Align tartronate semialdehyde reductase 2 (characterized)
to candidate GFF1146 Psest_1179 2-hydroxy-3-oxopropionate reductase
Query= ecocyc::G6278-MONOMER (292 letters) >FitnessBrowser__psRCH2:GFF1146 Length = 296 Score = 362 bits (929), Expect = e-105 Identities = 183/291 (62%), Positives = 224/291 (76%), Gaps = 1/291 (0%) Query: 2 KLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVADE-LLSLGAVSVETARQVTEASDIIF 60 K+GFIG GIMG PMA NL +AGH + ++T A L+ GAV++ ++V + ++ I Sbjct: 3 KIGFIGTGIMGLPMAQNLQKAGHDIFLSTHHDAAPAALIEAGAVALANPKEVAQEAEFII 62 Query: 61 IMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVS 120 +MVPDTP VE+VLF ENG + K ++DMSSISP TK FA ++N G YLDAPVS Sbjct: 63 VMVPDTPHVEDVLFRENGIAEGVGPNKLVIDMSSISPSATKTFAEKINATGAQYLDAPVS 122 Query: 121 GGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNI 180 GGE+GA+ TLSIMVGG E F R PLF+ +GKNITLVGGNGDGQT KVANQIIVALNI Sbjct: 123 GGEVGAKAATLSIMVGGSEESFARALPLFQAMGKNITLVGGNGDGQTAKVANQIIVALNI 182 Query: 181 EAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLN 240 +AV+EALLFA++ GADP +VR+ALMGGFA S+ILEVHGERMIK TF+PGF+I+LHQKDLN Sbjct: 183 QAVAEALLFAARNGADPAKVREALMGGFAGSKILEVHGERMIKGTFDPGFRISLHQKDLN 242 Query: 241 LALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKL 291 LAL A+ L LNLPNTA Q++F+TCAA GGS DHSAL++ LE MAN + Sbjct: 243 LALAGARELGLNLPNTANAQQVFSTCAAIGGSGWDHSALIKGLEHMANFSI 293 Lambda K H 0.318 0.135 0.376 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: 317 Number of extensions: 8 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: 292 Length of database: 296 Length adjustment: 26 Effective length of query: 266 Effective length of database: 270 Effective search space: 71820 Effective search space used: 71820 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 GFF1146 Psest_1179 (2-hydroxy-3-oxopropionate reductase)
to HMM TIGR01505 (2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60))
# 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/TIGR01505.hmm # target sequence database: /tmp/gapView.12441.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01505 [M=291] Accession: TIGR01505 Description: tartro_sem_red: 2-hydroxy-3-oxopropionate reductase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-122 391.9 7.1 9.8e-122 391.7 7.1 1.0 1 lcl|FitnessBrowser__psRCH2:GFF1146 Psest_1179 2-hydroxy-3-oxopropio Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1146 Psest_1179 2-hydroxy-3-oxopropionate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 391.7 7.1 9.8e-122 9.8e-122 1 289 [. 3 291 .. 3 293 .. 0.99 Alignments for each domain: == domain 1 score: 391.7 bits; conditional E-value: 9.8e-122 TIGR01505 1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqveevalG 75 k+gfiG GimG Pm++nl kaG+++ t ++ a + l+ aGa++ kev+++a+ i++mvPd+P+ve+v++ lcl|FitnessBrowser__psRCH2:GFF1146 3 KIGFIGTGIMGLPMAQNLQKAGHDIFLSTHHDAAPAALIEAGAVALANPKEVAQEAEFIIVMVPDTPHVEDVLFR 77 89************************************************************************* PP TIGR01505 76 enGileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdkavfdkvkplle 150 enGi e+ + k+++dmssi+P ++k +a+++++ G ++ldaPvsGGe+ga+ +tlsimvGG + f ++ pl++ lcl|FitnessBrowser__psRCH2:GFF1146 78 ENGIAEGVGPNKLVIDMSSISPSATKTFAEKINATGAQYLDAPVSGGEVGAKAATLSIMVGGSEESFARALPLFQ 152 *************************************************************************** PP TIGR01505 151 algksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlagstvleakkerlldrd 225 a+gk+i+lvG+nG+Gqt+kvanq+ivalni+av+eal++a + G+dp +v++al+GG+ags++le+++er+++ + lcl|FitnessBrowser__psRCH2:GFF1146 153 AMGKNITLVGGNGDGQTAKVANQIIVALNIQAVAEALLFAARNGADPAKVREALMGGFAGSKILEVHGERMIKGT 227 *************************************************************************** PP TIGR01505 226 fkPGfridlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhsalvraleklakd 289 f+PGfri lhqkdl+lal a+++g++lP+ta ++++++++a G+++ dhsal++ le++a+ lcl|FitnessBrowser__psRCH2:GFF1146 228 FDPGFRISLHQKDLNLALAGARELGLNLPNTANAQQVFSTCAAIGGSGWDHSALIKGLEHMANF 291 **************************************************************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (291 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 7.43 // [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