Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate 351943 BT2415 aspartate aminotransferase (NCBI ptt file)
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__Btheta:351943 Length = 397 Score = 162 bits (409), Expect = 2e-44 Identities = 122/399 (30%), Positives = 197/399 (49%), Gaps = 30/399 (7%) Query: 3 VSRLRPYATTVFAEMS--ALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPG 60 ++ L P AT ++ S A I +NL G PD + P + +AA+ AI ++Y P Sbjct: 8 LNSLSPSATLAMSQKSNELKAQGIDVINLSVGEPDFNTPDHIKEAAKKAIDDNFSRYSPV 67 Query: 61 PGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYD 120 PG LR AI + ++ G++Y ++ GA +++ A+L LV PG EV++ P++ Sbjct: 68 PGYPALRNAIVEKLKKENGLEYTA-AQISCANGAKQSVCNAILVLVNPGDEVIVPAPYWV 126 Query: 121 SYSPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATE 180 SY +V MA V V + + F + L A+TP+T+ALI+ SP NPTG+V S E Sbjct: 127 SYPEMVKMAEGTPVIVSAGIE-QDFKITPKQLEAAITPKTKALILCSPSNPTGSVYSKEE 185 Query: 181 LAAIAEI-AVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGW 239 LA +A + A +VVI DE+YEH+ + A H +A F M ERT+ ++ +K + TGW Sbjct: 186 LAGLAAVLAKYPQVVVIADEIYEHINYIGA-HQSIAQFPEMKERTVIVNGVSKAYAMTGW 244 Query: 240 KIGWACGPAELIAGVRAAK-QYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRL 298 +IG+ GP ++ + QY S + A A + T++ V ++ + RRD + Sbjct: 245 RIGFIAGPEWIVKACNKLQGQYTSGPCSVSQKAAEAAYVGTQEP-VKEMQKAFERRRDLI 303 Query: 299 AAGLTEI-GFAVHDSYG--------TYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMS 349 E+ GF V+ G +YF ++S + L E VA + + Sbjct: 304 VKLAKEVPGFEVNVPQGAFYLFPKCSYFFGKSNGERKIENSDDLAMYLLEDAHVACVGGT 363 Query: 350 AFCDPAAGQASQQADVWNHLVRFTFCKRDDTLDEAIRRL 388 +F P +R ++ D+ + EAIRR+ Sbjct: 364 SFGAP-------------ECIRMSYATSDENIVEAIRRI 389 Lambda K H 0.321 0.135 0.405 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: 310 Number of extensions: 16 Number of successful extensions: 6 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: 397 Length of database: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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