Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate RR42_RS11930 RR42_RS11930 succinyldiaminopimelate aminotransferase
Query= BRENDA::Q82IK5 (364 letters) >FitnessBrowser__Cup4G11:RR42_RS11930 Length = 405 Score = 155 bits (392), Expect = 2e-42 Identities = 138/396 (34%), Positives = 186/396 (46%), Gaps = 42/396 (10%) Query: 6 DRLPTFPWDKLEPYKARAAAHPDGI---VDLSVGTPVDPVPELIQKALVAAADS-PGYPT 61 D L +P++KL A P+G + +G P P PE I+ AL A YPT Sbjct: 6 DLLQPYPFEKLRVLLADVK--PNGALPAISFGIGEPKHPTPEFIKTALSNALQGLANYPT 63 Query: 62 VWGTPELRDALTGWVERRLGARGVTHH-HVLPIVGSKE-LVAWLPTQLGLG-PGDKVAHP 118 G+ LR + W++RR V VLP+ GS+E L A+ T + PG V P Sbjct: 64 TAGSDALRQCMAAWIQRRYNLPAVNATTQVLPVTGSREALFAFAQTVVDASQPGALVLCP 123 Query: 119 RLAYPTYEVGARLARADHVVYD-DPTE-----LDPTG------LKLLWLNSPSNPTGKVL 166 Y YE A LA A V + DP D G ++L+++ SP NPTG VL Sbjct: 124 NPFYQIYEGAALLAGATPVFANSDPARNFAPAFDRIGAETWAKVQLVFVCSPGNPTGAVL 183 Query: 167 SKAELTRIVAWAREHGILVFSDECYLELGWEAD--PVSVLHPDVCGGSYEG------IVS 218 S + + A + HG ++ SDECY E+ ++ P+ L G EG +V Sbjct: 184 SLEDWRELFALSDRHGFVIASDECYSEIYFKEGEPPLGALEAAHKLGRAEGAHPFERLVM 243 Query: 219 VHSLSKRSNLAGYRAAFLAGDPAVLGPLLQIRK-HGGMMTSAPTQAAVVAALGDDAHVRE 277 SLSKRSN+ G R+ F+AGD A+L L R HGG M A Q A VAA D+AHVR Sbjct: 244 FSSLSKRSNVPGLRSGFVAGDAALLKKFLLYRTYHGGAMNPA-VQTASVAAWNDEAHVRN 302 Query: 278 QRERYAARRTALRDALLSHGFRIEHSEASLYLWA---TRGESCWDTVAH-LADLGILVAP 333 R Y AR+ A +L+ + +A YLWA G S + A LA+ + V P Sbjct: 303 NRAAY-ARKFAEVTPMLAEVLDVALPDAGFYLWADVSRTGLSDTEFAARLLAEQNVTVLP 361 Query: 334 GDFYG------SAGEQFVRVALTATDERVAAAVRRL 363 G + + G VR+AL AT E RR+ Sbjct: 362 GSYLAREADGINPGANRVRMALVATPEECLEGARRI 397 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: 407 Number of extensions: 24 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: 364 Length of database: 405 Length adjustment: 30 Effective length of query: 334 Effective length of database: 375 Effective search space: 125250 Effective search space used: 125250 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 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