Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate WP_011385945.1 AMB_RS18155 3-hydroxyisobutyrate dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_05985 (294 letters) >NCBI__GCF_000009985.1:WP_011385945.1 Length = 296 Score = 302 bits (774), Expect = 5e-87 Identities = 160/290 (55%), Positives = 197/290 (67%) Query: 3 IAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELVIT 62 I FIGLGNMGAPM RNLIKAGH + DL++A LA A+ G T A +AA+GAE+V++ Sbjct: 4 IGFIGLGNMGAPMMRNLIKAGHKVAAFDLSEAALAAAAEAGATACTKATDAARGAEVVVS 63 Query: 63 MLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPVSG 122 MLPA HV+SV LGE G+ A +KG +D STID TAR ++ A++ G A+ DAPVSG Sbjct: 64 MLPAGAHVKSVMLGEGGLFAAASKGTLFIDSSTIDVATARLLSDEASRAGHALIDAPVSG 123 Query: 123 GTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAISMV 182 G GGA AGTLTFMVG + FA +P+LA MG+ IVH G G GQ AKICNN+LL ISM+ Sbjct: 124 GVGGAEAGTLTFMVGGADDSFARAEPILAVMGKTIVHAGGPGNGQAAKICNNMLLGISMI 183 Query: 183 GVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGAEL 242 G EA AL + LG+D Q L I + S+G+ WS Y P PG V +PA+R Y GF A + Sbjct: 184 GTCEAFALAEKLGLDAQKLFDISSKSSGQNWSMTSYCPVPGPVPASPANRDYKAGFAAAM 243 Query: 243 MLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAIINSYR 292 MLKDL LA EAA+ A + LGA A QLY M+ G+GG DFS II+ R Sbjct: 244 MLKDLKLAVEAAQTAGASIPLGAEAAQLYAMMAGMGQGGLDFSGIIHMLR 293 Lambda K H 0.317 0.132 0.382 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: 262 Number of extensions: 8 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: 294 Length of database: 296 Length adjustment: 26 Effective length of query: 268 Effective length of database: 270 Effective search space: 72360 Effective search space used: 72360 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_011385945.1 AMB_RS18155 (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.5575.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-130 419.6 15.5 3.6e-130 419.5 15.5 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011385945.1 AMB_RS18155 3-hydroxyisobutyrate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011385945.1 AMB_RS18155 3-hydroxyisobutyrate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 419.5 15.5 3.6e-130 3.6e-130 1 288 [] 6 293 .. 6 293 .. 1.00 Alignments for each domain: == domain 1 score: 419.5 bits; conditional E-value: 3.6e-130 TIGR01692 1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesv 69 fiGlGnmG+pm +nl+kagh+v +fdls +a+ + eaGa+a + a++a+ +a+vv++mlPag+hv+sv lcl|NCBI__GCF_000009985.1:WP_011385945.1 6 FIGLGNMGAPMMRNLIKAGHKVAAFDLSEAALAAAAEAGATACTKATDAARGAEVVVSMLPAGAHVKSV 74 9******************************************************************** PP TIGR01692 70 yagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaee 138 ++g+ g+ a ++k++l+idsstidv +ar +++ea+++G+ ++daPvsGGvgga+aGtltfmvGg +++ lcl|NCBI__GCF_000009985.1:WP_011385945.1 75 MLGEGGLFAAASKGTLFIDSSTIDVATARLLSDEASRAGHALIDAPVSGGVGGAEAGTLTFMVGGADDS 143 ********************************************************************* PP TIGR01692 139 faraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGr 207 faraep+l+ mgk ivhaG+ G GqaakiCnn+llgismiG++ea+al+eklGld++ l++i skssG+ lcl|NCBI__GCF_000009985.1:WP_011385945.1 144 FARAEPILAVMGKTIVHAGGPGNGQAAKICNNMLLGISMIGTCEAFALAEKLGLDAQKLFDISSKSSGQ 212 ********************************************************************* PP TIGR01692 208 cWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgag 276 +Ws+++y+PvPG+v+++Pa+++yk+Gfa+a+mlkdl+la eaa++++as++lGa a +ly+++a g g lcl|NCBI__GCF_000009985.1:WP_011385945.1 213 NWSMTSYCPVPGPVPASPANRDYKAGFAAAMMLKDLKLAVEAAQTAGASIPLGAEAAQLYAMMAGMGQG 281 ********************************************************************* PP TIGR01692 277 kkdfsavikllr 288 ++dfs++i++lr lcl|NCBI__GCF_000009985.1:WP_011385945.1 282 GLDFSGIIHMLR 293 *********998 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: 7.86 // [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