Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate WP_057507560.1 ABB28_RS04900 3-hydroxyisobutyrate dehydrogenase
Query= SwissProt::P28811 (298 letters) >NCBI__GCF_001431535.1:WP_057507560.1 Length = 296 Score = 362 bits (928), Expect = e-105 Identities = 189/293 (64%), Positives = 222/293 (75%), Gaps = 2/293 (0%) Query: 1 MTDIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEV 60 M+ IAF+GLGNMGGPMAANL KAGH V VFDL P AV V+ GA A SAL AEV Sbjct: 1 MSRIAFIGLGNMGGPMAANLAKAGHAVRVFDLVPAAVQAAVDAGATAASSALDTLADAEV 60 Query: 61 VISMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAP 120 VISMLPA +HVE +YLGDDGLLA + G L+IDCSTIAP TARKVAEAAAA+GL +LDAP Sbjct: 61 VISMLPASRHVEGVYLGDDGLLADIPGGALVIDCSTIAPATARKVAEAAAARGLQMLDAP 120 Query: 121 VSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGI 180 VSGG GA AGTL+FIVGG + RARP L+ MGRNIFH G GAGQVAK+CNNM LG+ Sbjct: 121 VSGGTAGATAGTLTFIVGGEEDALERARPYLQAMGRNIFHVGASGAGQVAKLCNNMALGV 180 Query: 181 LMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGFQ 240 +MA T E++ALGV +GLDP VLS++M S+G +WA + NPWPGV+ APAS GY+GGF Sbjct: 181 IMAVTGESIALGVAHGLDPKVLSQMMAVSTGRSWATEVCNPWPGVLENAPASRGYSGGFG 240 Query: 241 VRLMNKDLGLALANAQAVQASTPLGALARNLFSLHAQADAEHEGLDFSSIQKL 293 LM KD+GLA+ A +V AS PLG LARNL+S++ QA LDFSS+ +L Sbjct: 241 SDLMLKDMGLAVEAAMSVGASIPLGELARNLYSMNHQAG--RGKLDFSSVVQL 291 Lambda K H 0.317 0.135 0.395 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: 308 Number of extensions: 6 Number of successful extensions: 1 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: 298 Length of database: 296 Length adjustment: 26 Effective length of query: 272 Effective length of database: 270 Effective search space: 73440 Effective search space used: 73440 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: 48 (23.1 bits)
Align candidate WP_057507560.1 ABB28_RS04900 (3-hydroxyisobutyrate dehydrogenase)
to HMM TIGR01692 (mmsB: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))
# 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.carbon/TIGR01692.hmm # target sequence database: /tmp/gapView.14357.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01692 [M=288] Accession: TIGR01692 Description: HIBADH: 3-hydroxyisobutyrate dehydrogenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-128 412.6 11.4 4.9e-128 412.5 11.4 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057507560.1 ABB28_RS04900 3-hydroxyisobutyra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057507560.1 ABB28_RS04900 3-hydroxyisobutyrate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.5 11.4 4.9e-128 4.9e-128 1 286 [. 6 291 .. 6 293 .. 1.00 Alignments for each domain: == domain 1 score: 412.5 bits; conditional E-value: 4.9e-128 TIGR01692 1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesv 69 fiGlGnmGgpmaanl+kaghavrvfdl ++av+ +v+aGa+aa+sa ++ ++a+vvi+mlPa++hve v lcl|NCBI__GCF_001431535.1:WP_057507560.1 6 FIGLGNMGGPMAANLAKAGHAVRVFDLVPAAVQAAVDAGATAASSALDTLADAEVVISMLPASRHVEGV 74 9******************************************************************** PP TIGR01692 70 yagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaee 138 y+gd+g+la + +++l+id+sti++ +arkvae+aaa+G+++ldaPvsGG++ga aGtltf+vGge+++ lcl|NCBI__GCF_001431535.1:WP_057507560.1 75 YLGDDGLLADIPGGALVIDCSTIAPATARKVAEAAAARGLQMLDAPVSGGTAGATAGTLTFIVGGEEDA 143 ********************************************************************* PP TIGR01692 139 faraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGr 207 ++ra+p l+amg+ni+h+G++GaGq+ak+Cnn+ lg+ m+ + e++alg++ Gldpkvl++++ s+Gr lcl|NCBI__GCF_001431535.1:WP_057507560.1 144 LERARPYLQAMGRNIFHVGASGAGQVAKLCNNMALGVIMAVTGESIALGVAHGLDPKVLSQMMAVSTGR 212 ********************************************************************* PP TIGR01692 208 cWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgag 276 +W+ + nP+PGv+e+aPas+gy+gGf+++lmlkd+gla eaa sv+as++lG lar+lys+ ++g g lcl|NCBI__GCF_001431535.1:WP_057507560.1 213 SWATEVCNPWPGVLENAPASRGYSGGFGSDLMLKDMGLAVEAAMSVGASIPLGELARNLYSMNHQAGRG 281 ********************************************************************* PP TIGR01692 277 kkdfsavikl 286 k+dfs+v++l lcl|NCBI__GCF_001431535.1:WP_057507560.1 282 KLDFSSVVQL 291 ********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 1 (296 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: 7.08 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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