Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Dsui_2708 Dsui_2708 succinyldiaminopimelate transaminase
Query= BRENDA::Q82IK5 (364 letters) >FitnessBrowser__PS:Dsui_2708 Length = 401 Score = 165 bits (417), Expect = 2e-45 Identities = 130/374 (34%), Positives = 187/374 (50%), Gaps = 31/374 (8%) Query: 7 RLPTFPWDKLEPYKARAAAHPD-GIVDLSVGTPVDPVPELIQKALVAAADS-PGYPTVWG 64 +L +P++KL +PD + LS+G P P I++AL A YPT G Sbjct: 7 KLQPYPFEKLRQLFQGVTPNPDYQEIKLSIGEPQHATPGFIKEALTANLGGLANYPTSQG 66 Query: 65 TPELRDALTGWVERRLGARGVTHH-HVLPIVGSKE-LVAWLPTQLGLGPG--DKVAHPRL 120 TP LR A+ W+ERR G GV +LP+ GS+E L A+ T + G V P Sbjct: 67 TPALRQAIAAWMERRYGLAGVNPDTEILPVNGSREALFAFAQTVIDPSRGYVPLVVSPNP 126 Query: 121 AYPTYEVGARLARAD------------HVVYDDPTELDPTGLKLLWLNSPSNPTGKVLSK 168 Y YE A LA A+ + + +E D ++LL++ SP NPTGKVL Sbjct: 127 FYQIYEGAAYLAGAEPYFLNTLPENDFSLELEALSEADWARVQLLYVCSPGNPTGKVLDL 186 Query: 169 AELTRIVAWAREHGILVFSDECYLELGW-EADPV--SVLHPDVCGGSYEGIVSVHSLSKR 225 + ++ A + ++G ++ SDECY E+ + EA P + G +E +V SLSKR Sbjct: 187 EDWKKLFALSDKYGFVIASDECYSEIYFDEAKPPLGGLQAAKQLGRGFERLVMFSSLSKR 246 Query: 226 SNLAGYRAAFLAGDPAVLGPLLQIRK-HGGMMTSAPTQAAVVAALGDDAHVREQRERYAA 284 SN+ G R+ F+AGD AVL L R HGG M A QAA A ++AH RE R +Y Sbjct: 247 SNVPGLRSGFVAGDAAVLKKFLLYRTYHGGAMNPA-VQAASAIAWNEEAHARENRRQYKE 305 Query: 285 RRTALRDALLSHGFRIEHSEASLYLWATRGESCWDTVAH-LADLGILVAPGDFYG----- 338 + A+ +++ + +AS YLWA + + LAD ++V PG + Sbjct: 306 KFDAV-TPIVASVLQTGLPDASFYLWARTPIADTEFARRLLADYNVVVLPGSYLAREARG 364 Query: 339 -SAGEQFVRVALTA 351 + GE FVR+AL A Sbjct: 365 VNPGENFVRIALVA 378 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: 421 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: 401 Length adjustment: 30 Effective length of query: 334 Effective length of database: 371 Effective search space: 123914 Effective search space used: 123914 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 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