Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate AO356_21400 AO356_21400 isopropylmalate isomerase
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_21400 Length = 472 Score = 593 bits (1530), Expect = e-174 Identities = 301/468 (64%), Positives = 361/468 (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---DINACGE-MARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVT 118 HNV T + I A + ++R+Q+Q L NC E+G+ + +N QGIVHV+GPEQG T Sbjct: 64 HNVPTTPERKGGIEAIADQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGAT 123 Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178 LPGMT+VCGDSHT+THGAFGALA GIGTSEVEHVLATQ L + K M + V+GK G+ Sbjct: 124 LPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVRVEGKLPFGV 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 +PKG ++D AV WK L +D A FDTVV L A +I PQV+WGT+P V+ Sbjct: 244 TVEYVKGRPFSPKGAEWDMAVEAWKDLVSDADAKFDTVVELDATQIKPQVSWGTSPEMVL 303 Query: 299 SVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAA 358 +V+ N+PDPA D V+R S +AL YMGL +T++ +D+VFIGSCTNSRIEDLRAA Sbjct: 304 AVDQNVPDPAKEMDLVKRDSIVRALKYMGLSANQAITDIQLDRVFIGSCTNSRIEDLRAA 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: 743 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 AO356_21400 AO356_21400 (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.29866.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-238 776.0 1.6 6.8e-238 775.7 1.6 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 AO356_21400 isopropylmalate isom Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 AO356_21400 isopropylmalate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 775.7 1.6 6.8e-238 6.8e-238 2 466 .] 3 471 .. 2 471 .. 0.98 Alignments for each domain: == domain 1 score: 775.7 bits; conditional E-value: 6.8e-238 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhn 64 ktly+kl+d+h+vk+ ++++ l+yidrh++hevtspqafeglr agrk r+d +at dhn lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 3 GKTLYDKLWDSHLVKQRDDGSALIYIDRHIIHEVTSPQAFEGLRLAGRKPWRIDANIATPDHN 65 59************************************************************* PP TIGR00170 65 istesr....dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgkt 123 ++t+ i +++++lqv++l+ n++e+g+ f +++++qgivhv+gpe+g tlpg+t lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 66 VPTTPErkggIEAIADQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGATLPGMT 128 **9865466334578999********************************************* PP TIGR00170 124 ivcgdshtathgafgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiila 186 +vcgdsht+thgafgala gigtsevehvlatq l+ ++ k++ ++vegkl g+takdi+la lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 129 VVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVRVEGKLPFGVTAKDIVLA 191 *************************************************************** PP TIGR00170 187 iigkigvaggtgyvvefageairdlsmeermtvcnmaieagakagliapdettfeyvkdrkya 249 +igkig+agg g+ +efag airdls+e+rmt+cnm+ieaga+ gl+a de t eyvk+r+++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 192 VIGKIGTAGGNGHAIEFAGSAIRDLSVEGRMTICNMSIEAGARVGLVAADEKTVEYVKGRPFS 254 *************************************************************** PP TIGR00170 250 pkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpkslad 312 pkg+e++ av+ wk l +d +akfd+vv l+a++i pqv+wgt+p++vl+v+++vpdp++ d lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 255 PKGAEWDMAVEAWKDLVSDADAKFDTVVELDATQIKPQVSWGTSPEMVLAVDQNVPDPAKEMD 317 *************************************************************** PP TIGR00170 313 pvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklal 375 v++ s+ +al+y+gl +++ ++di++d+vfigsctnsriedlraaa ++kg+kva+++k+a+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 318 LVKRDSIVRALKYMGLSANQAITDIQLDRVFIGSCTNSRIEDLRAAAVIAKGRKVASTIKQAI 380 *************************************************************** PP TIGR00170 376 vvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438 vvpgsglvk+qae+egldkifleagfewre+gcs+cl+mn+d+l+++e castsnrnfegrqg lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 381 VVPGSGLVKAQAEAEGLDKIFLEAGFEWREPGCSMCLAMNPDRLESGEHCASTSNRNFEGRQG 443 *************************************************************** PP TIGR00170 439 kgarthlvspamaaaaavagkfvdirel 466 +g+rthlvspamaaaaav+g+fvd+rel lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 444 AGGRTHLVSPAMAAAAAVNGRFVDVREL 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.62 // [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