Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate Ga0059261_3686 Ga0059261_3686 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)
Query= SwissProt::P28811 (298 letters) >FitnessBrowser__Korea:Ga0059261_3686 Length = 295 Score = 281 bits (719), Expect = 1e-80 Identities = 152/293 (51%), Positives = 186/293 (63%), Gaps = 4/293 (1%) Query: 1 MTDIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEV 60 M + F+GLGNMGG MAANL KAGH V FDL A+ G +SA EGAE Sbjct: 1 MARVGFIGLGNMGGGMAANLAKAGHDVRAFDLSADALERAKAAGCLPVESAAAAAEGAEA 60 Query: 61 VISMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAP 120 VI+MLPAG+HVE +Y +D + +LIDCSTI TAR+VA+AA AKGL +DAP Sbjct: 61 VITMLPAGKHVEQVY--EDSVFGAADTGAILIDCSTIDVATARRVADAAQAKGLAAVDAP 118 Query: 121 VSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGI 180 VSGG+ A GTL+F+VGG A F RA L MG+ + HAG +GAGQ +KICNNMLLG Sbjct: 119 VSGGIAAAAGGTLTFMVGGDAAAFERAEVFLAAMGKAVIHAGGNGAGQASKICNNMLLGA 178 Query: 181 LMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGFQ 240 M T EAL L K GLDP ++ SSG W+LN Y P PG+ PQ PA NGY GGF Sbjct: 179 TMVATCEALLLAQKLGLDPQTFYDIASVSSGACWSLNTYAPLPGMGPQTPADNGYQGGFA 238 Query: 241 VRLMNKDLGLALANAQAVQASTPLGALARNLFSLHAQADAEHEGLDFSSIQKL 293 LM KDL LA+ A++ + TP+GA A L++ ADA + G+DFS I K+ Sbjct: 239 AGLMLKDLKLAMEAAESTHSETPMGARAAELYTKF--ADAGNAGVDFSGIIKM 289 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: 311 Number of extensions: 12 Number of successful extensions: 3 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: 295 Length adjustment: 26 Effective length of query: 272 Effective length of database: 269 Effective search space: 73168 Effective search space used: 73168 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 Ga0059261_3686 Ga0059261_3686 (3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))
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.16143.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-126 404.9 16.4 1.1e-125 404.8 16.4 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_3686 Ga0059261_3686 3-hydroxyisobutyr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_3686 Ga0059261_3686 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 404.8 16.4 1.1e-125 1.1e-125 1 287 [. 6 290 .. 6 291 .. 0.99 Alignments for each domain: == domain 1 score: 404.8 bits; conditional E-value: 1.1e-125 TIGR01692 1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesv 69 fiGlGnmGg+maanl+kagh vr+fdlsa+a+e++++aG+ +saa+a+e+a++vitmlPagkhve+v lcl|FitnessBrowser__Korea:Ga0059261_3686 6 FIGLGNMGGGMAANLAKAGHDVRAFDLSADALERAKAAGCLPVESAAAAAEGAEAVITMLPAGKHVEQV 74 9******************************************************************** PP TIGR01692 70 yagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaee 138 y ++ + + +++lid+stidv +ar+va++a+akG+ +daPvsGG+++a+ GtltfmvGg a++ lcl|FitnessBrowser__Korea:Ga0059261_3686 75 Y--EDSVFGAADTGAILIDCSTIDVATARRVADAAQAKGLAAVDAPVSGGIAAAAGGTLTFMVGGDAAA 141 *..59**************************************************************** PP TIGR01692 139 faraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGr 207 f+rae l+amgk ++haG++GaGqa+kiCnn+llg +m+ ++eal l++klGldp+++ +i+s ssG lcl|FitnessBrowser__Korea:Ga0059261_3686 142 FERAEVFLAAMGKAVIHAGGNGAGQASKICNNMLLGATMVATCEALLLAQKLGLDPQTFYDIASVSSGA 210 ********************************************************************* PP TIGR01692 208 cWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgag 276 cWsl+ty+P+PG+ +q+Pa+ngy+gGfa+ lmlkdl+la eaa+s+++++++Ga a ely+ fa++g lcl|FitnessBrowser__Korea:Ga0059261_3686 211 CWSLNTYAPLPGMGPQTPADNGYQGGFAAGLMLKDLKLAMEAAESTHSETPMGARAAELYTKFADAGNA 279 ********************************************************************* PP TIGR01692 277 kkdfsavikll 287 + dfs++ik+l lcl|FitnessBrowser__Korea:Ga0059261_3686 280 GVDFSGIIKML 290 ********986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 1 (295 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: 7.38 // [ok]
This GapMind analysis is from Sep 17 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