Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_092052812.1 BQ4888_RS01695 hypothetical protein
Query= BRENDA::Q939C9 (436 letters) >NCBI__GCF_900111775.1:WP_092052812.1 Length = 434 Score = 472 bits (1215), Expect = e-138 Identities = 239/430 (55%), Positives = 305/430 (70%), Gaps = 9/430 (2%) Query: 1 MNDAAKELNRTLSEENPHVLHMLSDLGRELFYPKGVLTQSAEAKAKAGKYNATIGIATSQ 60 MN A ELN LS+ NP+VL MLSDLG+ LF+PKG+LTQSAEAK KA KYNATIGIAT + Sbjct: 1 MNPLAVELNEQLSQHNPYVLEMLSDLGKNLFFPKGILTQSAEAKDKAHKYNATIGIATEK 60 Query: 61 GESMHFSHIQETLSAYNPDDIYDYAPPQGKEPLRQEWLKKMRLENPSLAGKDISTPIVTN 120 G M IQ+ LSA++P DIY YAPP GK LR W +KM ENPS+ GK S PIVTN Sbjct: 61 GGPMFLQCIQDKLSAFDPKDIYPYAPPAGKPELRSLWREKMLRENPSMQGKHFSNPIVTN 120 Query: 121 ALTHGLSIAADLFVNEGDTLLLPDKYWGNYNFIFGVRRKASIETYPLFQQDGRFNAAGLS 180 ALTHGLSI D+F+ GD L+LPD WGNYN FG A ++ +P F G ++ A Sbjct: 121 ALTHGLSIVGDMFLGVGDHLVLPDMLWGNYNLTFGTCNGAIVKKFPTFTATGGYDVAAFK 180 Query: 181 ELLKK---QEEKAIVVLNFPNNPTGYTPGEEEASEIVSVILEAAEAGKEIVVLVDDAYYN 237 +L ++ KA+V+LNFPNNP+GYTP E IV+ I E AE+G IV + DDAY+ Sbjct: 181 AVLTNTAAEKGKAVVLLNFPNNPSGYTPTIAEGDAIVAAIKEVAESGCNIVAITDDAYFG 240 Query: 238 LFYDETAIQESIFSKLAQVHDRVLCVKIDGATKENYAWGFRVGFITY----STKSEKALR 293 LFY E ++ES+F KLA +H R+L +K+DGATKE + WGFR GFIT+ S ++ L Sbjct: 241 LFY-EDCMKESLFGKLANLHPRILAIKLDGATKEEFVWGFRTGFITFADGKSGENAPVLT 299 Query: 294 VLEEKTKGIIRGTISSAPHPSQTFMLRAMQSPEYEKEKSLKYNIMKKRADKVKAVLAENK 353 LE+KT GIIR IS+ PHPSQTF++ A++SP++ ++K K+ +MK RA K KAVL K Sbjct: 300 ALEKKTMGIIRAKISNCPHPSQTFVIEALRSPKFLEQKEEKFQVMKGRALKTKAVLNSGK 359 Query: 354 HYEDVWTPYPFNSGYFMCVRLKDINAGELRVSLLEKRGIGTISINETDLRIAFSCVEEEH 413 Y+ W YPFNSGYFMC++LK ++A +LRV LL+K G+G ISIN+TDLRIAFSC+ EE+ Sbjct: 360 -YDKAWDYYPFNSGYFMCLKLKTVDAEKLRVHLLDKYGVGAISINKTDLRIAFSCIAEEN 418 Query: 414 IADLFEEIYQ 423 I +LF+ I+Q Sbjct: 419 IQELFDIIHQ 428 Lambda K H 0.315 0.133 0.377 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: 569 Number of extensions: 26 Number of successful extensions: 5 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: 436 Length of database: 434 Length adjustment: 32 Effective length of query: 404 Effective length of database: 402 Effective search space: 162408 Effective search space used: 162408 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: 42 (22.0 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