Align 3-hydroxyisobutyrate dehydrogenase subunit (EC 1.1.1.31) (characterized)
to candidate PP_4666 PP_4666 3-hydroxyisobutyrate dehydrogenase
Query= metacyc::MONOMER-11664 (295 letters) >FitnessBrowser__Putida:PP_4666 Length = 295 Score = 575 bits (1483), Expect = e-169 Identities = 292/295 (98%), Positives = 293/295 (99%) Query: 1 MRIAFIGLGNMGAPMARNLIKAGHQLNLFDLNKTVLAELAELGGQISPSPKDAAANSELV 60 MRIAFIGLGNMGAPMARNLIKAGHQLNLFDLNK VLAELAELGGQISPSPKDAAANSELV Sbjct: 1 MRIAFIGLGNMGAPMARNLIKAGHQLNLFDLNKAVLAELAELGGQISPSPKDAAANSELV 60 Query: 61 ITMLPAAAHVRSVYLNDDGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPV 120 ITMLPAAAHVRSVYLN+DGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPV Sbjct: 61 ITMLPAAAHVRSVYLNEDGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPV 120 Query: 121 SGGTGGAAAGTLTFMVGASAELFASLKPVLEQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180 SGGTGGAAAGTLTFMVGAS ELFASLKPVLEQMGRNIVHCGEVGTGQIAKICNNLLLGIS Sbjct: 121 SGGTGGAAAGTLTFMVGASTELFASLKPVLEQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180 Query: 181 MIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAPASRGYTGGFGA 240 MIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAPASRGYTGGFGA Sbjct: 181 MIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAPASRGYTGGFGA 240 Query: 241 ELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYRKKD 295 ELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYRKKD Sbjct: 241 ELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYRKKD 295 Lambda K H 0.317 0.134 0.386 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: 460 Number of extensions: 10 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: 295 Length of database: 295 Length adjustment: 26 Effective length of query: 269 Effective length of database: 269 Effective search space: 72361 Effective search space used: 72361 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 (21.6 bits) S2: 48 (23.1 bits)
Align candidate PP_4666 PP_4666 (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.16049.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-136 439.1 5.0 4.1e-136 439.0 5.0 1.0 1 lcl|FitnessBrowser__Putida:PP_4666 PP_4666 3-hydroxyisobutyrate deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4666 PP_4666 3-hydroxyisobutyrate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 439.0 5.0 4.1e-136 4.1e-136 1 288 [] 5 292 .. 5 292 .. 1.00 Alignments for each domain: == domain 1 score: 439.0 bits; conditional E-value: 4.1e-136 TIGR01692 1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesvyagdeg 75 fiGlGnmG+pma+nl+kagh++++fdl+ +++ el e G q+++s+++a+++++ vitmlPa++hv+svy+ ++g lcl|FitnessBrowser__Putida:PP_4666 5 FIGLGNMGAPMARNLIKAGHQLNLFDLNKAVLAELAELGGQISPSPKDAAANSELVITMLPAAAHVRSVYLNEDG 79 9************************************************************************** PP TIGR01692 76 ilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaeefaraepvleamg 150 +la ++ +++ +d+stid+++ar v+++aaakG + daPvsGG+gga+aGtltfmvG++ e fa +pvle+mg lcl|FitnessBrowser__Putida:PP_4666 80 VLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPVSGGTGGAAAGTLTFMVGASTELFASLKPVLEQMG 154 *************************************************************************** PP TIGR01692 151 knivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGrcWsldtynPvPGvveqaP 225 +nivh+G++G+Gq akiCnnlllgismiGv+ea+alg +lG+d+kvla i++ s+GrcWs+dtynP+PG++e+aP lcl|FitnessBrowser__Putida:PP_4666 155 RNIVHCGEVGTGQIAKICNNLLLGISMIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAP 229 *************************************************************************** PP TIGR01692 226 asngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgagkkdfsavikllr 288 as+gy+gGf+++lmlkdlgla eaa++++++v lGa+a++ly++++ +g g+kdfsa+++ +r lcl|FitnessBrowser__Putida:PP_4666 230 ASRGYTGGFGAELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYR 292 ***********************************************************9887 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 8.02 // [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