Align tartronate semialdehyde reductase 2 (characterized)
to candidate H281DRAFT_05314 H281DRAFT_05314 2-hydroxy-3-oxopropionate reductase
Query= ecocyc::G6278-MONOMER (292 letters) >FitnessBrowser__Burk376:H281DRAFT_05314 Length = 297 Score = 380 bits (975), Expect = e-110 Identities = 188/290 (64%), Positives = 227/290 (78%) Query: 2 KLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVADELLSLGAVSVETARQVTEASDIIFI 61 K GFIGLGIMG PMA NL + G L T V D+L GA + ++ V +D+IFI Sbjct: 3 KAGFIGLGIMGKPMAANLLKNGVTLAAFTRSAVPDDLTQAGAQACDSPAAVAAQADVIFI 62 Query: 62 MVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVSG 121 MVPDTP VE VLFGENG G+T+VDMSSISP+ T+ FA +V E G DYLDAPVSG Sbjct: 63 MVPDTPDVERVLFGENGLASGLRAGQTVVDMSSISPMATRDFAARVRETGADYLDAPVSG 122 Query: 122 GEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNIE 181 GE+GA+ G+L+IMVGG++A F+ VKPLF+++GKN+TL+G G GQ CKVANQ+IVA IE Sbjct: 123 GEVGAKAGSLTIMVGGEQATFDSVKPLFDMMGKNVTLIGAVGAGQVCKVANQVIVAATIE 182 Query: 182 AVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLNL 241 AV EALL ASKAG DP RVR+ALMGGFASSRILEVHGERM KRTF+PGF+I LHQKDLNL Sbjct: 183 AVGEALLLASKAGVDPARVREALMGGFASSRILEVHGERMTKRTFDPGFRIELHQKDLNL 242 Query: 242 ALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKL 291 ALQ+A+ L ++LPNTATCQ LFN C A+GG DHSA+V+ALE++ANH++ Sbjct: 243 ALQTAQTLGVSLPNTATCQALFNACVAHGGKAWDHSAMVRALEVLANHEI 292 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: 322 Number of extensions: 6 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: 297 Length adjustment: 26 Effective length of query: 266 Effective length of database: 271 Effective search space: 72086 Effective search space used: 72086 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 H281DRAFT_05314 H281DRAFT_05314 (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.9606.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-128 414.4 7.4 1.4e-128 414.2 7.4 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_05314 H281DRAFT_05314 2-hydroxy-3-oxop Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_05314 H281DRAFT_05314 2-hydroxy-3-oxopropionate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 414.2 7.4 1.4e-128 1.4e-128 1 291 [] 3 292 .. 3 292 .. 0.99 Alignments for each domain: == domain 1 score: 414.2 bits; conditional E-value: 1.4e-128 TIGR01505 1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPds 66 k gfiGlGimGkPm+ nllk G l ++t+ + d+l aGa++ ++ ++v+ +advi++mvPd+ lcl|FitnessBrowser__Burk376:H281DRAFT_05314 3 KAGFIGLGIMGKPMAANLLKNGVTLAAFTRS-AVPDDLTQAGAQACDSPAAVAAQADVIFIMVPDT 67 789***************************9.999******************************* PP TIGR01505 67 PqveevalGenGileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtls 132 P+ve v++GenG+ + + G+++vdmssi+P++++++a v+e G d+ldaPvsGGe+ga+ g l+ lcl|FitnessBrowser__Burk376:H281DRAFT_05314 68 PDVERVLFGENGLASGLRAGQTVVDMSSISPMATRDFAARVRETGADYLDAPVSGGEVGAKAGSLT 133 ****************************************************************** PP TIGR01505 133 imvGGdkavfdkvkpllealgksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpk 198 imvGG++a fd vkpl++++gk+++l+G GaGq++kvanqviva ieav eal+la+kaGvdp lcl|FitnessBrowser__Burk376:H281DRAFT_05314 134 IMVGGEQATFDSVKPLFDMMGKNVTLIGAVGAGQVCKVANQVIVAATIEAVGEALLLASKAGVDPA 199 ****************************************************************** PP TIGR01505 199 avlqalrGGlagstvleakkerlldrdfkPGfridlhqkdlalaldaakavgaalPvtavvaella 264 +v++al+GG+a+s++le+++er+ +r+f+PGfri+lhqkdl+lal++a+++g++lP+ta+++ l++ lcl|FitnessBrowser__Burk376:H281DRAFT_05314 200 RVREALMGGFASSRILEVHGERMTKRTFDPGFRIELHQKDLNLALQTAQTLGVSLPNTATCQALFN 265 ****************************************************************** PP TIGR01505 265 alradGdgtldhsalvraleklakdkv 291 a+ a+G+ dhsa+vrale la++++ lcl|FitnessBrowser__Burk376:H281DRAFT_05314 266 ACVAHGGKAWDHSAMVRALEVLANHEI 292 ************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (291 nodes) Target sequences: 1 (297 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: 00:00:00.00 # Mc/sec: 11.34 // [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