Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate RR42_RS24175 RR42_RS24175 isopropylmalate isomerase
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__Cup4G11:RR42_RS24175 Length = 469 Score = 604 bits (1557), Expect = e-177 Identities = 300/468 (64%), Positives = 360/468 (76%), Gaps = 3/468 (0%) Query: 1 MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60 MAKTLY+KL+D H V+ E+ T LLYIDRHL++EVTSPQAF+GLR PV + A Sbjct: 1 MAKTLYDKLWDDHAVHVEEDGTTLLYIDRHLLNEVTSPQAFEGLRMSEHPVWRISANLAV 60 Query: 61 MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120 DHNV T + ++++Q+ L NC FG+ + +N QGIVHV+GPEQG TLP Sbjct: 61 SDHNVPTTNRSQGIADPVSKLQVDTLDANCDSFGITQFKMNDHRQGIVHVIGPEQGATLP 120 Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180 GMT+VCGDSHT+THGAFGALA GIGTSEVEHV+ATQTL + M ++V+GK G TA Sbjct: 121 GMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVMATQTLLGKKTMNMLVKVEGKLPRGCTA 180 Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240 KDIVLAIIGK G+AGGTG+ +EF G AIRDL++EGRMT+CNMAIE GA+AGLVA D+ T Sbjct: 181 KDIVLAIIGKIGTAGGTGNTIEFAGSAIRDLTVEGRMTVCNMAIEAGARAGLVAVDDVTL 240 Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300 Y KGR +AP+G ++D AV YW+TL +D GA FD VV L+AEEI PQVTWGT+P VIS+ Sbjct: 241 EYFKGRPYAPQGVEWDQAVGYWRTLHSDAGAKFDLVVELRAEEIRPQVTWGTSPEMVISI 300 Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360 D +PDP DP +R + E+AL YMGL+P +P+ + IDKVFIGSCTNSRI+D+RAAA Sbjct: 301 EDRVPDPDKEKDPNKRTAMERALEYMGLQPNVPVESINIDKVFIGSCTNSRIDDMRAAAW 360 Query: 361 IAK--GRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417 + + GRKVA V+ ALVVPGSG VK QAE EGLD++F AGFEWR PGCSMCLAMN DR Sbjct: 361 VVQKLGRKVASNVKLALVVPGSGLVKEQAEREGLDEVFKAAGFEWREPGCSMCLAMNADR 420 Query: 418 LNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 L PGERCASTSNRNFEGRQG GGRTHLVSPAMAAAAA+ GHF D+R + Sbjct: 421 LEPGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAIEGHFVDVRKL 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: 735 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_RS24175 RR42_RS24175 (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.24149.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-239 779.9 0.4 4.3e-239 779.7 0.4 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS24175 RR42_RS24175 isopropylmalate iso Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS24175 RR42_RS24175 isopropylmalate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 779.7 0.4 4.3e-239 4.3e-239 1 466 [] 1 468 [. 1 468 [. 1.00 Alignments for each domain: == domain 1 score: 779.7 bits; conditional E-value: 4.3e-239 TIGR00170 1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistes 69 maktly+kl+d h v+ +e++t+llyidrhl+ evtspqafeglr + +v r++ la dhn++t++ lcl|FitnessBrowser__Cup4G11:RR42_RS24175 1 MAKTLYDKLWDDHAVHVEEDGTTLLYIDRHLLNEVTSPQAFEGLRMSEHPVWRISANLAVSDHNVPTTN 69 89******************************************************************* PP TIGR00170 70 rdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafg 138 r i + ++klqv +l+ n++ fg+ f +++++qgivhv+gpe+g tlpg+t+vcgdsht+thgafg lcl|FitnessBrowser__Cup4G11:RR42_RS24175 70 RSQGIADPVSKLQVDTLDANCDSFGITQFKMNDHRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFG 138 ********************************************************************* PP TIGR00170 139 alafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefagea 207 ala gigtsevehv+atqtl +++ ++ ++vegkl +g takdi+laiigkig+aggtg +efag a lcl|FitnessBrowser__Cup4G11:RR42_RS24175 139 ALAHGIGTSEVEHVMATQTLLGKKTMNMLVKVEGKLPRGCTAKDIVLAIIGKIGTAGGTGNTIEFAGSA 207 ********************************************************************* PP TIGR00170 208 irdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkv 276 irdl++e+rmtvcnmaieaga+agl+a d++t+ey k+r+yap+g e+++av yw+tl++d gakfd v lcl|FitnessBrowser__Cup4G11:RR42_RS24175 208 IRDLTVEGRMTVCNMAIEAGARAGLVAVDDVTLEYFKGRPYAPQGVEWDQAVGYWRTLHSDAGAKFDLV 276 ********************************************************************* PP TIGR00170 277 vtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfig 345 v l a++i pqvtwgt+p++v+s+++ vpdp++ dp +++ +e+al+y+gl+p++++++i++dkvfig lcl|FitnessBrowser__Cup4G11:RR42_RS24175 277 VELRAEEIRPQVTWGTSPEMVISIEDRVPDPDKEKDPNKRTAMERALEYMGLQPNVPVESINIDKVFIG 345 ********************************************************************* PP TIGR00170 346 sctnsriedlraaaevvk..gkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslcl 412 sctnsri+d+raaa vv+ g+kva+nvklalvvpgsglvk+qae+egld++f +agfewre+gcs+cl lcl|FitnessBrowser__Cup4G11:RR42_RS24175 346 SCTNSRIDDMRAAAWVVQklGRKVASNVKLALVVPGSGLVKEQAEREGLDEVFKAAGFEWREPGCSMCL 414 ****************97779************************************************ PP TIGR00170 413 gmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466 +mn d+l+++ercastsnrnfegrqg+g+rthlvspamaaaaa+ g+fvd+r+l lcl|FitnessBrowser__Cup4G11:RR42_RS24175 415 AMNADRLEPGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAIEGHFVDVRKL 468 ****************************************************85 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: 00:00:00.02 # Mc/sec: 10.55 // [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