Align asparagine-oxo-acid transaminase (EC 2.6.1.14); alanine-glyoxylate transaminase (EC 2.6.1.44); serine-glyoxylate transaminase (EC 2.6.1.45) (characterized)
to candidate 3607474 Dshi_0887 Serine--glyoxylate transaminase (RefSeq)
Query= BRENDA::Q56YA5 (401 letters) >FitnessBrowser__Dino:3607474 Length = 396 Score = 363 bits (932), Expect = e-105 Identities = 176/378 (46%), Positives = 250/378 (66%), Gaps = 1/378 (0%) Query: 12 LFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPTTGTG 71 +F+PGP N+P+ + R M+ D+RSPA A+ L + V+K+F T FP +GTG Sbjct: 7 IFIPGPTNVPDRLRRVMDMQTRDHRSPAFGAMLPELFDGVRKVFNTKDAAIITFPASGTG 66 Query: 72 AWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLASKLS 131 WE+A++NTLSPGD ++ G FS WID +R NV+++E WG GA + A +L Sbjct: 67 GWEAAVSNTLSPGDTVLIARYGMFSHRWIDLCQRHGLNVEIIECAWGSGAPADLFAERLK 126 Query: 132 QDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRMDEWG 191 D+ H IKA+ + HNETATGV +DI AVR +D HPA+L+VD VSS+ ++ F D WG Sbjct: 127 ADKGHEIKAVLVTHNETATGVRSDIGAVRRGMDSADHPAMLMVDCVSSLASMPFDFDGWG 186 Query: 192 VDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYWPYTP 251 VDVA+TGSQK L TG+ IV S KALE KT+K + FF ++D L G Y PYTP Sbjct: 187 VDVAITGSQKGFMLFTGMCIVAVSQKALEHRKTAKLPRTFFSFDDMLAANGAGGY-PYTP 245 Query: 252 SIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKEEWISNTVTAV 311 IQL++GL+ +L ++FEEGLEN+ ARH RL + R AV+AWGL+ C + + S+TV+A+ Sbjct: 246 PIQLMFGLQESLKMLFEEGLENVYARHFRLAEGVRRAVDAWGLRLCAESADLYSDTVSAI 305 Query: 312 MVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGVEMILK 371 VP D + + + A+ Y++S G+GL ++ G+ FRIGHLG + ++ +L LA +EM + Sbjct: 306 YVPKGFDSNALTQHAYDAYDISFGVGLGEMNGRAFRIGHLGALTDVTMLSGLATIEMAMA 365 Query: 372 DVGYPVVMGSGVAAASTY 389 D+ YP+ +GSGVAAA + Sbjct: 366 DLDYPIELGSGVAAAQQF 383 Lambda K H 0.320 0.137 0.419 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: 379 Number of extensions: 13 Number of successful extensions: 2 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: 401 Length of database: 396 Length adjustment: 31 Effective length of query: 370 Effective length of database: 365 Effective search space: 135050 Effective search space used: 135050 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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