Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_013554875.1 NITSA_RS09790 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000186245.1:WP_013554875.1 Length = 377 Score = 192 bits (487), Expect = 2e-53 Identities = 133/373 (35%), Positives = 203/373 (54%), Gaps = 18/373 (4%) Query: 6 MLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSGTG 65 +L PGPTPVPE V LAMA + HR+ +F I A L L T+ +V+ML +SGTG Sbjct: 2 LLFTPGPTPVPESVRLAMAGPTLHHRTPEFEAIFAVARTKLFELMVTD-EVVMLASSGTG 60 Query: 66 AMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTLLE 125 AMEA++ N ++L N GKFG R+ +A+ GL EI EW + +L Sbjct: 61 AMEAAVTNLCHR--KLLNVNAGKFGQRFGLIAQAHGLPHTEIVHEWDTPATVGEVMEILR 118 Query: 126 ADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIV-DAVTSLGATPVAIDDLG 184 +DS+ I AL I SE++ G+ + + I AA KA +M++ D +T++G ID Sbjct: 119 SDSE--IDALAIQISESAGGLRHPVEEIAAAVKAERPEVMVIADGITAVGVE--RIDTSN 174 Query: 185 LDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSPFTPP 244 +D + +GSQK M+PPGL + +S A + +Y +L K ++++ +T P Sbjct: 175 IDALIAGSQKALMLPPGLAILGLSNVAVEKIGNGR--GYYFNLASEIKKQRQNTTAYTAP 232 Query: 245 INLMYGLQASLQMMKAEG-LDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNAITAVA 303 L+ GL+A L+ ++ +G L ++ R ATR A++AL L + P A + T Sbjct: 233 TTLIIGLKAILEEIEKQGGLGKLYCDTARRAKATRFALEALGLHSY-PKTPARSMTTIDD 291 Query: 304 PLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATLIEL 363 P +A IRS ++ F + +AGGQDHLKGKIFRI +G + +++ + A+E L ++ Sbjct: 292 P---DANTIRSLLKSDFGVNVAGGQDHLKGKIFRINQMGLIEPHEMVWVVNAVELALAKM 348 Query: 364 GYEGVTPGSGVAA 376 G P G AA Sbjct: 349 GRR---PFDGTAA 358 Lambda K H 0.317 0.134 0.386 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: 312 Number of extensions: 18 Number of successful extensions: 7 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: 384 Length of database: 377 Length adjustment: 30 Effective length of query: 354 Effective length of database: 347 Effective search space: 122838 Effective search space used: 122838 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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