Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate WP_066328412.1 BLR17_RS00950 3-isopropylmalate dehydratase large subunit
Query= uniprot:A0A1X9Z7T5 (470 letters) >NCBI__GCF_900100165.1:WP_066328412.1 Length = 464 Score = 633 bits (1633), Expect = 0.0 Identities = 302/465 (64%), Positives = 368/465 (79%), Gaps = 1/465 (0%) Query: 1 MSKTLVEKIWDAHVVKSEEGFPDILYIDTHLIHEVTSPQAFDGLRKRGLPVFRPKQTVAT 60 MSKTL +K+WD+HVV+ E PD+ +ID H IHEVTSP AF GL+ RG+ V P++T AT Sbjct: 1 MSKTLFDKVWDSHVVRKIEDGPDVFFIDRHFIHEVTSPVAFLGLKTRGVSVLYPERTFAT 60 Query: 61 ADHNVPTLNQLLPIKEELSRYQVDMLTKNCAEFGVELYGLGHPFQGIVHVIGPELGITLP 120 ADHN PT+NQ LP+ + LS Q+ L N AE+G+ +GLGH GIVHV+GPE GITLP Sbjct: 61 ADHNTPTINQHLPVADALSANQLKALETNAAEYGISHWGLGHQKNGIVHVVGPENGITLP 120 Query: 121 GKTMVCGDSHTSTHGAFGAIAFGIGTSQVEQVFATQCLLQSKPKTMKIEVNGELGKGVGA 180 G T+VCGDSHTSTHGAFGAIAFGIGTS+VE V +TQC++Q KPK M+I VNG+L KGV Sbjct: 121 GATIVCGDSHTSTHGAFGAIAFGIGTSEVEMVLSTQCIMQPKPKKMRINVNGKLSKGVTP 180 Query: 181 KDIILYIIAKISAAGGTGYFIEYAGSAIEALSMEARMTICNMSIEMGARGGLIAPDQTTF 240 KD+ LYIIA+++ +GGTGYF+EYAG+ E ++ME RMT+CN+SIEMGARGG+IAPDQTTF Sbjct: 181 KDVALYIIAQLTTSGGTGYFVEYAGNVFEEMTMEGRMTVCNLSIEMGARGGMIAPDQTTF 240 Query: 241 DYIKGREFAPAGEEWDKALAYWKTLYSDADAKFDSVLTFDAADIAPMITYGTNPGMGMGI 300 D+++GR +AP GE W KA+ YWKTL +D DA FD+ L A DI PMITYGTNPGMG+GI Sbjct: 241 DFLEGRLYAPKGEAWTKAVEYWKTLKTDTDAVFDAELNIKAEDIEPMITYGTNPGMGIGI 300 Query: 301 QEHIPATGAQPEKEKLSYQKALDYMGFDDDSSLIGKPVDYVFIGSCTNSRIEDLREVADF 360 +HIP+ Q E + +Y+K+L+YMGF +D +IGKP+DYVF+GSCTN RIED R A Sbjct: 301 TKHIPSAD-QVEGGEETYKKSLNYMGFHEDDVMIGKPIDYVFLGSCTNGRIEDFRAFASI 359 Query: 361 VKDKRKADNVTVWIVPGSKQVEQQAKNEGLDKIFEAAGFQLREPGCSACLGMNEDKIPAG 420 VK ++KADNVT W+VPGS VE Q K EG+ I AGF LR+PGCSACL MN+DK+PAG Sbjct: 360 VKGRKKADNVTAWLVPGSHVVEAQIKEEGILDILTEAGFVLRQPGCSACLAMNDDKVPAG 419 Query: 421 KYCVSTSNRNFEGRQGQNARTLLASPLTAAAAAVTGKITDVRDLL 465 KY VSTSNRNFEGRQG +RTLLASP+ AAAAAVTGK+TD RDLL Sbjct: 420 KYAVSTSNRNFEGRQGPGSRTLLASPIMAAAAAVTGKLTDPRDLL 464 Lambda K H 0.317 0.135 0.399 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: 647 Number of extensions: 17 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: 470 Length of database: 464 Length adjustment: 33 Effective length of query: 437 Effective length of database: 431 Effective search space: 188347 Effective search space used: 188347 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_066328412.1 BLR17_RS00950 (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.2886858.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-198 643.4 0.1 1.1e-197 643.2 0.1 1.0 1 NCBI__GCF_900100165.1:WP_066328412.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066328412.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 643.2 0.1 1.1e-197 1.1e-197 1 465 [. 1 462 [. 1 463 [. 0.99 Alignments for each domain: == domain 1 score: 643.2 bits; conditional E-value: 1.1e-197 TIGR00170 1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve 73 m+ktl++k++d+hvv++ e+++d+++idrh++hevtsp af gl+++g v +++t+at dhn +t ++ + NCBI__GCF_900100165.1:WP_066328412.1 1 MSKTLFDKVWDSHVVRKIEDGPDVFFIDRHFIHEVTSPVAFLGLKTRGVSVLYPERTFATADHNTPTINQHLP 73 79*********************************************************************** PP TIGR00170 74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146 + + + q+k+le n+ e+g+ ++l ++++givhvvgpe+g+tlpg tivcgdsht+thgafga+afgigt NCBI__GCF_900100165.1:WP_066328412.1 74 VADALSANQLKALETNAAEYGISHWGLGHQKNGIVHVVGPENGITLPGATIVCGDSHTSTHGAFGAIAFGIGT 146 ************************************************************************* PP TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219 seve vl+tq ++q ++k+++i+v+gkl+kg+t kd+ l+ii +++++ggtgy ve+ag+++++++me+rmtv NCBI__GCF_900100165.1:WP_066328412.1 147 SEVEMVLSTQCIMQPKPKKMRINVNGKLSKGVTPKDVALYIIAQLTTSGGTGYFVEYAGNVFEEMTMEGRMTV 219 ************************************************************************* PP TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292 cn++ie+ga+ g+iapd+ttf+++ +r yapkg+ + kav+ywktlktd +a+fd +++++a+di p++t+gt NCBI__GCF_900100165.1:WP_066328412.1 220 CNLSIEMGARGGMIAPDQTTFDFLEGRLYAPKGEAWTKAVEYWKTLKTDTDAVFDAELNIKAEDIEPMITYGT 292 ************************************************************************* PP TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365 npg+ + +++++p+ +++ ++ +k+l+y+g++ + + +d vf+gsctn+ried+ra a++vkg+ NCBI__GCF_900100165.1:WP_066328412.1 293 NPGMGIGITKHIPSADQVEGGE--ETYKKSLNYMGFHEDDVMIGKPIDYVFLGSCTNGRIEDFRAFASIVKGR 363 **************99997654..56789******************************************** PP TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438 k+adnv a +vpgs v +q ++eg+ i+ eagf r++gcs cl+mn+d++++++ stsnrnfegrqg NCBI__GCF_900100165.1:WP_066328412.1 364 KKADNVT-AWLVPGSHVVEAQIKEEGILDILTEAGFVLRQPGCSACLAMNDDKVPAGKYAVSTSNRNFEGRQG 435 ******9.999************************************************************** PP TIGR00170 439 kgarthlvspamaaaaavagkfvdire 465 g+rt l sp maaaaav+gk+ d r+ NCBI__GCF_900100165.1:WP_066328412.1 436 PGSRTLLASPIMAAAAAVTGKLTDPRD 462 ************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (464 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 15.00 // [ok]
This GapMind analysis is from Jul 26 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