Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_015798108.1 AFER_RS03385 class I and II aminotransferase
Query= BRENDA::Q82IK5 (364 letters) >NCBI__GCF_000023265.1:WP_015798108.1 Length = 361 Score = 174 bits (441), Expect = 3e-48 Identities = 130/361 (36%), Positives = 171/361 (47%), Gaps = 34/361 (9%) Query: 21 ARAAAHPDGIVDLSVGTPVDPVPELIQKALVAAADSPGYPTVWGTPELRDALTGWVERRL 80 A AA +VD S+G+PVDP P + L + YP GTP L ++ T W Sbjct: 12 ALAADRHPFVVDASIGSPVDPPPAFVPHLLACQGEERAYPPAAGTPALVESATRWFH--- 68 Query: 81 GARGVT--HHHVLPIVGSKELVAWLPTQLGLGPGDK--VAHPRLAYPTYEVGARLARADH 136 RGVT V P +GSKE + L L D+ V P AYPTY GAR A + Sbjct: 69 ALRGVTLPDGAVAPTMGSKEAIGTLAWLLRERRPDRGVVLIPGRAYPTYAEGARAAGCEI 128 Query: 137 VVYDDPTELDPT----------GLKLLWLNSPSNPTGKVLSKAELTRIVAWAREHGILVF 186 V D P + W+NSPSNPTG V +VA AREHG ++ Sbjct: 129 VRVPDDCSGAPAFDAVAASVWDRTLVAWVNSPSNPTGAVYDPGP---VVALAREHGAVLA 185 Query: 187 SDECYLELGWEADPVSVLHPDVCGGSYEGIVSVHSLSKRSNLAGYRAAFLAGDPAVLGPL 246 SDE Y + W + S L + EG +++ SLSKRSNLAG R +AGDP ++ + Sbjct: 186 SDEAYGDFVWSGEAPSALRAGL-----EGTLALVSLSKRSNLAGLRLGLVAGDPMLVDEV 240 Query: 247 LQIRKHGGMMTSAPTQAAVVAALGDDAHVREQRERYAARRTALR---DALLSHGFRIEHS 303 + R+ G++ S P+QA AL D+ HV EQR RYA R L +A+ R+ Sbjct: 241 VARRRALGLLASGPSQAVAAEALADEGHVAEQRSRYAGRLRRLARVIEAVADVPVRV--P 298 Query: 304 EASLYLWATRGESCWDTVAH--LADLGILVAPGDFYGSAGEQFVRVALTATDERVAAAVR 361 + +YLW + A LGI+VA G YG FVR+A T D + A Sbjct: 299 DGGIYLWVRAPDDDGAAFARWLATRLGIVVADGADYGD--RAFVRIAATVKDRAIDALWE 356 Query: 362 R 362 R Sbjct: 357 R 357 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: 463 Number of extensions: 32 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: 361 Length adjustment: 29 Effective length of query: 335 Effective length of database: 332 Effective search space: 111220 Effective search space used: 111220 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: 49 (23.5 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