Align Alanine--glyoxylate aminotransferase; EC 2.6.1.44 (characterized)
to candidate WP_011321708.1 AVA_RS25680 alanine--glyoxylate aminotransferase family protein
Query= SwissProt::Q3LSM4 (393 letters) >NCBI__GCF_000204075.1:WP_011321708.1 Length = 381 Score = 339 bits (870), Expect = 7e-98 Identities = 169/368 (45%), Positives = 241/368 (65%), Gaps = 3/368 (0%) Query: 13 EPLVTPNKLLMGPGPSNAPQRVLDAMSRPILGHLHPETLKIMDDIKEGVRYLFQTNNIAT 72 EPL P++LL+GPGPSNA VL AM+ +GHL P L +MD+I+ +RY++QT N T Sbjct: 16 EPLEVPSRLLLGPGPSNAHPAVLQAMNVSPVGHLDPAFLALMDEIQSLLRYVWQTENPLT 75 Query: 73 FCLSASGHGGMEATLCNLLEDGDVILIGHTGHWGDRSADMATRYGADVRVVKSKVGQSLS 132 +S +G MEAT+ N +E GDV+LIG G++G+R DMA RYGADVR + GQ S Sbjct: 76 IAVSGTGTAAMEATIANAVEPGDVVLIGVAGYFGNRLVDMAGRYGADVRTISKPWGQVFS 135 Query: 133 LDEIRDALLIHKPSVLFLTQGDSSTGVLQGLEGVGALCHQHNCLLIVDTVASLGGAPMFM 192 L+E+R AL ++P++L L ++STG Q LEGVG LC + LL+VDTV SLGG P+F+ Sbjct: 136 LEELRTALENNRPAILALVHAETSTGARQPLEGVGELCREFGTLLLVDTVTSLGGVPIFL 195 Query: 193 DRWEIDAMYTGSQKVLGAPPGITPVSFSHRAVERYKRRNTKVKVYYWDMSLVGDYWGCFG 252 D W +D Y+ SQK LG PG +P + S RA+E+ +RR TKV +Y DM+L+G YW G Sbjct: 196 DGWGVDLAYSCSQKGLGCSPGASPFTMSSRAIEKLQRRRTKVANWYLDMNLLGKYW---G 252 Query: 253 RPRIYHHTISSTLLYGLREAIAMACEEGLPALIARHEDCAKRLYRGLQDAGFELYADPKD 312 R+YHHT L Y LREA+ + +EGL RH+ + L+ L+D G L+ + + Sbjct: 253 SERVYHHTAPINLYYALREALRLIAQEGLANCWQRHQKNVEYLWERLEDIGLSLHVEKEY 312 Query: 313 RLSTVTTIKVPQGVDWLKAAQYAMKTYLVEISGGLGPTAGQVFRIGLMGQNATTERVDRV 372 RL T+TT+++P GVD A+ + + +E+ GGLG AG+V+R+GLMG N+ E VD++ Sbjct: 313 RLPTLTTVRIPDGVDGKAVARQLLNEHNIEVGGGLGELAGKVWRVGLMGFNSRKESVDQL 372 Query: 373 LQVFQEAV 380 + ++ + Sbjct: 373 IPALEQVL 380 Lambda K H 0.321 0.137 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: 385 Number of extensions: 20 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: 393 Length of database: 381 Length adjustment: 30 Effective length of query: 363 Effective length of database: 351 Effective search space: 127413 Effective search space used: 127413 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