Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate 200847 SO1682 3-hydroxyisobutyrate dehydrogenase (NCBI ptt file)
Query= SwissProt::P28811 (298 letters) >FitnessBrowser__MR1:200847 Length = 300 Score = 328 bits (840), Expect = 1e-94 Identities = 176/293 (60%), Positives = 208/293 (70%), Gaps = 5/293 (1%) Query: 1 MTDIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEV 60 M+ +AF+GLGNMGGPMAANLLKAG V VFDL A+ L EQGA + +A GA V Sbjct: 1 MSTVAFIGLGNMGGPMAANLLKAGMTVRVFDLVHTAMQTLAEQGALVSSTACGAAAGANV 60 Query: 61 VISMLPAGQHVESLYLG---DDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLL 117 VI+MLPAG+HV++LYLG + GLL VA LLIDCSTI ++A+ VA AA GL + Sbjct: 61 VITMLPAGKHVKNLYLGSGSEKGLLDVVASDTLLIDCSTIDAQSAQLVATQAAKNGLEFM 120 Query: 118 DAPVSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNML 177 DAPVSGG GA AGTL+FI GG F RA+PVL MG+NIFHAG GAGQ+AKICNNML Sbjct: 121 DAPVSGGTSGAAAGTLTFICGGSDTAFERAQPVLNAMGKNIFHAGGPGAGQIAKICNNML 180 Query: 178 LGILMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAG 237 L +LM GT+EAL +G+ +GLDP VLS +MK SSGGNW L YNP PGVM P+S GY G Sbjct: 181 LSVLMVGTSEALQMGIDHGLDPKVLSNIMKVSSGGNWTLEKYNPCPGVMENVPSSKGYQG 240 Query: 238 GFQVRLMNKDLGLALANAQAVQASTPLGALARNLFSLHAQADAEHEGLDFSSI 290 GF V LM KDLGL+ A +STP+GALAR+L+ HA+ H DFSSI Sbjct: 241 GFMVDLMVKDLGLSFEAALLSNSSTPMGALARSLYVSHARQGNGHR--DFSSI 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: 327 Number of extensions: 7 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: 298 Length of database: 300 Length adjustment: 27 Effective length of query: 271 Effective length of database: 273 Effective search space: 73983 Effective search space used: 73983 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 200847 SO1682 (3-hydroxyisobutyrate dehydrogenase (NCBI ptt file))
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.5399.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-124 399.9 9.8 3.6e-124 399.8 9.8 1.0 1 lcl|FitnessBrowser__MR1:200847 SO1682 3-hydroxyisobutyrate dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200847 SO1682 3-hydroxyisobutyrate dehydrogenase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.8 9.8 3.6e-124 3.6e-124 1 285 [. 6 293 .. 6 296 .. 0.98 Alignments for each domain: == domain 1 score: 399.8 bits; conditional E-value: 3.6e-124 TIGR01692 1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesvyag...degi 76 fiGlGnmGgpmaanllkag +vrvfdl +a+++l e+Ga ++++a a+++a+vvitmlPagkhv+++y+g ++g+ lcl|FitnessBrowser__MR1:200847 6 FIGLGNMGGPMAANLLKAGMTVRVFDLVHTAMQTLAEQGALVSSTACGAAAGANVVITMLPAGKHVKNLYLGsgsEKGL 84 9*********************************************************************97333589* PP TIGR01692 77 lakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaeefaraepvleamgknivh 155 l v+ ++llid+stid++sa+ va +aa++G+ f+daPvsGG+ ga+aGtltf+ Gg++ +f+ra+pvl+amgkni+h lcl|FitnessBrowser__MR1:200847 85 LDVVASDTLLIDCSTIDAQSAQLVATQAAKNGLEFMDAPVSGGTSGAAAGTLTFICGGSDTAFERAQPVLNAMGKNIFH 163 ******************************************************************************* PP TIGR01692 156 aGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGrcWsldtynPvPGvveqaPasngykgGf 234 aG+ GaGq akiCnn+ll++ m+G++eal++g+ Gldpkvl++i++ ssG +W+l+ ynP PGv+e++P+s+gy+gGf lcl|FitnessBrowser__MR1:200847 164 AGGPGAGQIAKICNNMLLSVLMVGTSEALQMGIDHGLDPKVLSNIMKVSSGGNWTLEKYNPCPGVMENVPSSKGYQGGF 242 ******************************************************************************* PP TIGR01692 235 atalmlkdlglaqeaaksvkasvllGalarelyslfaskgagkkdfsavik 285 ++lm+kdlgl+ eaa ++s+++Galar ly +a +g g +dfs++++ lcl|FitnessBrowser__MR1:200847 243 MVDLMVKDLGLSFEAALLSNSSTPMGALARSLYVSHARQGNGHRDFSSIFE 293 *************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 1 (300 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.21 // [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