Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate 3608350 Dshi_1752 3-hydroxyisobutyrate dehydrogenase (RefSeq)
Query= reanno::psRCH2:GFF2390 (296 letters) >FitnessBrowser__Dino:3608350 Length = 291 Score = 259 bits (663), Expect = 4e-74 Identities = 143/293 (48%), Positives = 184/293 (62%), Gaps = 10/293 (3%) Query: 1 MHIGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAEL 60 M IGF+GLGNMGAPMA NL AGH ++ FDL A E + GA + A A AE+ Sbjct: 1 MKIGFVGLGNMGAPMARNLAAAGHAVTGFDLTAPVPEGVTGAAS------AAEAAAGAEV 54 Query: 61 IITMLPAAAHVKGVYLGVNGLIAHSRAGVMLIDCSTIDPHSAREVAKAAAEHGNPMLDAP 120 +ITMLP A ++ V LI G +L+DCST+D SAR VA A G LDAP Sbjct: 55 VITMLPNGAILRSV---AAELIPAMAPGAVLLDCSTVDVESARAVAAQAEAAGLGALDAP 111 Query: 121 VSGGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCGAAGNGQVAKVANNMLLGI 180 VSGGTGGA AGTLTFMVGGSD F A+P+ MG+ VHCG AGNGQ AK+ NNM+LG+ Sbjct: 112 VSGGTGGAEAGTLTFMVGGSDAAFATARPLFDIMGQKAVHCGGAGNGQAAKICNNMILGV 171 Query: 181 SMIGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSRGYSGGFG 240 +M+ E AL LG+D + L V++TSSG WS + Y P PG+ P+ R Y+ GF Sbjct: 172 TMVATCEGFALADKLGLDRQALFDVVSTSSGYSWSMNVYCPAPGIGPESPADRDYAPGFA 231 Query: 241 SDLMLKDLGLATEAAKQVRQPVILGALAQQLYQSF-SAQGHGGLDFSAIINQY 292 ++LMLKDL L+ +AA+ V GA A L+++F +G G DF+AI+ ++ Sbjct: 232 AELMLKDLRLSQQAAEAVDADTPTGATATALFETFVETEGMGKKDFTAILPRF 284 Lambda K H 0.318 0.134 0.392 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: 269 Number of extensions: 11 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: 296 Length of database: 291 Length adjustment: 26 Effective length of query: 270 Effective length of database: 265 Effective search space: 71550 Effective search space used: 71550 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 3608350 Dshi_1752 (3-hydroxyisobutyrate dehydrogenase (RefSeq))
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.25040.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-113 363.6 10.9 4.6e-113 363.3 10.9 1.0 1 lcl|FitnessBrowser__Dino:3608350 Dshi_1752 3-hydroxyisobutyrate d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3608350 Dshi_1752 3-hydroxyisobutyrate dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 363.3 10.9 4.6e-113 4.6e-113 1 284 [. 5 281 .. 5 284 .. 0.98 Alignments for each domain: == domain 1 score: 363.3 bits; conditional E-value: 4.6e-113 TIGR01692 1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesvyagdegil 77 f+GlGnmG+pma+nl+ aghav+ fdl+a v +G++ aasaaea+++a+vvitmlP g+ +sv a +++ lcl|FitnessBrowser__Dino:3608350 5 FVGLGNMGAPMARNLAAAGHAVTGFDLTAP-----VPEGVTGAASAAEAAAGAEVVITMLPNGAILRSVAA---ELI 73 9**************************986.....577999****************************95...999 PP TIGR01692 78 akvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaeefaraepvleamgkniv 154 + ++ +++l+d+st+dv+sar+va++a+a+G+ ldaPvsGG+gga+aGtltfmvGg++++fa a+p+++ mg++ v lcl|FitnessBrowser__Dino:3608350 74 PAMAPGAVLLDCSTVDVESARAVAAQAEAAGLGALDAPVSGGTGGAEAGTLTFMVGGSDAAFATARPLFDIMGQKAV 150 ***************************************************************************** PP TIGR01692 155 haGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGrcWsldtynPvPGvveqaPasngyk 231 h+G+aG GqaakiCnn++lg++m+ ++e +al+ klGld ++l++++s+ssG +Ws++ y+P PG+ +++Pa+++y+ lcl|FitnessBrowser__Dino:3608350 151 HCGGAGNGQAAKICNNMILGVTMVATCEGFALADKLGLDRQALFDVVSTSSGYSWSMNVYCPAPGIGPESPADRDYA 227 ***************************************************************************** PP TIGR01692 232 gGfatalmlkdlglaqeaaksvkasvllGalarelyslfa.skgagkkdfsavi 284 +Gfa++lmlkdl+l+q+aa++v a+++ Ga+a +l+++f +g+gkkdf+a++ lcl|FitnessBrowser__Dino:3608350 228 PGFAAELMLKDLRLSQQAAEAVDADTPTGATATALFETFVeTEGMGKKDFTAIL 281 *************************************9975899********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 1 (291 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: 7.10 // [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