Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate PfGW456L13_3948 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 Length = 472 Score = 592 bits (1527), 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 HNVPTTPERKGGIDAIVDQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGAT 123 Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178 LPGMT+VCGDSHT+THGAFGALA GIGTSEVEHVLATQ L + K M + V+G+ G+ Sbjct: 124 LPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVRVEGQLPFGV 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 ATFDTVV L A +I PQV+WGT+P V+ Sbjct: 244 TVAYVKGRPFAPKGAEWDLAVEAWKDLVSDADATFDTVVELDATQIKPQVSWGTSPEMVL 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 VKAQAE+EGLDKIF+EAGFEWR PGCSMCLAMN DR Sbjct: 364 AVIAKGRKVASTIKQAIVVPGSGLVKAQAESEGLDKIFLEAGFEWREPGCSMCLAMNPDR 423 Query: 418 LNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 L GE CASTSNRNFEGRQG GGRTHLVSPAMAAAAA+ G F D+R + Sbjct: 424 LESGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAINGRFVDVREL 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: 746 Number of extensions: 25 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 PfGW456L13_3948 (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.2392264.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-237 774.0 1.5 2.9e-237 773.7 1.5 1.0 1 FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 Domain annotation for each sequence (and alignments): >> FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 773.7 1.5 2.9e-237 2.9e-237 2 466 .] 3 471 .. 2 471 .. 0.98 Alignments for each domain: == domain 1 score: 773.7 bits; conditional E-value: 2.9e-237 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlat 60 ktly+kl+d+h+vk+ ++++ l+yidrh++hevtspqafeglr agrk r+d +at FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 3 GKTLYDKLWDSHLVKQRDDGSALIYIDRHIIHEVTSPQAFEGLRLAGRKPWRIDANIAT 61 59********************************************************* PP TIGR00170 61 ldhnistesr....dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpee 115 dhn++t+ i++++++lqv++l+ n++e+g+ f +++++qgivhv+gpe+ FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 62 PDHNVPTTPErkggIDAIVDQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQ 120 ******986546743357899************************************** PP TIGR00170 116 gltlpgktivcgdshtathgafgalafgigtsevehvlatqtlkqaraktlkievegkl 174 g tlpg+t+vcgdsht+thgafgala gigtsevehvlatq l+ ++ k++ ++veg+l FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 121 GATLPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVRVEGQL 179 *********************************************************** PP TIGR00170 175 akgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagakagli 233 g+takdi+la+igkig+agg g+ +efag airdls+e+rmt+cnm+ieaga+ gl+ FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 180 PFGVTAKDIVLAVIGKIGTAGGNGHAIEFAGSAIRDLSVEGRMTICNMSIEAGARVGLV 238 *********************************************************** PP TIGR00170 234 apdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292 a de t +yvk+r++apkg+e++ av+ wk l +d +a+fd+vv l+a++i pqv+wgt FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 239 AADEKTVAYVKGRPFAPKGAEWDLAVEAWKDLVSDADATFDTVVELDATQIKPQVSWGT 297 *********************************************************** PP TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsr 351 +p++vl+v+++vpdp++ d v++ s+ +al+y+gl++++ ++di++d+vfigsctnsr FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 298 SPEMVLAVDQNVPDPAKEMDLVKRDSIVRALKYMGLTANQAITDIQLDRVFIGSCTNSR 356 *********************************************************** PP TIGR00170 352 iedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcsl 410 iedlraaa ++kg+kva+++k+a+vvpgsglvk+qae egldkifleagfewre+gcs+ FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 357 IEDLRAAAVIAKGRKVASTIKQAIVVPGSGLVKAQAESEGLDKIFLEAGFEWREPGCSM 415 *********************************************************** PP TIGR00170 411 clgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466 cl+mn+d+l+++e castsnrnfegrqg+g+rthlvspamaaaaa++g+fvd+rel FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 416 CLAMNPDRLESGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAINGRFVDVREL 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: 28.35 // [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