Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_012283431.1 HM1_RS10910 LL-diaminopimelate aminotransferase
Query= BRENDA::Q82IK5 (364 letters) >NCBI__GCF_000019165.1:WP_012283431.1 Length = 393 Score = 143 bits (361), Expect = 7e-39 Identities = 115/375 (30%), Positives = 171/375 (45%), Gaps = 29/375 (7%) Query: 13 WDKLEPYKARAAAHPDGIVDLSVGTPVDPVPELIQKALVAAA---DSPGYPTVWGTPELR 69 + +++ + A +++L +G+P P +++ L+ A D+ GY G E + Sbjct: 18 FSRMDALRQEVEASGVDVINLGIGSPDRPPAPHVRQTLMDALVRDDAYGYALTDGLIEFK 77 Query: 70 DALTGWVERRLGARGVTHHHVLPIVGSKELVAWLPTQLGLGPGDKVAHPRLAYPTYEVGA 129 A+ W + R G VL ++GS++ + L L L PGD P YP Y G Sbjct: 78 SAVADWYQERFGVALDPKTEVLSLMGSQDGLGHLGLAL-LDPGDVALIPDPGYPIYRAGV 136 Query: 130 RLARADHVVYDDPTELDPTGL--------------KLLWLNSPSNPTGKVLSKAELTRIV 175 LA Y P E + L KL+ LN PSNP T +V Sbjct: 137 LLAEG--FPYPLPLERERDYLPDLDAVPEDILRRAKLMILNYPSNPVAATAELNFFTGVV 194 Query: 176 AWAREHGILVFSDECYLELGWEA-DPVSVLHPDVCGGSYEGIVSVHSLSKRSNLAGYRAA 234 +AR + I+V D Y EL ++ PVS L G+ E + HSLSK NLAG R Sbjct: 195 DFARRNNIIVLHDIAYSELAYDGYRPVSFLQAP---GAKEVGIEFHSLSKSYNLAGCRLG 251 Query: 235 FLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAAL-GDDAHVREQRERYAARRTALRDAL 293 G+ VL L ++ + Q A VAAL G A V E Y RR L D L Sbjct: 252 MAVGNREVLALLANLKSNIDYGVFKAVQWAAVAALRGPQAIVEENARAYQRRRDVLVDGL 311 Query: 294 LSHGFRIEHSEASLYLWATRGESCWDTVAHLADL----GILVAPGDFYGSAGEQFVRVAL 349 G++++ +AS+++WA + + A +L G+LV PG+ +G GE +VR+AL Sbjct: 312 NRIGWQMDKPKASMFVWAPVPKGFTSSFAFAEELLRETGVLVVPGNAFGERGEGYVRIAL 371 Query: 350 TATDERVAAAVRRLA 364 + R+ AV R+A Sbjct: 372 VVPEGRLEEAVERIA 386 Lambda K H 0.319 0.135 0.420 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: 372 Number of extensions: 16 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: 364 Length of database: 393 Length adjustment: 30 Effective length of query: 334 Effective length of database: 363 Effective search space: 121242 Effective search space used: 121242 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 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