Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_009562813.1 AFE_RS01930 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000021485.1:WP_009562813.1 Length = 388 Score = 239 bits (609), Expect = 1e-67 Identities = 142/369 (38%), Positives = 209/369 (56%), Gaps = 26/369 (7%) Query: 1 MPLYRKRLRL----VRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKI 56 MPL RL RGEGV+++D +GRRYLD +AGI V LGH+HP + Q ++ Sbjct: 1 MPLMSTYARLPVAFARGEGVWLYDTEGRRYLDALAGIAVCGLGHSHPAVTRALQTQAGQL 60 Query: 57 VVAGPMFEHDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARL-----ATGRSEIV 111 + ++ +E++ + L + + NSG EA EAAIK ARL +I+ Sbjct: 61 LHTSNLYRIPAQEKLSDTLCAVSGMDAAFFCNSGAEANEAAIKIARLHGHGKGIAEPQIL 120 Query: 112 AMTNAFHGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKE--TAAVIFE 169 +NAFHGRTL +L+AT + +EGF PL+PGF P+ ++ + + A++ E Sbjct: 121 VFSNAFHGRTLATLTATGNFRIQEGFSPLLPGFVRAPYGDLSTVRALVQANPGICAILAE 180 Query: 170 PIQGEGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHY-GVRPDIVT 227 P+QGEGG+ PA E F+ LR++ + G LL+ DEVQ+G+ RTG F A + G+RPD+++ Sbjct: 181 PLQGEGGVRPAPEGFLTGLREVCDAHGLLLMLDEVQTGIGRTGAFFAYQQIPGLRPDVLS 240 Query: 228 MGKGIGNGFPVSLTL----TDLEIPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAG 283 + KG+GNG P+ L T GKHG+TFGG PL C A L ++++ L AG Sbjct: 241 LAKGLGNGVPIGAMLAGQSTAALFGPGKHGTTFGGGPLVCAAAQAVLDTMQQEDLPAHAG 300 Query: 284 -------EKFMEFSG--ERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVI 334 ++ + G V++ RG GLM+GI L V+ E G+L+N +VI Sbjct: 301 RMGALLRQRLQKRLGGHPEVLEIRGMGLMVGIELAHKPERLVERALEAGLLINVTAEKVI 360 Query: 335 RLLPPLIIE 343 RLLPPLI++ Sbjct: 361 RLLPPLILQ 369 Lambda K H 0.320 0.140 0.410 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: 384 Number of extensions: 16 Number of successful extensions: 6 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: 362 Length of database: 388 Length adjustment: 30 Effective length of query: 332 Effective length of database: 358 Effective search space: 118856 Effective search space used: 118856 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 10 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