Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate 7023122 Shewana3_0360 alanine-glyoxylate aminotransferase (RefSeq)
Query= BRENDA::P74281 (384 letters) >FitnessBrowser__ANA3:7023122 Length = 377 Score = 186 bits (471), Expect = 1e-51 Identities = 120/366 (32%), Positives = 195/366 (53%), Gaps = 12/366 (3%) Query: 4 KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTS- 62 +++LM PGP+ V +VL A A+ +GH F ++ EL + +++ QT+N++ M ++ Sbjct: 14 RRILMGPGPSDVYPEVLAAQARPTVGHLDPLFVGMMDELKSLIQYAFQTKNEMTMAVSAP 73 Query: 63 GTGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKT 122 G+ ME +N + PG++V+V NG FG+R + + G + EWG +D + Sbjct: 74 GSAGMETCFVNLVEPGEKVIVCRNGVFGERMRQNVERVGAIAVLVDNEWGTPVDAAAVEA 133 Query: 123 LLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAIDD 182 L+A+ D K L H+ETSTG L+D + A AK +G L IVDAVTSLG + +D+ Sbjct: 134 ALKANPDA--KFLAFVHAETSTGALSDAKTLCALAKQYG-CLSIVDAVTSLGGVELRVDE 190 Query: 183 LGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIP--RFYLD----LKKYKKSTDE 236 G+D + SGSQK PGL VS S A + + P ++LD + + + + Sbjct: 191 WGIDAIYSGSQKCLSCVPGLSPVSFSPNAVEKLKNRKTPVQSWFLDQSLVMAYWTSAGGK 250 Query: 237 DSSPFTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAAS 296 S T P+N +Y L SL+++ EGL+ + RHQ R ++ L L + + Sbjct: 251 RSYHHTAPVNALYALHESLRLLAEEGLENAWKRHQDMHLVLRAGLEKLGLKFVVAEASRL 310 Query: 297 NAITAV-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRD-ILSCIG 354 + A+ P GV+ +R+ + K +++ + G L GK +RIG +GF R+ + C+ Sbjct: 311 PQLNAIYIPEGVDDAAVRARLLKDYNLEIGAGLGALAGKAWRIGLMGFGARRENVALCLR 370 Query: 355 ALEATL 360 ALE L Sbjct: 371 ALEEVL 376 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: 316 Number of extensions: 13 Number of successful extensions: 6 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 Aug 03 2021. The underlying query database was built on Aug 03 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