Align aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_075387886.1 BK574_RS21330 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::Q9SIE1 (475 letters) >NCBI__GCF_002019605.1:WP_075387886.1 Length = 393 Score = 281 bits (720), Expect = 2e-80 Identities = 175/408 (42%), Positives = 246/408 (60%), Gaps = 27/408 (6%) Query: 65 SSSVDMSLSPRVQSLKPSKTMVITDLAATLVQSGVPVIRLAAGEPDFDTPKVVAEAGINA 124 S+ V+ LS VQS++PS DLA+T+ +I L GEPDF TP V EA ++ Sbjct: 4 STKVNRRLSKSVQSIQPSGIRRFFDLASTMDN----IISLGVGEPDFVTPWNVREAAFSS 59 Query: 125 IREGFTRYTLNAGITELREAICRKLKEENGLSYAPD-QILVSNGAKQSLLQAVLAVCSPG 183 + GFT YT NAG+ ELRE I + + ++ L Y+PD ++LV+ GA +++ A+ A+ PG Sbjct: 60 LERGFTAYTANAGLLELREEISKYMSQQFALPYSPDSEVLVTVGASEAIDLAIRALVDPG 119 Query: 184 DEVIIPAPYWVSYTEQARLADATPVVIPTKISNNFLLDPKDLESKLTEKSRLLILCSPSN 243 DEVI+ P +VSY LA PV + TK + F + P LE+ +T K++L+++C P+N Sbjct: 120 DEVIVVEPTFVSYAPIVSLAGGVPVSVGTKKEDEFKVTPAQLEAAITPKTKLVMICFPNN 179 Query: 244 PTGSVYPKSLLEEIARIIAKHPRLLVLSDEIYEHIIYAPATHTSFASLPDMYERTLTVNG 303 PTG+V K LE I+ +I KH LLVLSDEIY + Y +H S A LPDM +RT+ ++G Sbjct: 180 PTGAVMTKEELELISHVIKKHD-LLVLSDEIYAELSY-ETSHYSIARLPDMRDRTVVISG 237 Query: 304 FSKAFAMTGWRLGYLAGPKHIVAACSKLQGQVSSGASSIAQKAGVAALGLGKAGGETVAE 363 FSKAFAMTGWRLG+ P+ I AA K+ AS+ AQ + AL G A V + Sbjct: 238 FSKAFAMTGWRLGFTLAPEDITAAMLKIHQYTMMCASTPAQYGALEALQNGLA---DVKK 294 Query: 364 MVKAYRERRDFLVKSLGDIKGVKISEPQGAFYLF--IDFSAYYGSEAEGFGLINDSSSLA 421 MV++Y +RR+F+VKS +I G+ P GAFY F I + Y DS A Sbjct: 295 MVQSYNQRRNFIVKSYAEI-GLPCHTPGGAFYAFPSIKNTGY------------DSGEFA 341 Query: 422 LYFLDKFQVAMVPGDAFGD--DSCIRISYATSLDVLQAAVEKIRKALE 467 L + +VA+VPGD FG+ + IR SYATS++ L+ +V +I + LE Sbjct: 342 EKLLLEERVAVVPGDVFGEGGEGHIRCSYATSMENLEESVRRIGRFLE 389 Lambda K H 0.317 0.132 0.370 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: 411 Number of extensions: 25 Number of successful extensions: 8 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: 475 Length of database: 393 Length adjustment: 32 Effective length of query: 443 Effective length of database: 361 Effective search space: 159923 Effective search space used: 159923 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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