|FitnessBrowser__pseudo3_N2E3:AO353_20620 393 EAEGLDKIFLEAGFEWREPGCSMCLAMNPDRLESGEHCASTSNRNFEGRQGAGGRTHLVSPAMAA 457 ***************************************************************** PP TIGR00170 453 aaavagkfvdirel 466 aaav+g+fvd+rel lcl|FitnessBrowser__pseudo3_N2E3:AO353_20620 458 AAAVNGRFVDVREL 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8.54 // [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