Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_013459667.1 SULKU_RS04095 hypothetical protein
Query= BRENDA::O66630 (387 letters) >NCBI__GCF_000183725.1:WP_013459667.1 Length = 378 Score = 137 bits (345), Expect = 5e-37 Identities = 117/368 (31%), Positives = 182/368 (49%), Gaps = 38/368 (10%) Query: 34 IDLGVGDPDMPTPKPIVEAAKKALENPENHKYPSYVGKYEFRKAVADWYKRRFDVDLDPN 93 I L +G+P TP I ++ K E E +YP G+ ++ + +RRF V L N Sbjct: 27 IALTIGEPQFETPAFIQKSLAKHSE--ELRRYPKTAGESYLNDSMRGFVERRFGVKLKAN 84 Query: 94 TEVITLIGSKEGIAHFP--LAFVNPGDIVLCPDPAYPVYRIGAIFAGGTPYTVPLKEENN 151 E+++ G++E + +FP F ++ +P Y +Y AI + + L E+N Sbjct: 85 -ELVSSFGTREVLFNFPQYYLFDKKEPVMAYTNPFYQIYEGSAIASRAKVIHLNLSEQNG 143 Query: 152 FLPDLDSIPEDVAKKAKIIWINYPNNPTSAPPTLEFYKKLVDWAK---EYNVIIASDNAY 208 F P +D E ++ +N+PNNPT++ +LE +L DW K +++ + +D Y Sbjct: 144 FKPVID---EAELAGCDLVILNFPNNPTASVLSLE---ELGDWVKLALKHDFCLINDECY 197 Query: 209 SEIYTGQEKPPSILQV------PGAKDVAIEFHSLSKTYNMTGWRIGMAVGNKELVAGLG 262 SEIYT Q K PS+L+ K+V + +S+SK + G R G G+ ++ G Sbjct: 198 SEIYTDQ-KIPSLLEASLYVGNSSFKNVLV-INSISKRSSAPGLRSGFIAGDGSILKGYA 255 Query: 263 KVKTNVDSGQFGAVQDAGIVALNLPEEEVEKIRDVYRERKKIMTEALEKIGLEIYRSDYT 322 + +T V +Q A +A E V K R+VY E K A E +G+E SD T Sbjct: 256 QYRTYVGCASPLPLQAAAAMAW-ADEYHVAKAREVYAENFK---AAQEILGIE--TSDAT 309 Query: 323 FYLWIKVPEGYTSAEFVGRLIDEAGIVCTPG------NGFGEY-GEGYFRISLTVPTERL 375 FY+W+KVP + EF RL + + PG + GE G GY RI+L T R Sbjct: 310 FYVWLKVP---NALEFTQRLYRDYNVKVLPGEFLAREDARGENPGIGYIRIALVEETVRT 366 Query: 376 LEAAERIK 383 ++A ER+K Sbjct: 367 IQALERLK 374 Lambda K H 0.317 0.139 0.413 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: 368 Number of extensions: 26 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: 387 Length of database: 378 Length adjustment: 30 Effective length of query: 357 Effective length of database: 348 Effective search space: 124236 Effective search space used: 124236 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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