Align Aspartate aminotransferase; AspAT; Transaminase A; EC 2.6.1.1 (characterized)
to candidate 14737 b0600 putative aminotransferase (NCBI)
Query= SwissProt::Q9X0Y2 (377 letters) >FitnessBrowser__Keio:14737 Length = 386 Score = 175 bits (443), Expect = 2e-48 Identities = 112/378 (29%), Positives = 191/378 (50%), Gaps = 17/378 (4%) Query: 9 IPISKTMELDAKA---KALIKKGEDVINLTAGEPDFPTPEPVVEEAVRFLQKGEVKYTDP 65 IP SK +L + + + INL+ G PDF P + E + +G +Y Sbjct: 7 IPQSKLPQLGTTIFTQMSALAQQHQAINLSQGFPDFDGPRYLQERLAHHVAQGANQYAPM 66 Query: 66 RGIYELREGIAKRIGERYKKDISPDQ-VVVTNGAKQALFNAFMALLDPGDEVIVFSPVWV 124 G+ LRE IA++ Y D + VT GA +AL+ A AL+ GDEVI F P + Sbjct: 67 TGVQALREAIAQKTERLYGYQPDADSDITVTAGATEALYAAITALVRNGDEVICFDPSYD 126 Query: 125 SYIPQIILAGGTVNVVETFMSKNFQPSLEEVEGLLVGKTKAVLINSPNNPTGVVYRREFL 184 SY P I L+GG V + +F+ +E LL +T+ V++N+P+NP+ V+++ Sbjct: 127 SYAPAIALSGGIVKRM-ALQPPHFRVDWQEFAALLSERTRLVILNTPHNPSATVWQQADF 185 Query: 185 EGLVRLAKKRNFYIISDEVYDSLVYTDE-FTSILDVSEGFDRIVYINGFSKSHSMTGWRV 243 L + ++ISDEVY+ + ++ + S+L + +R V ++ F K++ MTGW+V Sbjct: 186 AALWQAIAGHEIFVISDEVYEHINFSQQGHASVLAHPQLRERAVAVSSFGKTYHMTGWKV 245 Query: 244 GYLISSEKVATAVSKIQSHTTSCINTVAQYAALKALEVDNSY---MVQTFKERKNFVVER 300 GY ++ ++ + K+ + T +NT AQ A L + + + ++++++ +V Sbjct: 246 GYCVAPAPISAEIRKVHQYLTFSVNTPAQLALADMLRAEPEHYLALPDFYRQKRDILVNA 305 Query: 301 LKKMGVKFVEPEGAFYLFFKVRG----DDVKFCERLLEEKKVALVPGSAFLKPGF----V 352 L + ++ + EG ++L DDV+FC+ L +E VA +P S F F + Sbjct: 306 LNESRLEILPCEGTYFLLVDYSAVSTLDDVEFCQWLTQEHGVAAIPLSVFCADPFPHKLI 365 Query: 353 RLSFATSIERLTEALDRI 370 RL FA L A +R+ Sbjct: 366 RLCFAKKESTLLAAAERL 383 Lambda K H 0.319 0.137 0.384 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: 295 Number of extensions: 17 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: 377 Length of database: 386 Length adjustment: 30 Effective length of query: 347 Effective length of database: 356 Effective search space: 123532 Effective search space used: 123532 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 (21.7 bits) S2: 50 (23.9 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