Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate HSERO_RS16515 HSERO_RS16515 isopropylmalate isomerase
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__HerbieS:HSERO_RS16515 Length = 466 Score = 592 bits (1527), Expect = e-174 Identities = 290/466 (62%), Positives = 356/466 (76%), Gaps = 1/466 (0%) Query: 1 MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60 M KTLY+KL+++HVV+ ++ T +LYIDRHL+HEVTSPQAF+GL+ GR + Sbjct: 1 MLKTLYDKLWESHVVHTEDDGTAILYIDRHLLHEVTSPQAFEGLKLAGRQPWRNSANLMV 60 Query: 61 MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120 DHNV T + ++R+Q++ L N KE+ + + +N QGIVHV+GPEQG TLP Sbjct: 61 ADHNVPTTDRAHGIADPISRLQVETLDGNAKEYSLTYFGMNDKRQGIVHVIGPEQGATLP 120 Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180 GMT+VCGDSHT+THGAF ALA GIGTSEVEHVLATQTL ++K M ++V G G+TA Sbjct: 121 GMTVVCGDSHTSTHGAFAALAHGIGTSEVEHVLATQTLLARKSKAMLVQVDGALPAGVTA 180 Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240 KDIVLA+IGK G+AGGTG+ +EF G IR LSMEGRMT+CNMAIE GA+AG+VA D+TT Sbjct: 181 KDIVLAVIGKIGTAGGTGYAIEFAGSTIRSLSMEGRMTVCNMAIEAGARAGMVAFDDTTL 240 Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300 Y+KGR +P G ++ AV+YW++L +D GA FD VVTL A EI PQVTWGT+P V++V Sbjct: 241 EYLKGRPFSPSGPHWERAVSYWRSLHSDPGAKFDMVVTLNAAEIKPQVTWGTSPEMVVAV 300 Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360 + +PDP DP +R EKALAYM LKP P+ ++ IDKVFIGSCTNSRIEDLR AA+ Sbjct: 301 DARVPDPDKEKDPTKRDGMEKALAYMALKPNTPIEDIRIDKVFIGSCTNSRIEDLREAAK 360 Query: 361 IAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419 + +G+ A V+ A+VVPGSG VK QAE EGLDKIF +AGFEWR PGCSMCLAMN DRL Sbjct: 361 VVRGKFRASNVKLAMVVPGSGLVKEQAEREGLDKIFRDAGFEWREPGCSMCLAMNADRLE 420 Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 PGERCASTSNRNFEGRQG GGRTHLVSPAMAAAA + GHF D+R++ Sbjct: 421 PGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAGIAGHFVDVRSL 466 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: 729 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: 466 Length adjustment: 33 Effective length of query: 433 Effective length of database: 433 Effective search space: 187489 Effective search space used: 187489 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 HSERO_RS16515 HSERO_RS16515 (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.1146.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-240 782.9 0.0 5.3e-240 782.7 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS16515 HSERO_RS16515 isopropylmalate is Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS16515 HSERO_RS16515 isopropylmalate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 782.7 0.0 5.3e-240 5.3e-240 1 465 [. 1 465 [. 1 466 [] 1.00 Alignments for each domain: == domain 1 score: 782.7 bits; conditional E-value: 5.3e-240 TIGR00170 1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhniste 68 m ktly+kl+++hvv+ ++++t +lyidrhl+hevtspqafegl+ agr+ r + l dhn++t+ lcl|FitnessBrowser__HerbieS:HSERO_RS16515 1 MLKTLYDKLWESHVVHTEDDGTAILYIDRHLLHEVTSPQAFEGLKLAGRQPWRNSANLMVADHNVPTT 68 679***************************************************************** PP TIGR00170 69 srdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathga 136 r i + ++lqv++l+ n+ke+ + +f++++++qgivhv+gpe+g tlpg+t+vcgdsht+thga lcl|FitnessBrowser__HerbieS:HSERO_RS16515 69 DRAHGIADPISRLQVETLDGNAKEYSLTYFGMNDKRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGA 136 ******************************************************************** PP TIGR00170 137 fgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefa 204 f ala gigtsevehvlatqtl ++k++ ++v+g l g+takdi+la+igkig+aggtgy +efa lcl|FitnessBrowser__HerbieS:HSERO_RS16515 137 FAALAHGIGTSEVEHVLATQTLLARKSKAMLVQVDGALPAGVTAKDIVLAVIGKIGTAGGTGYAIEFA 204 ******************************************************************** PP TIGR00170 205 geairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegak 272 g +ir+lsme+rmtvcnmaieaga+ag++a d+tt+ey+k+r+++p g ++e av+yw++l++d+gak lcl|FitnessBrowser__HerbieS:HSERO_RS16515 205 GSTIRSLSMEGRMTVCNMAIEAGARAGMVAFDDTTLEYLKGRPFSPSGPHWERAVSYWRSLHSDPGAK 272 ******************************************************************** PP TIGR00170 273 fdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvd 340 fd vvtl+a +i pqvtwgt+p++v++v+ vpdp++ dp ++ ++ekalay+ l+p+t+++di++d lcl|FitnessBrowser__HerbieS:HSERO_RS16515 273 FDMVVTLNAAEIKPQVTWGTSPEMVVAVDARVPDPDKEKDPTKRDGMEKALAYMALKPNTPIEDIRID 340 ******************************************************************** PP TIGR00170 341 kvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagc 408 kvfigsctnsriedlr+aa+vv+gk a+nvkla+vvpgsglvk+qae+egldkif +agfewre+gc lcl|FitnessBrowser__HerbieS:HSERO_RS16515 341 KVFIGSCTNSRIEDLREAAKVVRGKFRASNVKLAMVVPGSGLVKEQAEREGLDKIFRDAGFEWREPGC 408 ******************************************************************** PP TIGR00170 409 slclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465 s+cl+mn d+l+++ercastsnrnfegrqg+g+rthlvspamaaaa++ag+fvd+r lcl|FitnessBrowser__HerbieS:HSERO_RS16515 409 SMCLAMNADRLEPGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAGIAGHFVDVRS 465 *******************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (466 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: 7.46 // [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