Align Alanine--glyoxylate aminotransferase; AGT; EC 2.6.1.44 (characterized)
to candidate WP_011384845.1 AMB_RS12385 alanine--glyoxylate aminotransferase family protein
Query= SwissProt::Q9W3Z3 (394 letters) >NCBI__GCF_000009985.1:WP_011384845.1 Length = 400 Score = 185 bits (470), Expect = 2e-51 Identities = 125/390 (32%), Positives = 202/390 (51%), Gaps = 15/390 (3%) Query: 5 PPLVLKRPLYVPSKTL--MGPGPSNCSHRVLEAMSNP-VLGHMHPECLQIMDEVKEGIKY 61 PP V+ +P + L MG GP +V AM+N ++ H+ ++++VK +Y Sbjct: 6 PPTVIPLDNILPDEPLLMMGAGPVPIPPKV--AMANSLIINHLGDTMNAVIEQVKTMGRY 63 Query: 62 IFQTLNDATMCISGAGHSGMEAALCNLIEDGDVVLMGITGVWGHRAGDMARRYGAEVHYV 121 +FQT + M ++G + ME A+ NL+E G VL G++ R +MA R G +V + Sbjct: 64 VFQTNSPHVMGVAGPASAAMEMAIANLVEPGTRVLSICNGLFSRRLAEMADRVGGDVTRL 123 Query: 122 EASFGRALSHEEITFAFEAHRPKVFFIAQGDSSTGIIQQNIRELGELCRKYDCFLIVDTV 181 +A RA+S E++ A + R ++ + QG++S + +++ E+ L ++Y C IVD V Sbjct: 124 DAPDKRAISAEDVEKALKTGRFQILTVVQGETSNTVWNRDLVEICRLGKQYGCLNIVDAV 183 Query: 182 ASLGGTEFLMDEWKVDVAYTGSQKSLGGPAGLTPISFSKRALTRIRKRKTKPKVYYFDIL 241 +L MDEW VD TG QK L G++ I+FS+ A RI R + + D Sbjct: 184 CTLSTMPMEMDEWMVDAIITGGQKGLSSIPGVSLIAFSEEAFARIEARNSPMAHWCLDAR 243 Query: 242 LIGQYWGCYGTPRIYHHTISSTLLYGLREALAHFCAVGLKAVVRRHQECSKRLQLGIEEL 301 L Q+W + YH+T + + L EAL L RRH +CSK LQ G+E + Sbjct: 244 LAHQFWHNHS----YHYTAPVSGILALHEALRLIGDETLPGRFRRHAQCSKALQNGVEAM 299 Query: 302 GLEMFVSREEERLPTVNTIKVPFGVDWKKVAEYAMRKYSVEISGGLGPTVEHVFRIGLMG 361 GL++ ++ E+ RL +V I++P + +V + + VEISG G + RIG MG Sbjct: 300 GLKLLIA-EDSRLNSVVGIELPEVISADQVRHIMSQVHKVEISGAFGLP---IVRIGQMG 355 Query: 362 ENATVERVDMVLSILNEAIQSSKLGIKTDL 391 E + + L L A++++ G K D+ Sbjct: 356 EQSRAPNLFRTLHALGSAMRAA--GGKVDM 383 Lambda K H 0.321 0.138 0.417 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: 376 Number of extensions: 20 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: 394 Length of database: 400 Length adjustment: 31 Effective length of query: 363 Effective length of database: 369 Effective search space: 133947 Effective search space used: 133947 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 (21.9 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