Align alanine-glyoxylate transaminase (EC 2.6.1.44); serine-glyoxylate transaminase (EC 2.6.1.45) (characterized)
to candidate 3609943 Dshi_3325 aminotransferase class V (RefSeq)
Query= BRENDA::Q56YA5 (401 letters) >FitnessBrowser__Dino:3609943 Length = 422 Score = 337 bits (865), Expect = 3e-97 Identities = 175/392 (44%), Positives = 242/392 (61%), Gaps = 3/392 (0%) Query: 2 DYMYGPGRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGT 61 D M GRH L +PGP +P+ ++RA++ D+R P + + L+ +K IF+T Sbjct: 26 DPMRKAGRHFLQIPGPSAVPDRILRAISMQTIDHRGPDFADVGQKALKGMKTIFRTDQNV 85 Query: 62 PFLFPTTGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGA 121 F+FP++GTGAWE+AL NT+SPGD ++ + G F+ LW K++ N +E DW GA Sbjct: 86 -FIFPSSGTGAWEAALVNTMSPGDTVLMYETGHFATLWQKMAKKIGLNPVFIEGDWRGGA 144 Query: 122 NLQVLASKLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSIC 181 + Q + L +D +H IKA+C+VHNET+TG + I+ VR +D HPALL+VD +S + Sbjct: 145 DPQAIEDALRKDTDHEIKAVCVVHNETSTGSVSPIAEVRAAMDATGHPALLMVDSISGLA 204 Query: 182 ALDFRMDEWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFY 241 ++ F D WGVDV ++GSQK L LP GL S KALE K++K + ++DW D + Sbjct: 205 SVPFEFDAWGVDVCVSGSQKGLMLPPGLSFNAVSDKALEVAKSAKMQRSYWDWLDMVGPN 264 Query: 242 KLGTYWPYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKE 301 G Y+PYTP LLYGL A+D++ EEGLEN+ RH R G ATR AV AWGL+ ++ Sbjct: 265 ATG-YFPYTPGTNLLYGLNEAVDMLHEEGLENVFERHRRHGAATRAAVRAWGLEVLCARQ 323 Query: 302 EWISNTVTAVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLG 361 S +TAVM+P Y++SLG GL+KVA KVFRIGHLG+ N+L L+ Sbjct: 324 GQESGVLTAVMMPEGHSADAFRATTLAHYDISLGNGLSKVADKVFRIGHLGDFNDLMLMA 383 Query: 362 CLAGVEMILKDVGYPVVMGSGVAAASTYLQHH 393 L+GVEM L G P G GV AA +L+ H Sbjct: 384 TLSGVEMGLAKAGVPHESG-GVQAAMDHLKTH 414 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: 442 Number of extensions: 13 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: 401 Length of database: 422 Length adjustment: 31 Effective length of query: 370 Effective length of database: 391 Effective search space: 144670 Effective search space used: 144670 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 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