Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_012977708.1 AZL_RS27700 aminotransferase
Query= BRENDA::Q82IK5 (364 letters) >NCBI__GCF_000010725.1:WP_012977708.1 Length = 418 Score = 149 bits (375), Expect = 2e-40 Identities = 127/392 (32%), Positives = 180/392 (45%), Gaps = 44/392 (11%) Query: 6 DRLPTFPWDKLE----PYKARAAAHPDGIVDLSVGTPVDPVPELIQKALVAAADSPG-YP 60 D L +P+ +L P RA P + L+VG P P L+++ L A+A YP Sbjct: 24 DLLTDYPFTRLANLLAPITPRANVSP---ILLTVGEPQHAPPVLLEETLRASASGWNKYP 80 Query: 61 TVWGTPELRDALTGWVERRLGA-RGVTH--HHVLPIVGSKE------LVAWLPTQLGLGP 111 V GTPE R A W+ RR G G+ H VLP+ G++E L+A + G P Sbjct: 81 PVGGTPEFRAAAGDWLTRRYGLPAGLLHADSSVLPLSGTREALFMLALLAVPARKAGRQP 140 Query: 112 GDKVAHPRLAYPTYEVGARLARADHVVYDDPTE------LDPTGLKLL------WLNSPS 159 V P Y YE A +A A+ V E LD +LL +L +P+ Sbjct: 141 A--VLMPNPFYAPYEGAAVMAGAEPVFLSATRETGFLPDLDALAPELLERTALFYLCTPA 198 Query: 160 NPTGKVLSKAELTRIVAWAREHGILVFSDECYLELGWEADPVSVLH-----PDVCGGSYE 214 NP G S A L + + AR +G ++ DECY E+ +A P L P G + Sbjct: 199 NPQGAAASPAYLAKAIGLARRYGFVLAVDECYAEIWLDAPPAGALQVAAGLPHDDGKPWA 258 Query: 215 GIVSVHSLSKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAH 274 ++ HSLSKRS+ AG R+ F+AGDPA++G ++R +G P QAA A D+AH Sbjct: 259 NLLVFHSLSKRSSAAGLRSGFVAGDPALIGRFSRLRSYGCAGMPLPIQAASTALWRDEAH 318 Query: 275 VREQRERYAARRTALRDALLSHGFRIEHSEASLYLWATRGESCWDTVAHLADLGILVAPG 334 V E R Y A + A +A L + +LW G+ A+ + V PG Sbjct: 319 VEENRAAYRA-KFAAAEAELGGRYGYYRPAGGFFLWLEVGDGEEAAKRLWAEGAVRVLPG 377 Query: 335 DFYG-------SAGEQFVRVALTATDERVAAA 359 + + G+ F+RVAL + VA A Sbjct: 378 AYLSRGNPGEPNPGDAFIRVALVQDADTVAQA 409 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: 454 Number of extensions: 39 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: 418 Length adjustment: 31 Effective length of query: 333 Effective length of database: 387 Effective search space: 128871 Effective search space used: 128871 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 10 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