Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_013683744.1 ARCVE_RS05320 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_000194625.1:WP_013683744.1 Length = 375 Score = 298 bits (764), Expect = 1e-85 Identities = 168/387 (43%), Positives = 243/387 (62%), Gaps = 22/387 (5%) Query: 4 LSRRVQAMKPSATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTK 63 +SRR ++++PSAT+++++ A EL RQG ++ + GEPDF TP+H+ EAA +AL +GKT Sbjct: 2 ISRRAKSIQPSATLSISSTAKELARQGKPVINMGVGEPDFVTPKHIIEAAIKALNEGKTF 61 Query: 64 YAPPAGIPELREALAEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSP 123 Y P GIPEL +A+ EK +++GL V E IVT G K A+F A+++ GDEVI+L P Sbjct: 62 YTPTRGIPELVDAIVEK-AKQDGLDVKAENVIVTPGAKYAIFEAILAVIEEGDEVILLDP 120 Query: 124 YWVSYPEMVRFAGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPK 183 WVSY V+ AGG VV V EGF P + + +TK +++NSP+NP G VYPK Sbjct: 121 SWVSYEPCVQVAGGKVVWVP--HSEGFSDAP--IEEYVKQKTKLIIINSPSNPLGVVYPK 176 Query: 184 EVLEALARLAVEHDFYLVSDEIYEHLLYEGEHFSPGRV--APEHTLTVNGAAKAFAMTGW 241 E L+ + +AV++D ++SDEIY+ +++EGE S PE T+ +NG +K +AMTGW Sbjct: 177 EFLKKVRDIAVDNDILVMSDEIYDKIIFEGEFVSIAGFDGMPERTIVINGFSKTYAMTGW 236 Query: 242 RIGYACGPKEVIKAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRD 301 R+GYA P+E+ K M + S S + P + Q+A + AL + + EM E ++ RRD Sbjct: 237 RLGYAIAPEEITKHMLRIQSHSVSHPTSFVQYAGVAALKGDQ--KCVEEMVAE-FKVRRD 293 Query: 302 LLLEGLTALGLKAVRPSGAFYVLMDTSPIAPDEVRAAERLLEAG-VAVVPGTDFAAFGH- 359 +L+EGL +GLK P GAFY+ +D + D ++ E L+ VA PG +AFG Sbjct: 294 MLMEGLDEIGLKYAPPKGAFYMFVD---VGQDSMKFCEEFLKKEYVAATPG---SAFGRV 347 Query: 360 ----VRLSYATSEENLRKALERFARVL 382 VRLSYATS EN+ +A+ R R L Sbjct: 348 FTTWVRLSYATSRENIEEAIRRLKRFL 374 Lambda K H 0.317 0.133 0.379 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: 391 Number of extensions: 22 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: 385 Length of database: 375 Length adjustment: 30 Effective length of query: 355 Effective length of database: 345 Effective search space: 122475 Effective search space used: 122475 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 (21.7 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