Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_089323238.1 CHB58_RS06165 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_900188395.1:WP_089323238.1 Length = 392 Score = 281 bits (720), Expect = 2e-80 Identities = 151/377 (40%), Positives = 225/377 (59%), Gaps = 7/377 (1%) Query: 4 KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSG 63 K+ LM PGPTPVPE+VL AMA H + HRS F +I AE LK L +TE D L+LT+SG Sbjct: 5 KERLMTPGPTPVPERVLQAMASHTMYHRSPKFKEIFAETIERLKRLFKTERDTLILTSSG 64 Query: 64 TGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTL 123 TGAMEA++ N SPGD +V GKFG RW ++ +TFG+ I+ EWGK+++P D K Sbjct: 65 TGAMEAAVSNLFSPGDSAVVIVGGKFGQRWKELCETFGVNPVVIELEWGKSVNPEDVKKK 124 Query: 124 LEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAIDDL 183 +E ++ IK +++ ETSTG ND+ A+ + +++ D +T+ G + +DD Sbjct: 125 IE--ENRNIKGVLVQICETSTGAFNDVKALGEITARYDNVILVADGITAFGVYDIPVDDW 182 Query: 184 GLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSPFTP 243 +DV +GSQK M PPGL +S+S KA ++ + +Y DL K K+ + + +TP Sbjct: 183 NIDVAITGSQKALMTPPGLAVISLSEKA-KSRLSRKKWAYYFDLSKEIKNQAKGQTAYTP 241 Query: 244 PINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNAITAVA 303 +NL+ GL +L+M++ EGL+ + RH+ + R +KAL L L P++ A+ Sbjct: 242 AVNLIVGLNEALKMIEEEGLENVAKRHEILAKSARAGIKALELELL-PEHPANGVTAVKL 300 Query: 304 PLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATLIEL 363 P ++ +K S +R + I +AGGQ+HLKGKIFR+ H+G++ DI + LEA L Sbjct: 301 PEHIDGQKFVSWIRDRLGIVIAGGQEHLKGKIFRLSHMGYI---DIFDLLTQLEAVEFAL 357 Query: 364 GYEGVTPGSGVAAAAGV 380 + P G A AA + Sbjct: 358 TRMEMYPAYGKAVAAAM 374 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: 346 Number of extensions: 11 Number of successful extensions: 4 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: 392 Length adjustment: 30 Effective length of query: 354 Effective length of database: 362 Effective search space: 128148 Effective search space used: 128148 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