Align Alanine--glyoxylate aminotransferase; AGT; Serine--pyruvate aminotransferase, mitochondrial; SPT; EC 2.6.1.44; EC 2.6.1.51 (characterized)
to candidate WP_024851959.1 N745_RS0109870 alanine--glyoxylate aminotransferase family protein
Query= SwissProt::P09139 (414 letters) >NCBI__GCF_000526715.1:WP_024851959.1 Length = 371 Score = 280 bits (715), Expect = 7e-80 Identities = 149/365 (40%), Positives = 222/365 (60%), Gaps = 3/365 (0%) Query: 43 PKRLLLGPGPSNLAPRVLAAGSLRMIGHMQKEMFQIMDEIKQGIQYVFQTRNPLTLVVSG 102 P R L+GPGPS++ PR+L+A + IGH+ +MDE+K ++Y FQT N +T+ VS Sbjct: 7 PVRTLMGPGPSDVHPRILSAMARPTIGHLDPAFVGMMDEVKAMLKYAFQTENEMTMPVSA 66 Query: 103 SGHCAMETALFNLLEPGDSFLVGTNGIWGIRAAEIAERIGARVHQMIKKPGEHYTLQEVE 162 G MET NL+EPGD +V NG++G+R E ER G ++ G+ + ++V+ Sbjct: 67 PGSAGMETCFANLVEPGDKVVVCINGVFGMRMKENVERAGGICVEVNDDWGKAVSAEKVD 126 Query: 163 EGLAQHKPV-LLFLTHGESSTGVLQPLDGFGELCHRYQCLLLVDSVASLGGVPIYMDQQG 221 E LA + +L H E+STG E+ ++ CL +VD+V SLGGV + +D+ G Sbjct: 127 ETLAANPDAKILAFVHAETSTGACSDAKTLCEIARKHDCLSIVDAVTSLGGVELRVDEWG 186 Query: 222 IDILYSGSQKVLNAPPGISLISFNDKAKSKVYSRKTKPVSFYTDITYLSKLWGCEGKTRV 281 ID +YSG+QK L+ PG+S +SF++KA KV +RKTK S++ D+ + WG +G R Sbjct: 187 IDAIYSGTQKCLSCTPGLSPVSFSEKALDKVRNRKTKVQSWFLDLNLVMGYWG-QGTKRA 245 Query: 282 IHHTLPVISLYCLRESLALISEQGLENSWRRHREATAHLHKCLRELGLKFFVKDPEIRLP 341 HHT P+ +LY L ESL ++ E+GLEN+W RH+ L L E+G+ F V D +RLP Sbjct: 246 YHHTAPINALYALHESLLMLQEEGLENAWARHKAMHDKLKVGLEEMGIGFVV-DESVRLP 304 Query: 342 TITTVTVPAGYNWRDIVSYVLDHFNIEISGGLGPSEDKVLRIGLLGYNATTENADRVAEA 401 + +V +P G + + S +L+ +N+EI GLG KV RIGL+G++A EN A Sbjct: 305 QLNSVWIPEGVDDAAVRSELLNTYNLEIGAGLGDFAGKVWRIGLMGFSAKEENVLFCVSA 364 Query: 402 LREAL 406 L++ L Sbjct: 365 LKKVL 369 Lambda K H 0.320 0.137 0.412 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: 363 Number of extensions: 14 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: 414 Length of database: 371 Length adjustment: 31 Effective length of query: 383 Effective length of database: 340 Effective search space: 130220 Effective search space used: 130220 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