Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_104010003.1 AVA_RS00800 LL-diaminopimelate aminotransferase
Query= BRENDA::Q8TQ40 (389 letters) >NCBI__GCF_000204075.1:WP_104010003.1 Length = 404 Score = 324 bits (830), Expect = 3e-93 Identities = 164/398 (41%), Positives = 245/398 (61%), Gaps = 19/398 (4%) Query: 6 YSDRINALPPYLFAAIDEAKDEMIAKGVDVIDLGVGDPDLPTHPHIVEAMREAVCDPKTH 65 +S R+ L +FA +D+AK +A G ++IDL +G DLP H++EA+ +++ DP TH Sbjct: 3 FSQRLQPLQSNVFADMDKAKALALAAGKELIDLSLGSSDLPAEAHVIEAIAKSLYDPSTH 62 Query: 66 QYPSYAGMPEFREAAAEWCKKYKGIELDPATEVLSLIGSKEAVAHIPLAFVNPGDVVLYT 125 Y + G +FR+AAA W ++ G+++DP TEVL LIGS+E AH+PLA +NPGD L Sbjct: 63 GYLLFNGTRDFRQAAANWYEQKFGVKVDPETEVLPLIGSQEGTAHLPLALLNPGDFALLL 122 Query: 126 DPGYPVYKIGTLFAGGEPYSLPLKAENSFLPDLDSIPADILKRAKLFFFNYPNNPTSATA 185 DPGYP + G A G+ Y +PLKAEN FLP IP D+L R+++ +YP+NPT+A A Sbjct: 123 DPGYPSHAGGVYLASGQIYPMPLKAENDFLPVFTDIPTDVLARSRMMVLSYPHNPTAAIA 182 Query: 186 DMKFFEKVVEFCKKNDIIAVHDNAYSQMVYDGYD-----------------APSFLAAEG 228 + FF++ V FC++++I VHD Y MV++ PS L A+ Sbjct: 183 PLSFFKEAVAFCQEHNIALVHDFPYVDMVFEDSSNWDQNLSQSPIPNHRSLVPSILQADP 242 Query: 229 AMDIGIELYSHSKTYNMTGWRLGFAVGSKALIKGLGKVKSNVDSGVFDAIQIAGIAALSS 288 + IE ++ SK+YNM G+R+G+A+G+ +I+ L ++K+ VD + I IAAL+ Sbjct: 243 DKSVSIEFFTLSKSYNMGGFRIGYAIGNAQMIQALRQIKAAVDFNQYRGILNGAIAALTG 302 Query: 289 SQACVDDTNKIYEERRNVLIEGLTAMGLEVKPPKATFYVWAPVPTGFT--SIEFAKLLLE 346 QA V+ + +RR+ I L +G V PKAT Y+WA +P+ ++ SIEF L++ Sbjct: 303 PQAGVEAAVSTFRQRRDAFIHALHHIGWYVPTPKATMYIWAKLPSSWSQNSIEFCTQLVK 362 Query: 347 EAGIVATPGVGFGDAGEGYVRFALTKPVERIKEAVERM 384 + G+ A+PG GFG +GEGYVRFAL ++ AVER+ Sbjct: 363 QTGVAASPGAGFGKSGEGYVRFALVHEPSILRTAVERI 400 Lambda K H 0.319 0.137 0.409 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: 446 Number of extensions: 18 Number of successful extensions: 3 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: 389 Length of database: 404 Length adjustment: 31 Effective length of query: 358 Effective length of database: 373 Effective search space: 133534 Effective search space used: 133534 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