Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_013460298.1 SULKU_RS07245 threonine ammonia-lyase
Query= BRENDA::Q2PGG3 (331 letters) >NCBI__GCF_000183725.1:WP_013460298.1 Length = 403 Score = 216 bits (551), Expect = 6e-61 Identities = 123/314 (39%), Positives = 191/314 (60%), Gaps = 11/314 (3%) Query: 11 DILSIKEAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACNAVLSL 70 D+ +I EAH+RIK I TP + L+ SG +++ K E LQ GAFK RGA N + SL Sbjct: 3 DLKTIYEAHERIKNVITETPFAHAPRLSQESGCNVYLKKENLQVTGAFKIRGAYNKIASL 62 Query: 71 DAEQAAKGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKVIWSEA 130 E+ ++GV+ S+GNHA +++AA+I G A IV+P+ P K++ V YG +VI + + Sbjct: 63 SDEERSRGVIAASAGNHAQGVAMAAQIFGTRALIVMPESTPLTKINGVSYYGAEVILAGS 122 Query: 131 TMSSREEIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQEIDAIVVPISGGGLI 190 A++ +E G V +HP+ D +++GQGTIA+E++E + ++DAIV+P+ GGGLI Sbjct: 123 NYDEAYAYAARYGEEHGMVFVHPFADEAVMAGQGTIAIEMIESMNDMDAIVIPVGGGGLI 182 Query: 191 SGVALAAKSIKPSIRIIAAEPKGADDAAQSKVAGKIITLPVTNTIADGLRA-SLGDLTWP 249 SG+A A K++ P IR++ GA +S A + I TIADG+ +T Sbjct: 183 SGMASAIKALAPHIRVVGVGAVGAPAMRESYDAKQAIDSTSVRTIADGIAVRDTSPITLS 242 Query: 250 VVRDLVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNS---FRNNPSCRDC 306 + + VD+ V++++ EI A+ E K+ VE +GA+G+AA+L + FRN Sbjct: 243 HILETVDEFVSVDDEEIANAILFLLEKQKLVVEGAGAVGVAALLHHKLDHFRN------- 295 Query: 307 KNIGIVLSGGNVDL 320 K +G+VLSGGN+D+ Sbjct: 296 KKVGVVLSGGNMDV 309 Lambda K H 0.316 0.133 0.380 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: 294 Number of extensions: 15 Number of successful extensions: 3 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: 331 Length of database: 403 Length adjustment: 30 Effective length of query: 301 Effective length of database: 373 Effective search space: 112273 Effective search space used: 112273 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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