Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_013450502.1 CALNI_RS01845 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::A2V838 (392 letters) >NCBI__GCF_000183405.1:WP_013450502.1 Length = 383 Score = 162 bits (409), Expect = 2e-44 Identities = 112/344 (32%), Positives = 178/344 (51%), Gaps = 13/344 (3%) Query: 25 LLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHC 84 LL PGP+ +P +++ + MI + + I E++EG++ +F TR + L+++GSG Sbjct: 6 LLSPGPTPVPEKVLLDMAMPMIHHRTSEFSNIFKEVREGLKPIFGTRQDV-LILAGSGTA 64 Query: 85 ALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLA 144 A+EAA+VN L GD LV G +G+R V+I G V + + G +VE L Sbjct: 65 AMEAAVVNTLNEGDKVLVVNAGKFGKRWVEIATTYGLDVITIDIEWGRSVKPDQVESKLI 124 Query: 145 QHKPVLLFLTHG-ESSTGVLQPLDGFGELCH-RYKCLLLVDSVASLGGTPLYMDRQGIDI 202 H + L E+ST P++ G++ R + LL+VD + S+G MD GIDI Sbjct: 125 AHPEIKAVLVQASETSTTAYHPIEEIGKIVSLRDETLLIVDGITSVGVYETKMDEWGIDI 184 Query: 203 LYSGSQKALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFKGCDDQPRMYHH 262 L +GSQKA PPG +LI+ S+KA K ++ K++ FYL++K K Q Sbjct: 185 LITGSQKAFMLPPGLALIALSEKAWK--FTEKSRIPKFYLNLK-----KERKSQLENTTS 237 Query: 263 TIPVISL-YSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTV 321 P +SL L+ L ++ ++GL N +++H A L A+G +L KD + + Sbjct: 238 WTPAVSLIIGLKSVLEIMNKEGLPNVYKRHALCAEATRKGLMAMGFELLAKD--IPSNSA 295 Query: 322 TTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIGLLG 365 T + +P G+D V + + + GG GK+LR+ LG Sbjct: 296 TGIVLPEGFDGGKFVKLMREKAGLTFAGGQDHLKGKILRVSHLG 339 Lambda K H 0.320 0.138 0.418 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: 332 Number of extensions: 20 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: 392 Length of database: 383 Length adjustment: 30 Effective length of query: 362 Effective length of database: 353 Effective search space: 127786 Effective search space used: 127786 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 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