Align tartronate semialdehyde reductase 2 (characterized)
to candidate RR42_RS23235 RR42_RS23235 tartronate semialdehyde reductase
Query= ecocyc::G6278-MONOMER (292 letters) >FitnessBrowser__Cup4G11:RR42_RS23235 Length = 286 Score = 387 bits (994), Expect = e-112 Identities = 194/282 (68%), Positives = 227/282 (80%) Query: 11 MGTPMAINLARAGHQLHVTTIGPVADELLSLGAVSVETARQVTEASDIIFIMVPDTPQVE 70 MGTPMA NL GH++ +++ V LL G V+ + ++V E +D+IF+MVPDTP VE Sbjct: 1 MGTPMAANLIAGGHEVSLSSRSGVPQSLLDSGGVACSSGKEVAERADVIFLMVPDTPHVE 60 Query: 71 EVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVSGGEIGAREGT 130 LF G GK +VDMSSISPI TK FA +VN LG YLDAPVSGGE+GAR T Sbjct: 61 AALFNNGGIAAGLSAGKIVVDMSSISPIATKAFAERVNALGCQYLDAPVSGGEVGARNAT 120 Query: 131 LSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNIEAVSEALLFA 190 LSIMVGG +A FE V+PLFEL+GKNITLVG NG GQT KVANQIIVALNIEAV+EALLFA Sbjct: 121 LSIMVGGPQATFETVRPLFELMGKNITLVGDNGAGQTAKVANQIIVALNIEAVAEALLFA 180 Query: 191 SKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLNLALQSAKALA 250 SKAGADP RVRQALMGGFASS++LEVHGERMIKRTF+PGF+I LHQKDLNLAL +A+ + Sbjct: 181 SKAGADPARVRQALMGGFASSKVLEVHGERMIKRTFDPGFRIGLHQKDLNLALSNAREMG 240 Query: 251 LNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKLA 292 ++LPNTATCQELFN CA++GGS DHSALV+ALELMANH++A Sbjct: 241 VSLPNTATCQELFNACASHGGSDWDHSALVRALELMANHEVA 282 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: 341 Number of extensions: 7 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: 292 Length of database: 286 Length adjustment: 26 Effective length of query: 266 Effective length of database: 260 Effective search space: 69160 Effective search space used: 69160 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 RR42_RS23235 RR42_RS23235 (tartronate semialdehyde 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.31240.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-124 400.9 4.3 1.7e-124 400.8 4.3 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS23235 RR42_RS23235 tartronate semialde Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS23235 RR42_RS23235 tartronate semialdehyde reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 400.8 4.3 1.7e-124 1.7e-124 10 291 .] 1 281 [. 1 281 [. 0.99 Alignments for each domain: == domain 1 score: 400.8 bits; conditional E-value: 1.7e-124 TIGR01505 10 mGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqveevalGenG 78 mG+Pm+ nl+ G+++ ++ + + ll G+++ ++ kev+e advi+ mvPd+P+ve+ ++ + G lcl|FitnessBrowser__Cup4G11:RR42_RS23235 1 MGTPMAANLIAGGHEVSLSSRS-GVPQSLLDSGGVACSSGKEVAERADVIFLMVPDTPHVEAALFNNGG 68 9****************99998.999******************************************* PP TIGR01505 79 ileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdkavfdkvkp 147 i + Gk++vdmssi+P+++k +a+ v+++G ++ldaPvsGGe+ga+++tlsimvGG +a f+ v+p lcl|FitnessBrowser__Cup4G11:RR42_RS23235 69 IAAGLSAGKIVVDMSSISPIATKAFAERVNALGCQYLDAPVSGGEVGARNATLSIMVGGPQATFETVRP 137 ********************************************************************* PP TIGR01505 148 llealgksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlagstvlea 216 l+e++gk+i+lvG+nGaGqt+kvanq+ivalnieav+eal++a+kaG+dp +v+qal+GG+a+s+vle+ lcl|FitnessBrowser__Cup4G11:RR42_RS23235 138 LFELMGKNITLVGDNGAGQTAKVANQIIVALNIEAVAEALLFASKAGADPARVRQALMGGFASSKVLEV 206 ********************************************************************* PP TIGR01505 217 kkerlldrdfkPGfridlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhsalvralek 285 ++er+++r+f+PGfri lhqkdl+lal a+++g++lP+ta+++el++a++++G+++ dhsalvrale+ lcl|FitnessBrowser__Cup4G11:RR42_RS23235 207 HGERMIKRTFDPGFRIGLHQKDLNLALSNAREMGVSLPNTATCQELFNACASHGGSDWDHSALVRALEL 275 ********************************************************************* PP TIGR01505 286 lakdkv 291 +a+++v lcl|FitnessBrowser__Cup4G11:RR42_RS23235 276 MANHEV 281 ****97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (291 nodes) Target sequences: 1 (286 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: 6.93 // [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