Align tartronate semialdehyde reductase 2 (characterized)
to candidate AO353_01930 AO353_01930 2-hydroxy-3-oxopropionate reductase
Query= ecocyc::G6278-MONOMER (292 letters) >FitnessBrowser__pseudo3_N2E3:AO353_01930 Length = 296 Score = 374 bits (959), Expect = e-108 Identities = 189/291 (64%), Positives = 231/291 (79%), Gaps = 1/291 (0%) Query: 2 KLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVAD-ELLSLGAVSVETARQVTEASDIIF 60 K+GFIG GIMG PMA+NL +AGH L ++ A +LL+ GAV++ + ++V + ++ I Sbjct: 3 KIGFIGTGIMGHPMALNLQKAGHSLFLSAHHDAAPADLLAAGAVALASPKEVAQEAEFII 62 Query: 61 IMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVS 120 IMVPDTPQV++VLF +G KGK ++DMSSISP TK FA ++NE G YLDAPVS Sbjct: 63 IMVPDTPQVDDVLFRADGVAAGVGKGKVVIDMSSISPTATKAFAAKINEKGAQYLDAPVS 122 Query: 121 GGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNI 180 GGE+GA+ TLSIMVGGD FER PLF+ +GKNITLVGGNGDGQT KVANQIIVALNI Sbjct: 123 GGEVGAKAATLSIMVGGDSDAFERALPLFQSMGKNITLVGGNGDGQTAKVANQIIVALNI 182 Query: 181 EAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLN 240 +AV+EALLFASK GADP +VR+ALMGGFASS+ILEVHGERMIK TF+PGF+I+LHQKDLN Sbjct: 183 QAVAEALLFASKNGADPAKVREALMGGFASSKILEVHGERMIKGTFDPGFRISLHQKDLN 242 Query: 241 LALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKL 291 LAL A+ L +NLPNTA Q++F+TCAA GGS DHSAL++ LE MAN + Sbjct: 243 LALAGARELGINLPNTAGTQQVFSTCAALGGSNWDHSALIKGLEHMANFSI 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: 327 Number of extensions: 6 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 AO353_01930 AO353_01930 (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.30412.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-124 398.7 8.6 8e-124 398.5 8.6 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_01930 AO353_01930 2-hydroxy-3-oxopropi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_01930 AO353_01930 2-hydroxy-3-oxopropionate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 398.5 8.6 8e-124 8e-124 1 289 [. 3 291 .. 3 293 .. 0.99 Alignments for each domain: == domain 1 score: 398.5 bits; conditional E-value: 8e-124 TIGR01505 1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPd 65 k+gfiG GimG+Pm+ nl kaG++l ++ a ++llaaGa++ + kev+++a+ i++mvPd lcl|FitnessBrowser__pseudo3_N2E3:AO353_01930 3 KIGFIGTGIMGHPMALNLQKAGHSLFLSAHHDAAPADLLAAGAVALASPKEVAQEAEFIIIMVPD 67 89*****************************9********************************* PP TIGR01505 66 sPqveevalGenGileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegt 130 +Pqv++v++ +G+ + kGkv++dmssi+P ++k +a +++ekG ++ldaPvsGGe+ga+ +t lcl|FitnessBrowser__pseudo3_N2E3:AO353_01930 68 TPQVDDVLFRADGVAAGVGKGKVVIDMSSISPTATKAFAAKINEKGAQYLDAPVSGGEVGAKAAT 132 ***************************************************************** PP TIGR01505 131 lsimvGGdkavfdkvkpllealgksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGv 195 lsimvGGd f+++ pl++ +gk+i+lvG+nG+Gqt+kvanq+ivalni+av+eal++a+k G+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_01930 133 LSIMVGGDSDAFERALPLFQSMGKNITLVGGNGDGQTAKVANQIIVALNIQAVAEALLFASKNGA 197 ***************************************************************** PP TIGR01505 196 dpkavlqalrGGlagstvleakkerlldrdfkPGfridlhqkdlalaldaakavgaalPvtavva 260 dp +v++al+GG+a+s++le+++er+++ +f+PGfri lhqkdl+lal a+++g++lP+ta + lcl|FitnessBrowser__pseudo3_N2E3:AO353_01930 198 DPAKVREALMGGFASSKILEVHGERMIKGTFDPGFRISLHQKDLNLALAGARELGINLPNTAGTQ 262 ***************************************************************** PP TIGR01505 261 ellaalradGdgtldhsalvraleklakd 289 +++++++a G+++ dhsal++ le++a+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_01930 263 QVFSTCAALGGSNWDHSALIKGLEHMANF 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.60 // [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