Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_068460068.1 APY04_RS04325 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_001541235.1:WP_068460068.1 Length = 397 Score = 255 bits (652), Expect = 1e-72 Identities = 151/383 (39%), Positives = 217/383 (56%), Gaps = 5/383 (1%) Query: 4 KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSG 63 + L IPGPTPVPE+V AMA+ + HR F + +L A++K + +T+ V++ +SG Sbjct: 7 RHFLQIPGPTPVPERVHNAMARSMMDHRGPAFCEFGQKLFADVKGIFKTQQPVIIFPSSG 66 Query: 64 TGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTL 123 TG+ EA++ N LSPGD VLV G+F W K+A+ GL E I +W D N + Sbjct: 67 TGSWEAALTNTLSPGDHVLVMETGQFAVLWTKMAERMGLKPEVIANDWRSGADANALEAR 126 Query: 124 LEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHG-GALMIVDAVTSLGATPVAIDD 182 L ADS + IKA+ + +ETSTG + I A A G AL++VD ++SL A D+ Sbjct: 127 LRADSSQQIKAVCVVQNETSTGARTHIDEIRKAMDAAGHSALLMVDTISSLAAMDYRHDE 186 Query: 183 LGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSPFT 242 G+D+ SGSQKG M+PPGL F +VS KA A + AT+ R Y + P+T Sbjct: 187 WGVDITISGSQKGLMLPPGLSFTAVSQKALAASKKATLARAYFSWDDMLAINGSGTFPYT 246 Query: 243 PPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPD-NAASNAITA 301 PPI L++GL ++ M+ EGL +F RH+R ATR A+KA L ++ D A S +TA Sbjct: 247 PPIGLLFGLAETITMLNEEGLSNVFARHERLAEATRRAVKAWGLEVWCQDARAYSPVVTA 306 Query: 302 V-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATL 360 V P G ++ R + + F++++ G L GK FRI HLG+ + I+ + +E L Sbjct: 307 VEMPEGHNSDAFRKIVLENFNMSLGTGLSKLAGKAFRIAHLGYTNELTIMGALAGVEMGL 366 Query: 361 IELGYEGVTPGSGVAAAAGVLAK 383 EL G GV+AA LA+ Sbjct: 367 -ELARVPHNKG-GVSAAMAYLAQ 387 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: 340 Number of extensions: 14 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: 384 Length of database: 397 Length adjustment: 31 Effective length of query: 353 Effective length of database: 366 Effective search space: 129198 Effective search space used: 129198 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 10 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