Align 3-isopropylmalate dehydratase large subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate WP_077243460.1 B1A74_RS00520 3-isopropylmalate dehydratase large subunit
Query= SwissProt::P15717 (466 letters) >NCBI__GCF_001995255.1:WP_077243460.1 Length = 469 Score = 590 bits (1520), Expect = e-173 Identities = 293/460 (63%), Positives = 353/460 (76%), Gaps = 1/460 (0%) Query: 3 KTLYEKLFDAHVVFEAPNETPLLYIDRHLVHEVTSPQAFDGLRAHHRPVRQPGKTFATMD 62 KTLY+KL++AHVV E P+ + LLYIDRHLVHEVTSPQAF+GLR R + A D Sbjct: 4 KTLYDKLWEAHVVREEPDGSTLLYIDRHLVHEVTSPQAFEGLRLAGRKPWRGDSVLAVPD 63 Query: 63 HNVSTQTKDINASGEMARIQMQELIKNCNEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122 HNV T +D ++R Q++ L N + FG++ + + QGIVHV+GPEQG TLPGM Sbjct: 64 HNVPTTNRDAGIEDPVSRTQVETLESNVSGFGLKFFPMADVRQGIVHVIGPEQGATLPGM 123 Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVTGNAAPGITAKD 182 T+VCGDSHT+THGA GALAFGIGTSEVEHVLATQ L Q + K M+I V G PG+TAKD Sbjct: 124 TVVCGDSHTSTHGALGALAFGIGTSEVEHVLATQCLWQKKTKAMQIRVEGELRPGVTAKD 183 Query: 183 IVLAIIGKTGSAGGTGHVVEFCGDAIRALSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242 IVLAIIG+ G+AGGTG+ +EF G AIR+LS+EGRM++CNM+IE GA+AG+VA DE T Y Sbjct: 184 IVLAIIGRIGTAGGTGYAIEFAGSAIRSLSIEGRMSICNMSIEAGARAGMVAVDEKTIEY 243 Query: 243 VKGRLHAPKGRDFDEAVEYWKTLKTDDGATFDTVVALRAEEIAPQVTWGTNPGQVISVTD 302 V+G+ AP G F+ A EYW+TL +D A FD VV L A EIAPQV+WGT+P V + Sbjct: 244 VRGKPQAPTGEMFERAAEYWRTLVSDPDAEFDAVVELDAAEIAPQVSWGTSPEMVAPIDG 303 Query: 303 IIPDPASFSDPVERASAEKALAYMGLQPGVPLTDVAIDKVFIGSCTNSRIEDLRAAAEVA 362 +PDPA+ SDPV ++AL YM L+ P+T++ DKVFIGSCTNSRIEDLRAAAEV Sbjct: 304 RVPDPAAESDPVRAEGMQRALEYMDLKANTPMTEIRPDKVFIGSCTNSRIEDLRAAAEVV 363 Query: 363 KGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421 KGR+ A ++ A+VVPGSG VK QAE EGLD+IF++AGFEWR PGCSMCLAMN DRL PG Sbjct: 364 KGRRKADNIKLAMVVPGSGLVKQQAEQEGLDRIFLDAGFEWREPGCSMCLAMNADRLEPG 423 Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFAD 461 ERCASTSNRNFEGRQG+GGRTHLVSPA+AAAAAV GHF + Sbjct: 424 ERCASTSNRNFEGRQGQGGRTHLVSPALAAAAAVAGHFIE 463 Lambda K H 0.318 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: 779 Number of extensions: 26 Number of successful extensions: 2 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: 469 Length adjustment: 33 Effective length of query: 433 Effective length of database: 436 Effective search space: 188788 Effective search space used: 188788 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 WP_077243460.1 B1A74_RS00520 (3-isopropylmalate dehydratase large subunit)
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.32263.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-237 774.6 0.0 1.9e-237 774.3 0.0 1.0 1 lcl|NCBI__GCF_001995255.1:WP_077243460.1 B1A74_RS00520 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001995255.1:WP_077243460.1 B1A74_RS00520 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 774.3 0.0 1.9e-237 1.9e-237 2 462 .. 3 463 .. 2 467 .. 0.99 Alignments for each domain: == domain 1 score: 774.3 bits; conditional E-value: 1.9e-237 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr 70 ktly+kl++ahvv+e+ ++++llyidrhlvhevtspqafeglr agrk r d+ la dhn++t++r lcl|NCBI__GCF_001995255.1:WP_077243460.1 3 GKTLYDKLWEAHVVREEPDGSTLLYIDRHLVHEVTSPQAFEGLRLAGRKPWRGDSVLAVPDHNVPTTNR 71 59******************************************************************* PP TIGR00170 71 dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafga 139 d i + +++ qv++le nv fg+k+f + +++qgivhv+gpe+g tlpg+t+vcgdsht+thga+ga lcl|NCBI__GCF_001995255.1:WP_077243460.1 72 DAGIEDPVSRTQVETLESNVSGFGLKFFPMADVRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGALGA 140 ********************************************************************* PP TIGR00170 140 lafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageai 208 lafgigtsevehvlatq l+q+++k+++i+veg+l +g+takdi+laiig+ig+aggtgy +efag ai lcl|NCBI__GCF_001995255.1:WP_077243460.1 141 LAFGIGTSEVEHVLATQCLWQKKTKAMQIRVEGELRPGVTAKDIVLAIIGRIGTAGGTGYAIEFAGSAI 209 ********************************************************************* PP TIGR00170 209 rdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvv 277 r+ls+e+rm++cnm+ieaga+ag++a de t+eyv+++++ap g+ fe a +yw+tl +d++a+fd vv lcl|NCBI__GCF_001995255.1:WP_077243460.1 210 RSLSIEGRMSICNMSIEAGARAGMVAVDEKTIEYVRGKPQAPTGEMFERAAEYWRTLVSDPDAEFDAVV 278 ********************************************************************* PP TIGR00170 278 tleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigs 346 l+a +i+pqv+wgt+p++v ++++ vpdp+ +dpv+ +++++al+y+ l+++t++++i+ dkvfigs lcl|NCBI__GCF_001995255.1:WP_077243460.1 279 ELDAAEIAPQVSWGTSPEMVAPIDGRVPDPAAESDPVRAEGMQRALEYMDLKANTPMTEIRPDKVFIGS 347 ********************************************************************* PP TIGR00170 347 ctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmn 415 ctnsriedlraaaevvkg+++adn+kla+vvpgsglvk+qae+egld+ifl+agfewre+gcs+cl+mn lcl|NCBI__GCF_001995255.1:WP_077243460.1 348 CTNSRIEDLRAAAEVVKGRRKADNIKLAMVVPGSGLVKQQAEQEGLDRIFLDAGFEWREPGCSMCLAMN 416 ********************************************************************* PP TIGR00170 416 ndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvd 462 d+l+++ercastsnrnfegrqg+g+rthlvspa+aaaaavag+f++ lcl|NCBI__GCF_001995255.1:WP_077243460.1 417 ADRLEPGERCASTSNRNFEGRQGQGGRTHLVSPALAAAAAVAGHFIE 463 *********************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (469 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 6.98 // [ok]
This GapMind analysis is from Apr 10 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