Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate Synpcc7942_2545 Synpcc7942_2545 aspartate aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__SynE:Synpcc7942_2545 Length = 392 Score = 175 bits (444), Expect = 2e-48 Identities = 122/366 (33%), Positives = 181/366 (49%), Gaps = 7/366 (1%) Query: 3 VSRLRPYATTVFAEMSAL--ATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPG 60 V R+ P T A + A + + G PD + P + AA A+A G +Y P Sbjct: 7 VGRVSPSLTLAIAAQAKAMKAEGLDVCSFSAGEPDFETPLHIRNAAAQALAEGKTRYGPA 66 Query: 61 PGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYD 120 G LR AIA + R G+DY +LVT G +++ + L++PG EV++ P++ Sbjct: 67 AGEPDLREAIAQKLRADNGLDYQA-ANILVTNGGKQSLYNLMQVLLDPGDEVIIPAPYWL 125 Query: 121 SYSPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATE 180 SY +V +AG V V GF L L A+TPRTR L++NSP NPTG V S E Sbjct: 126 SYPEMVKLAGGVPVIVETFASD-GFKLQPQQLAGAITPRTRLLVLNSPSNPTGMVYSRQE 184 Query: 181 LAAIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFD-GMAERTITISSAAKMFNCTGW 239 L AIA I A + V++DE+YE +++D A H + ERT+ + AK ++ TGW Sbjct: 185 LEAIAPIIEAHDFWVVSDEIYEKILYDGADHHSIGSLSPACFERTLISNGFAKAYSMTGW 244 Query: 240 KIGWACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLA 299 ++G+ GP+ELIA + + + + Q AL VA + + RR + Sbjct: 245 RVGYLAGPSELIAAAASLQSHSTSNVCTFAQYGAIAALQGPQDCVAEMLAAFTERRQLIL 304 Query: 300 AGLTEI-GFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQ 358 GL +I G + G +++ D G D T +C L ++ VAAIP AF D + + Sbjct: 305 NGLNQIAGLSCPIPEGAFYVFVDISKTGLDSMT-YCRQLLDQHQVAAIPGIAFGDDRSIR 363 Query: 359 ASQQAD 364 S D Sbjct: 364 LSYATD 369 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: 356 Number of extensions: 22 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: 397 Length of database: 392 Length adjustment: 31 Effective length of query: 366 Effective length of database: 361 Effective search space: 132126 Effective search space used: 132126 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 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