Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_043742980.1 AMB_RS00085 aspartate aminotransferase
Query= BRENDA::Q82IK5 (364 letters) >NCBI__GCF_000009985.1:WP_043742980.1 Length = 399 Score = 139 bits (350), Expect = 1e-37 Identities = 125/395 (31%), Positives = 179/395 (45%), Gaps = 38/395 (9%) Query: 1 MSAVSDRLPTFPWDKLEPYKARAAAHPDGIVDLSVGTPVDPVPELIQKALVAAADSPG-Y 59 + A D LP +P+ +L A A PD V +S+G P P L+ + L A S G Y Sbjct: 7 LDARLDGLPDYPFARLAKLLG-APARPDSTV-MSIGEPQHRPPALVAEVLAANTSSWGKY 64 Query: 60 PTVWGTPELRDALTGWVERRLGA-RGVTHHH--VLPIVGSKELVAWLP-TQLGLGPGDK- 114 P G ELR A+ W RR +G+ +LP+ G++E + + T G G + Sbjct: 65 PPANGPAELRQAVADWAGRRYDLPQGLIDPEKAILPVAGTREALYLIAQTVCGDREGQRP 124 Query: 115 -VAHPRLAYPTYEVGARLARADHVVYDD-------------PTEL-DPTGLKLLWLNSPS 159 V P Y Y A +A A+ V P +L D T L ++ SP+ Sbjct: 125 LVLMPNPFYQVYAGAAVMAGAEPVFVPGANGPASQPDFSTLPADLLDRTALA--YVCSPA 182 Query: 160 NPTGKVLSKAELTRIVAWAREHGILVFSDECYLELGWEADPVSVLHPDVCGGSYEGIVSV 219 NP G V A L R V AR+HG ++ DECY E+ + P VL C EG+ +V Sbjct: 183 NPQGSVADAALLERQVRTARDHGFVLAVDECYSEIWDKVPPPGVLK--TCAALGEGLANV 240 Query: 220 ---HSLSKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVR 276 +SLSKRS++ G R+ + GD V+ ++R +GG T P AA A D+AHV Sbjct: 241 LMFNSLSKRSSVPGLRSGVVVGDERVIHAFARLRSYGGAATPLPIAAAAAALWRDEAHVT 300 Query: 277 EQRERYAARRTALRDALLSHGFRIEHSEASLYLWATRGESCWDTVAHLADLGILVAPGDF 336 E + Y A + + + +L F +LW G+ V + I V PG + Sbjct: 301 ESNDLYRA-KLDVAERVLGGRFGFYRPPGGFFLWLDVGDGEAAAVKLWQEGNIRVLPGAY 359 Query: 337 Y-------GSAGEQFVRVALTATDERVAAAVRRLA 364 G+ G +F+RVAL AA+ RLA Sbjct: 360 LAAEDSEEGNPGSRFIRVALVHDLAGTEAALTRLA 394 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: 434 Number of extensions: 30 Number of successful extensions: 4 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: 399 Length adjustment: 30 Effective length of query: 334 Effective length of database: 369 Effective search space: 123246 Effective search space used: 123246 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 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