Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_004041085.1 C498_RS01375 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000337315.1:WP_004041085.1 Length = 436 Score = 190 bits (483), Expect = 5e-53 Identities = 143/421 (33%), Positives = 207/421 (49%), Gaps = 64/421 (15%) Query: 1 MPLYRK-RLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVA 59 MP+++ + + R G + D G YLD+ +GI V +GH + V + QLE+ V Sbjct: 19 MPIWKSLNVPVERASGCTLEDFDGNEYLDVFSGISVTNVGHNNEAVVEAATEQLEEFV-H 77 Query: 60 GPMFEHDERE--EMLEELSHWV--DYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTN 115 G + H R ++ E ++ D + + NSGTEAVE AIK AR TG E++++ Sbjct: 78 GCSYVHPNRPVADLAETIAEVTPGDLQKTFFCNSGTEAVEGAIKLARKYTGSKEVISLEM 137 Query: 116 AFHGRTLGSLSATWKKKYREGFGPLVPGFKHI--PF--------------NNVEAAKEAI 159 FHGRTLGSL+ T + Y++ P + H P+ + +A + I Sbjct: 138 GFHGRTLGSLALTGNRAYKQDMAPTINDVAHTAPPYAYRCPRCDGDTCGADCADALERVI 197 Query: 160 TKET----AAVIFEPIQGEGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFL 214 T AAV+ EP+ GE GIV E ++K +RD+ D GALLIADEVQ+G RTG+ Sbjct: 198 GSHTSGDLAAVVVEPVMGEAGIVVPSEAWLKRVRDIAHDHGALLIADEVQTGYGRTGELF 257 Query: 215 AIEHYGVRPDIVTMGKGIGNGFPVSLTLTDLEIP----RGKHGSTFGGNPLACRAVATTL 270 A + +GV PDI+T KGI NG P+ +I G H STFGGNP+AC A T+ Sbjct: 258 ASKQFGVEPDILTQAKGIANGLPLGAFTAPADIADAFGSGDHLSTFGGNPVACAAALATI 317 Query: 271 RILRRDRLVEKAGEK---------FMEFSGERVVKTRGRGLMIGIVLRRP---------- 311 L ++ +V+ A E +E + V + RG GLM GI L P Sbjct: 318 EEL-QNGIVDNACENGEWLSAELATLESDYDVVGEARGLGLMQGIELVDPETTGPQHVAP 376 Query: 312 ---------AGNYVKALQERGILVNTAG--NRVIRLLPPLIIEGDTLEEARKEIEGVLND 360 G +++ +E +++ G V+R PPL I L EA + LND Sbjct: 377 APDKELAAAVGEHLR--EESNVVMGVGGYYKNVMRFQPPLTISQAQLGEAVDALRTALND 434 Query: 361 I 361 + Sbjct: 435 L 435 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: 400 Number of extensions: 20 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: 436 Length adjustment: 31 Effective length of query: 331 Effective length of database: 405 Effective search space: 134055 Effective search space used: 134055 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 09 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