Align Alanine--glyoxylate aminotransferase; EC 2.6.1.44 (characterized)
to candidate SMa1495 SMa1495 aminotransferase
Query= SwissProt::Q3LSM4 (393 letters) >FitnessBrowser__Smeli:SMa1495 Length = 370 Score = 272 bits (695), Expect = 1e-77 Identities = 151/369 (40%), Positives = 213/369 (57%), Gaps = 6/369 (1%) Query: 18 PNKLLMGPGPSNAPQRVLDAMSRPILGHLHPETLKIMDDIKEGVRYLFQTNNIATFCLSA 77 P +LLMGPGPSN VL A +RP +GHL P + +MD IK+ +R F+T+N TF LSA Sbjct: 7 PPRLLMGPGPSNVSPEVLAAQARPTIGHLDPSFVGLMDRIKDQLRLAFRTDNRVTFPLSA 66 Query: 78 SGHGGMEATLCNLLEDGDVILIGHTGHWGDRSADMATRYGADVRVVKSKVGQSLSLDEIR 137 ME L LLE GD +I G +G R A++A R GA+VR+V + G+ + + +R Sbjct: 67 PASLAMEMALVTLLEPGDTAIIAQNGVFGGRMAEIAQRAGAEVRLVSVEWGKPVDPEAVR 126 Query: 138 DALL-IHKPSVLFLTQGDSSTGVLQGLEGVGALCHQHNCLLIVDTVASLGGAPMFMDRWE 196 ++L + +L ++STGV + AL + L +VDTV LGG P+ +D W+ Sbjct: 127 ASILEAPQAKLLAFVHAETSTGVRSDAASLCALAREAGLLSVVDTVTGLGGIPVSVDEWQ 186 Query: 197 IDAMYTGSQKVLGAPPGITPVSFSHRAVERYKRRNTKVKVYYWDMSLVGDYWGCFGRPRI 256 DA+Y G+QK L APPG+ P++FS RAV K R T ++ ++ D+ L+ YW G R Sbjct: 187 ADAVYAGTQKCLSAPPGLAPITFSDRAVSAVKARKTPIQSWFLDLGLMLGYWEGEG-ARS 245 Query: 257 YHHTISSTLLYGLREAIAMACEEGLPALIARHEDCAKRLYRGLQDAGFELYADPKDRLST 316 YHHT LYGL E+++ EGL ARH RL LQ G D + RL Sbjct: 246 YHHTAPVNALYGLHESLSRLLGEGLETAWARHRAAHDRLVERLQGLGIAFVVDKEHRLPQ 305 Query: 317 VTTIKVPQGVDWLKAAQYAMKTYLVEISGGLGPTAGQVFRIGLMGQNATTERVDRVLQVF 376 + T+ +P+GV + + + + +EI GGLGP AG+++RIGLMG+ E VDR+ Sbjct: 306 LNTVWLPEGVKDVPERRRLLDEFGIEIGGGLGPLAGRIWRIGLMGETCRIENVDRL---- 361 Query: 377 QEAVAAVKP 385 EA+AAV P Sbjct: 362 AEAIAAVLP 370 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: 378 Number of extensions: 18 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: 393 Length of database: 370 Length adjustment: 30 Effective length of query: 363 Effective length of database: 340 Effective search space: 123420 Effective search space used: 123420 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