Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate BWI76_RS07600 BWI76_RS07600 aspartate aminotransferase family protein
Query= reanno::SB2B:6938540 (460 letters) >FitnessBrowser__Koxy:BWI76_RS07600 Length = 445 Score = 224 bits (571), Expect = 4e-63 Identities = 145/453 (32%), Positives = 241/453 (53%), Gaps = 33/453 (7%) Query: 12 LQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRK 71 ++ +D A+ H ++ +L VI A+G +WD +GN LD + L VN+GY Sbjct: 16 VRQLDRAYVFHSWSMQGNLHPL---VIAGAKGCELWDYEGNTYLDFSSQLVNVNIGYQHP 72 Query: 72 SIADAAYAQLQTLPFYNNFFQCTHEPAI------RLASKIASLAPGHMNRVFFTGSGSEA 125 + A AQL+ L T PA A +I LAP ++VFFT +G++A Sbjct: 73 RVLAAMKAQLEAL--------VTIAPATANLARGEAAKRIVELAPEGFSKVFFTNAGADA 124 Query: 126 NDTNLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHI 185 N+ +RM R Y + ++S +YHG+T G+++ G + + G VH Sbjct: 125 NENAIRMARLY------TGRDKVLSAYRSYHGNT--GSAIAATGDWRRVPNEYSRGHVHF 176 Query: 186 DQPYWFGEGRDMSPEAFGIKTAQALEAKILEL-GEDKVAAFIAEPFQGAGGVIIPPDSYW 244 PY + + + E + A A +++E G + +AA + E G G+++PP+ Y Sbjct: 177 FNPYLYRSEFNATTEEEECQRALAHLRRMIECEGPNAIAAILLESIPGTAGILVPPEGYM 236 Query: 245 NEIKRILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIV 304 ++ + +++ I+ ILDEV++GFGRTG+WFA + G+ PDL+T AKG+ +GY+P GGV++ Sbjct: 237 QGVRALADEFGIILILDEVMAGFGRTGSWFAFEQDGVVPDLVTFAKGVNAGYVPAGGVLI 296 Query: 305 SDRVADVLISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQ 364 S+ +A D FA G TYSGHP+A A + I ++EE++V+ T L+ L+ Sbjct: 297 SEPIARYF--DDHFFAGGLTYSGHPLAMAAIVATIDAMKEEKVVENAATIGNEVLRPGLE 354 Query: 365 TLS-AHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDT 423 L+ H ++G VRG G+ A+ELV+ + G+ A + + A E+GL+ V + Sbjct: 355 ALAEKHAIIGNVRGRGLFQALELVSSREHKTPLGAADMAAI--KGALTEAGLLAFVVENR 412 Query: 424 MIISPPLCITRDEIDE--LIFKASQALSLTLEK 454 + + PP I+ +++ + IF A A +L K Sbjct: 413 IHVVPPCTISAEQVAKGLAIFDAVFARFASLAK 445 Lambda K H 0.321 0.137 0.408 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: 524 Number of extensions: 35 Number of successful extensions: 5 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: 460 Length of database: 445 Length adjustment: 33 Effective length of query: 427 Effective length of database: 412 Effective search space: 175924 Effective search space used: 175924 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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