Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_013420082.1 RVAN_RS12540 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000166055.1:WP_013420082.1 Length = 463 Score = 187 bits (476), Expect = 4e-52 Identities = 139/385 (36%), Positives = 197/385 (51%), Gaps = 54/385 (14%) Query: 11 VRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQ-----LEKIVVAGPMFEH 65 VRG+G Y+WD G +YLDL++G GV LG +P+ V D RQ L +V Sbjct: 42 VRGQGAYLWDRAGDKYLDLLSGWGVFALGRNNPK-VNDALRQVLDSELPNLVQMDVSPLA 100 Query: 66 DEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSL 125 E L + W+D + NSGTE+VEAAIKF R ATGR+ + +AFHG + GSL Sbjct: 101 GVVAERLLARAPWLDK--AFFANSGTESVEAAIKFVRAATGRAGLAHCGHAFHGLSYGSL 158 Query: 126 SATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAI-TKETAAVIFEPIQGEGGIVPADEEF 184 S + +R+GF + +PFN++ A ++A+ TK+ A EPIQG+G VP D+ + Sbjct: 159 SLNGDQIFRKGFEGFLTDTVEVPFNDLTALEDALKTKKIAGFFVEPIQGKGVHVP-DDGY 217 Query: 185 VKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHY-GVRPDIVTMGKGIGNG-FPVSLT 241 +K +++L + G L +ADE+Q+G+ RTGKF AI+H+ GV PD+V + K + G PV Sbjct: 218 LKGVQELCKKYGTLFVADEIQTGVGRTGKFFAIDHWPGVEPDLVLVAKALSGGHVPVGAV 277 Query: 242 LTDLEI---------PRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEK------- 285 LT I HGSTF N +A A TL IL D ++E A K Sbjct: 278 LTRKWIFDKLFNRMDRAVVHGSTFAKNDMAMAAALATLSILEEDGVIENAAAKGERLAAS 337 Query: 286 FMEFSG--ERVVKTRGRGLMIGIVLRRPAGNYVK---------------------ALQER 322 F G E + RG+GLMIGI P ++ +E Sbjct: 338 FRSMIGRHELMKDVRGKGLMIGIEFGEPKSFALRMSWHALETANKGLFSQMITIPLFKEH 397 Query: 323 GILVNTAGN--RVIRLLPPLIIEGD 345 +L AG+ +++LLP L + D Sbjct: 398 KVLCQVAGHGMNIVKLLPALTLTED 422 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: 416 Number of extensions: 21 Number of successful extensions: 7 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: 463 Length adjustment: 31 Effective length of query: 331 Effective length of database: 432 Effective search space: 142992 Effective search space used: 142992 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