Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_011316915.1 AVA_RS00085 aspartate aminotransferase
Query= BRENDA::Q82IK5 (364 letters) >NCBI__GCF_000204075.1:WP_011316915.1 Length = 403 Score = 163 bits (413), Expect = 7e-45 Identities = 121/377 (32%), Positives = 188/377 (49%), Gaps = 24/377 (6%) Query: 7 RLPTFPWDKLEPYKARAAAHPDGIVDLSVGTPVDPVPELIQKALVAAADSP---GYPTVW 63 +LP + + +L+ KA+A ++DL +G P P+ + A + A +P GYP Sbjct: 14 QLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQNPANHGYPPFE 73 Query: 64 GTPELRDALTGWVERRLGARGVTHHHVLPIVGSKELVAWLPTQLGLGPGDKVAHPRLAYP 123 GT R A+T W RR G LP++GSKE ++ L + PGD V P AYP Sbjct: 74 GTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAY-VNPGDVVLVPSPAYP 132 Query: 124 TYEVGARLARAD-HVVYDDPTE---LDPTGL--------KLLWLNSPSNPTGKVLSKAEL 171 + G +A H + P +D T + K+L+ N PSNPTG + Sbjct: 133 AHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPREFF 192 Query: 172 TRIVAWAREHGILVFSDECYLELGWEA-DPVSVLHPDVCGGSYEGIVSVHSLSKRSNLAG 230 IVA+AR++ IL+ D CY EL ++ P S+L ++ G G V H+LSK N+AG Sbjct: 193 EEIVAFARKYEILLVHDLCYAELAFDGYQPTSLL--EIPGAKDIG-VEFHTLSKTYNMAG 249 Query: 231 YRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALG-DDAHVREQRERYAARRTAL 289 +R F+ G+ V+ L ++ + A Q A AL D ++ E ++RY RR L Sbjct: 250 WRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFL 309 Query: 290 RDALLSHGFRIEHSEASLYLWATRGESCWDT---VAHLADLGILVAPGDFYGSAGEQFVR 346 L G+ + ++A++YLW T + L G++V PG+ +G AGE +VR Sbjct: 310 IQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGYVR 369 Query: 347 VALTATDERVAAAVRRL 363 ++L A +R+ A+ R+ Sbjct: 370 ISLIADCDRLGEALGRI 386 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: 402 Number of extensions: 36 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: 364 Length of database: 403 Length adjustment: 30 Effective length of query: 334 Effective length of database: 373 Effective search space: 124582 Effective search space used: 124582 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