Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate GFF1185 HP15_1162 aminotransferase, class I and II
Query= BRENDA::Q82IK5 (364 letters) >FitnessBrowser__Marino:GFF1185 Length = 400 Score = 159 bits (401), Expect = 2e-43 Identities = 125/388 (32%), Positives = 183/388 (47%), Gaps = 32/388 (8%) Query: 6 DRLPTFPWDKLEPYKARAAAHPDGI--VDLSVGTPVDPVPELIQKALVAAADS-PGYPTV 62 DRL +P++KL KA + PD + + L +G P P P+ +++ + D YPT Sbjct: 6 DRLHPYPFEKLAKLKAGISV-PDHLRPISLGIGEPKHPSPDFVKQVIANNLDKLANYPTT 64 Query: 63 WGTPELRDALTGWVERRLGARGVT---HHHVLPIVGSKELV-AWLPTQLGLGPGDKVAHP 118 GT ELR+A++GW RR + + ++++P+ G++E + + + + V P Sbjct: 65 RGTDELREAISGWATRRFNLKAGSLSAANNIVPVNGTREAIFSLVQAVVDATKPATVVSP 124 Query: 119 RLAYPTYEVGARLARADHVV------------YDDPTELDPTGLKLLWLNSPSNPTGKVL 166 Y YE A LA A V +D E ++L+L SP NP+G V+ Sbjct: 125 NPFYQVYEGAAFLAGATPVYIPCDGSNGFIPDFDSVPESIWQECQILFLCSPGNPSGAVI 184 Query: 167 SKAELTRIVAWAREHGILVFSDECYLELGWEAD--PVSVLHPDVCGG--SYEGIVSVHSL 222 S+ LTR++A A +H +V SDECY EL E P +L G Y V HSL Sbjct: 185 SREALTRVIALADKHDFIVASDECYSELYPEEGNAPEGLLQTCAAIGRDDYARCVVFHSL 244 Query: 223 SKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQRERY 282 SKRSNL G R+ F+AGD +L L+ R + G Q A +AA D+ HVRE R Y Sbjct: 245 SKRSNLPGLRSGFVAGDANILDGYLKYRTYHGCAMPIHNQLASIAAWSDEDHVRENRAAY 304 Query: 283 AARRTALRDALLSHGFRIEHSEASLYLWATRGESCWDTVAHL-ADLGILVAPGDFYG--- 338 A+ A+ +L ++ +A YLW L A + V PG + Sbjct: 305 RAKFEAV-VPILREVMDVDFPDAGFYLWPITPMDDETFARELSAQQNVHVLPGRYLSRTV 363 Query: 339 ---SAGEQFVRVALTATDERVAAAVRRL 363 + GE VR+AL A E A R+ Sbjct: 364 DGHNPGENRVRMALVAPLEECVEAAERI 391 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: 419 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: 400 Length adjustment: 30 Effective length of query: 334 Effective length of database: 370 Effective search space: 123580 Effective search space used: 123580 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