Align Alanine--glyoxylate aminotransferase; AGT; Serine--pyruvate aminotransferase, mitochondrial; SPT; EC 2.6.1.44; EC 2.6.1.51 (characterized)
to candidate WP_077278474.1 B1C78_RS07145 alanine--glyoxylate aminotransferase family protein
Query= SwissProt::P09139 (414 letters) >NCBI__GCF_002000365.1:WP_077278474.1 Length = 393 Score = 285 bits (728), Expect = 2e-81 Identities = 157/365 (43%), Positives = 212/365 (58%), Gaps = 3/365 (0%) Query: 43 PKRLLLGPGPSNLAPRVLAAGSLRMIGHMQKEMFQIMDEIKQGIQYVFQTRNPLTLVVSG 102 P R L+GPGPS++ PRVLAA S IGH+ +MDE+K +QY FQT+N LTL VS Sbjct: 9 PVRTLMGPGPSDVNPRVLAAMSRPTIGHLDPVFVDMMDEMKALLQYAFQTKNELTLPVSA 68 Query: 103 SGHCAMETALFNLLEPGDSFLVGTNGIWGIRAAEIAERIGARVHQMIKKPGEHYTLQEVE 162 G ME NL++PGD+ +V NG++G+R E ER GA + G Q++E Sbjct: 69 PGSAGMEMCFVNLVQPGDTVIVCINGVFGMRMKENVERCGATAVVVEDTWGHPVDPQKLE 128 Query: 163 EGLAQHKPV-LLFLTHGESSTGVLQPLDGFGELCHRYQCLLLVDSVASLGGVPIYMDQQG 221 + L H + H E+STG E+ HR+ CL++VDSV LGGV + +D G Sbjct: 129 DALKAHPEANTVAFVHAETSTGACSDAKTLTEIAHRHDCLVIVDSVTGLGGVELRVDDWG 188 Query: 222 IDILYSGSQKVLNAPPGISLISFNDKAKSKVYSRKTKPVSFYTDITYLSKLWGCEGKTRV 281 ID +YSGSQK L+ PG+S +SFND A +++ +R+ K S++ D+T + WG G R Sbjct: 189 IDAIYSGSQKCLSCTPGLSPVSFNDAAVARIKAREHKVQSWFLDLTLVMGYWG-SGTKRA 247 Query: 282 IHHTLPVISLYCLRESLALISEQGLENSWRRHREATAHLHKCLRELGLKFFVKDPEIRLP 341 HHT P+ +LY L ESL ++ E+GLENSW RHR L L LGL+ V + RLP Sbjct: 248 YHHTAPINALYALHESLVILQEEGLENSWARHRAHHEALRAGLESLGLELIV-PRDHRLP 306 Query: 342 TITTVTVPAGYNWRDIVSYVLDHFNIEISGGLGPSEDKVLRIGLLGYNATTENADRVAEA 401 + V VP G + + +LD F++EI GLGP KV RIGL+GY A N A Sbjct: 307 QLNAVRVPDGIDEAAVRKMLLDDFSLEIGAGLGPLAGKVWRIGLMGYGANRRNVLLCLSA 366 Query: 402 LREAL 406 L A+ Sbjct: 367 LESAM 371 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: 407 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 414 Length of database: 393 Length adjustment: 31 Effective length of query: 383 Effective length of database: 362 Effective search space: 138646 Effective search space used: 138646 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