Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate RR42_RS14400 RR42_RS14400 isopropylmalate isomerase
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__Cup4G11:RR42_RS14400 Length = 469 Score = 604 bits (1557), Expect = e-177 Identities = 298/468 (63%), Positives = 361/468 (77%), Gaps = 3/468 (0%) Query: 1 MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60 MAKTLY+KL+D H V+ ++ T +LYIDRHL+HEVTSPQAF+GL+ RPV + A Sbjct: 1 MAKTLYDKLWDDHTVHVEDDGTTMLYIDRHLLHEVTSPQAFEGLKLAQRPVWRISANLAV 60 Query: 61 MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120 DHNV T + ++++Q+ L NC +G+ + +N QGIVHV+GPEQG TLP Sbjct: 61 SDHNVPTTDRSQGIADPVSKLQVDTLDNNCDAYGITQFKMNDLRQGIVHVIGPEQGATLP 120 Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180 GMT+VCGDSHT+THGAFGALA GIGTSEVEHVLATQTL +AK M + V+GK G TA Sbjct: 121 GMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQTLLGKKAKNMLVRVEGKLPRGCTA 180 Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240 KDIVLA+IGK G+AGGTG+ +EF G AIRDLSMEGRMT+CNMAIE GA+AGLVA D+ T Sbjct: 181 KDIVLAVIGKIGTAGGTGYTIEFAGSAIRDLSMEGRMTVCNMAIEAGARAGLVAVDDVTL 240 Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300 YVKGR +P+G +++ AV YW+TL +D GA FD VV L+AE++ PQVTWGT+P V+S+ Sbjct: 241 EYVKGRPFSPQGVEWEQAVGYWRTLHSDAGAHFDQVVELRAEDVRPQVTWGTSPEMVVSI 300 Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360 D +PDP DP +R + E+AL YMGL+P +P+ + IDKVFIGSCTNSRIED+RAAA Sbjct: 301 EDRVPDPEKEKDPNKRNAMERALEYMGLQPNVPVDSIKIDKVFIGSCTNSRIEDMRAAAW 360 Query: 361 IAK--GRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417 + + GR+VA V+ A+VVPGSG VK QAE EGLDK+F AGFEWR PGCSMCLAMN DR Sbjct: 361 VVQKLGRRVASNVKLAMVVPGSGLVKEQAEREGLDKVFKAAGFEWREPGCSMCLAMNADR 420 Query: 418 LNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 L GERCASTSNRNFEGRQG GGRTHLVSPAMAAAAA+ GHF DIR + Sbjct: 421 LEAGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAIEGHFVDIRQL 468 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: 722 Number of extensions: 21 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 RR42_RS14400 RR42_RS14400 (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.12413.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-243 794.6 0.5 1.5e-243 794.4 0.5 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS14400 RR42_RS14400 isopropylmalate iso Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS14400 RR42_RS14400 isopropylmalate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 794.4 0.5 1.5e-243 1.5e-243 1 465 [. 1 467 [. 1 468 [. 0.99 Alignments for each domain: == domain 1 score: 794.4 bits; conditional E-value: 1.5e-243 TIGR00170 1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistes 69 maktly+kl+d h v+ ++++t++lyidrhl+hevtspqafegl+ a+r+v r++ la dhn++t+ lcl|FitnessBrowser__Cup4G11:RR42_RS14400 1 MAKTLYDKLWDDHTVHVEDDGTTMLYIDRHLLHEVTSPQAFEGLKLAQRPVWRISANLAVSDHNVPTTD 69 89******************************************************************* PP TIGR00170 70 rdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafg 138 r i + ++klqv +l++n++++g+ f +++ +qgivhv+gpe+g tlpg+t+vcgdsht+thgafg lcl|FitnessBrowser__Cup4G11:RR42_RS14400 70 RSQGIADPVSKLQVDTLDNNCDAYGITQFKMNDLRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFG 138 ********************************************************************* PP TIGR00170 139 alafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefagea 207 ala gigtsevehvlatqtl ++ak++ ++vegkl +g takdi+la+igkig+aggtgy +efag a lcl|FitnessBrowser__Cup4G11:RR42_RS14400 139 ALAHGIGTSEVEHVLATQTLLGKKAKNMLVRVEGKLPRGCTAKDIVLAVIGKIGTAGGTGYTIEFAGSA 207 ********************************************************************* PP TIGR00170 208 irdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkv 276 irdlsme+rmtvcnmaieaga+agl+a d++t+eyvk+r+++p+g e+e+av yw+tl++d ga+fd+v lcl|FitnessBrowser__Cup4G11:RR42_RS14400 208 IRDLSMEGRMTVCNMAIEAGARAGLVAVDDVTLEYVKGRPFSPQGVEWEQAVGYWRTLHSDAGAHFDQV 276 ********************************************************************* PP TIGR00170 277 vtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfig 345 v l a+d+ pqvtwgt+p++v+s+++ vpdp++ dp +++ +e+al+y+gl+p++++++ik+dkvfig lcl|FitnessBrowser__Cup4G11:RR42_RS14400 277 VELRAEDVRPQVTWGTSPEMVVSIEDRVPDPEKEKDPNKRNAMERALEYMGLQPNVPVDSIKIDKVFIG 345 ********************************************************************* PP TIGR00170 346 sctnsriedlraaaevvk..gkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslcl 412 sctnsried+raaa vv+ g++va+nvkla+vvpgsglvk+qae+egldk+f +agfewre+gcs+cl lcl|FitnessBrowser__Cup4G11:RR42_RS14400 346 SCTNSRIEDMRAAAWVVQklGRRVASNVKLAMVVPGSGLVKEQAEREGLDKVFKAAGFEWREPGCSMCL 414 ****************97779************************************************ PP TIGR00170 413 gmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465 +mn d+l+++ercastsnrnfegrqg+g+rthlvspamaaaaa+ g+fvdir+ lcl|FitnessBrowser__Cup4G11:RR42_RS14400 415 AMNADRLEAGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAIEGHFVDIRQ 467 ****************************************************8 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12.03 // [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