Align Alanine--glyoxylate aminotransferase; AGT; Serine--pyruvate aminotransferase, mitochondrial; SPT; EC 2.6.1.44; EC 2.6.1.51 (characterized)
to candidate 7023122 Shewana3_0360 alanine-glyoxylate aminotransferase (RefSeq)
Query= SwissProt::P09139 (414 letters) >FitnessBrowser__ANA3:7023122 Length = 377 Score = 271 bits (694), Expect = 2e-77 Identities = 150/365 (41%), Positives = 211/365 (57%), Gaps = 2/365 (0%) Query: 43 PKRLLLGPGPSNLAPRVLAAGSLRMIGHMQKEMFQIMDEIKQGIQYVFQTRNPLTLVVSG 102 P+R+L+GPGPS++ P VLAA + +GH+ +MDE+K IQY FQT+N +T+ VS Sbjct: 13 PRRILMGPGPSDVYPEVLAAQARPTVGHLDPLFVGMMDELKSLIQYAFQTKNEMTMAVSA 72 Query: 103 SGHCAMETALFNLLEPGDSFLVGTNGIWGIRAAEIAERIGARVHQMIKKPGEHYTLQEVE 162 G MET NL+EPG+ +V NG++G R + ER+GA + + G VE Sbjct: 73 PGSAGMETCFVNLVEPGEKVIVCRNGVFGERMRQNVERVGAIAVLVDNEWGTPVDAAAVE 132 Query: 163 EGL-AQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYQCLLLVDSVASLGGVPIYMDQQG 221 L A L H E+STG L L +Y CL +VD+V SLGGV + +D+ G Sbjct: 133 AALKANPDAKFLAFVHAETSTGALSDAKTLCALAKQYGCLSIVDAVTSLGGVELRVDEWG 192 Query: 222 IDILYSGSQKVLNAPPGISLISFNDKAKSKVYSRKTKPVSFYTDITYLSKLWGCEGKTRV 281 ID +YSGSQK L+ PG+S +SF+ A K+ +RKT S++ D + + W G R Sbjct: 193 IDAIYSGSQKCLSCVPGLSPVSFSPNAVEKLKNRKTPVQSWFLDQSLVMAYWTSAGGKRS 252 Query: 282 IHHTLPVISLYCLRESLALISEQGLENSWRRHREATAHLHKCLRELGLKFFVKDPEIRLP 341 HHT PV +LY L ESL L++E+GLEN+W+RH++ L L +LGLKF V + RLP Sbjct: 253 YHHTAPVNALYALHESLRLLAEEGLENAWKRHQDMHLVLRAGLEKLGLKFVVAEAS-RLP 311 Query: 342 TITTVTVPAGYNWRDIVSYVLDHFNIEISGGLGPSEDKVLRIGLLGYNATTENADRVAEA 401 + + +P G + + + +L +N+EI GLG K RIGL+G+ A EN A Sbjct: 312 QLNAIYIPEGVDDAAVRARLLKDYNLEIGAGLGALAGKAWRIGLMGFGARRENVALCLRA 371 Query: 402 LREAL 406 L E L Sbjct: 372 LEEVL 376 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: 365 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: 414 Length of database: 377 Length adjustment: 31 Effective length of query: 383 Effective length of database: 346 Effective search space: 132518 Effective search space used: 132518 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