Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_069661945.1 BCR25_RS02115 pyridoxal phosphate-dependent aminotransferase
Query= CharProtDB::CH_004890 (393 letters) >NCBI__GCF_001730305.1:WP_069661945.1 Length = 396 Score = 427 bits (1098), Expect = e-124 Identities = 213/394 (54%), Positives = 278/394 (70%), Gaps = 1/394 (0%) Query: 1 MKLAKRVSALTPSTTLAITAKAKELKAAGHDVIGLGAGEPDFNTPQHIIDAAVRSMNEGH 60 M ++ R L PS TLA +AKA LKA G +V+ L GEPDF TP++I AA++++ G Sbjct: 1 MDISMRAQKLEPSVTLAASAKANALKAQGQNVLSLTVGEPDFTTPKNIQQAAIQAIESGK 60 Query: 61 TKY-TPSGGLAELKNSIAEKFKRDQNIEYKPSQIIVCTGAKHALYTLFQVILDEEDEVII 119 Y TPS G+ EL+ ++A K + ++Y+ +IV GAK ALY LFQ +L+ DEVII Sbjct: 61 ASYYTPSAGIKELRQAVATYIKSNYQLDYQVENVIVTDGAKFALYLLFQAVLNPLDEVII 120 Query: 120 PTPYWVSYPEQVKLAGGKPVYVEGLEENHFKISPEQLKNAITEKTKAIVINSPSNPTGVM 179 P PYWVSY EQVKLA G PV+V +E FK++ QL+ A TEKTK +++NSPSNPTG++ Sbjct: 121 PVPYWVSYGEQVKLAEGVPVFVSCAQEQEFKVTVAQLEEARTEKTKILILNSPSNPTGMI 180 Query: 180 YTEEELSALGEVCLEHDILIVSDEIYEKLTYGGKKHVSIAQLSDRLKEQTVIINGVSKSH 239 Y+E+EL A+GE + HDILIVSD+IY KL Y G IA LS+ +++QT+IINGVSKS+ Sbjct: 181 YSEKELRAIGEWAVLHDILIVSDDIYGKLVYNGAVFTPIATLSEAIQKQTIIINGVSKSY 240 Query: 240 SMTGWRIGYAAGSEDIIKAMTNLASHSTSNPTSIAQYGAIAAYNGPSEPLEEMREAFEHR 299 +MTGWRIGYA G + II M ++AS STSNPT+++QY AI A +G + +E MR+AFE R Sbjct: 241 AMTGWRIGYAVGDKAIIATMNDIASQSTSNPTAVSQYAAIEALSGEQDTVETMRQAFEER 300 Query: 300 LNTIYAKLIEIPGFSCVKPEGAFYLFPNAKEAAQSCGFKDVDEFVKALLEEEKVAIVPGS 359 LN +Y +PGF KP GAFYLFPN KE CG+ DV ++V LL E VA+V G+ Sbjct: 301 LNKVYPMFAALPGFKIEKPHGAFYLFPNIKETMDLCGYTDVTDWVDDLLAEAHVALVTGA 360 Query: 360 GFGSPENVRLSYATSLDLLEEAIERIKRFVEKHS 393 GFG+PENVR+SYAT LD LEEA+ RI F+E S Sbjct: 361 GFGAPENVRISYATDLDTLEEAVARIAAFIEAKS 394 Lambda K H 0.313 0.131 0.370 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: 437 Number of extensions: 18 Number of successful extensions: 2 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: 396 Length adjustment: 31 Effective length of query: 362 Effective length of database: 365 Effective search space: 132130 Effective search space used: 132130 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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