Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_012971471.1 ALVIN_RS11365 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= CharProtDB::CH_017144 (393 letters) >NCBI__GCF_000025485.1:WP_012971471.1 Length = 410 Score = 255 bits (651), Expect = 2e-72 Identities = 149/393 (37%), Positives = 224/393 (56%), Gaps = 14/393 (3%) Query: 2 KLAKRVASLTPSATLAITEKAKELKAAGHDVIGLGAGEPDFNTPQHILDAAIKAMNEGHT 61 +LA+R + P + + +A+EL+AAG ++ L GEPDF+TP+ IL A A++ G T Sbjct: 18 RLAERACRVEPFHVMRLLGRARELEAAGRSIVHLEVGEPDFSTPEPILAAGRAALDAGLT 77 Query: 62 KYTPSGGLPALKEEIIKKFARDQGLDYEPAEVIVCVGAKHALYTLFQVLLDEGDEVIIPT 121 YTP+ GLPAL++ I + R G++ +PA V+V GA AL +F VLL+ GD V++ Sbjct: 78 HYTPAAGLPALRQAIAAHYGRRHGVEVDPARVLVTPGASGALQLVFSVLLEPGDRVMLGD 137 Query: 122 PYWVSYPEQVKLAGGVPVYVEGLEQNHFKITPEQLKQAITPRTKAVIINSPSNPTGMIYT 181 P + Y + + L G PV V + +++TPE+L+ P T+AV++ SP+NPTG + + Sbjct: 138 PSYPCYRQMLGLMGAEPVAVPLGPETGYRLTPERLEAVWAPGTRAVVVASPANPTGAVTS 197 Query: 182 AEELKALGEVCLAHGVLIVSDEIYEKLTYGGAKHVSIAELSPELKAQTVIINGVSKSHSM 241 +EL+AL +C A G ++ DEIY LTYG ++A +L +I+ SK M Sbjct: 198 LDELRALHAICRARGAALIVDEIYRGLTYGVPDTTALALAGEDL----YVIDSFSKYFGM 253 Query: 242 TGWRIGYAAGPKDIIKAMTDLASHSTSNPTSIAQYAAIAAYSGPQEPV--EQMRQAFEQR 299 TGWR+G+ AGP++ + M LA + + AQ+AA+AA+S P+ V EQ R F+QR Sbjct: 254 TGWRVGWVAGPEEAVAVMDRLAQNFFIAANTPAQHAALAAFS-PETAVILEQRRVIFQQR 312 Query: 300 LNIIYDKLVQIPGFTCVKPQGAFYLFPNAREAAAMAGCRTVDEFVAALLEEAKVALVPGS 359 + + L + P GAFYL+ E + +F LLEEA VAL PG Sbjct: 313 RDRLLPALRDLGFGLSGAPDGAFYLYARLPEWLEIDSM----DFATRLLEEAGVALTPGQ 368 Query: 360 GFGAPD---NVRLSYATSLDALETAVERIHRFM 389 FG+ + +VRL+Y D L+ V RI F+ Sbjct: 369 DFGSHECDRHVRLAYTRDFDVLDEGVRRIGDFL 401 Lambda K H 0.316 0.133 0.381 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: 411 Number of extensions: 23 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: 410 Length adjustment: 31 Effective length of query: 362 Effective length of database: 379 Effective search space: 137198 Effective search space used: 137198 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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