Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_035239975.1 Q366_RS13815 hypothetical protein
Query= BRENDA::Q939C9 (436 letters) >NCBI__GCF_000745975.1:WP_035239975.1 Length = 436 Score = 382 bits (980), Expect = e-110 Identities = 192/437 (43%), Positives = 280/437 (64%), Gaps = 9/437 (2%) Query: 1 MNDAAKELNRTLSEENPHVLHMLSDLGRELFYPKGVLTQSAEAKAKAGKYNATIGIATSQ 60 MN A+ELN T+ + PHV MLSD+G+ LF+P+G+LTQSAEAK KA + NATIGIA Sbjct: 1 MNPIAQELNNTIKQAAPHVYEMLSDMGKNLFFPEGILTQSAEAKLKAHRINATIGIARQG 60 Query: 61 GESMHFSHIQETLSAYNPDDIYDYAPPQGKEPLRQEWLKKMRLENPSLAGKDISTPIVTN 120 + + + ++ PD+ YA G LR++WLK++ ++NPSL G +S P+VT+ Sbjct: 61 SCVLSLPSVTKYITEIEPDNYLSYASSFGLLELREKWLKELYVKNPSLGGTAVSLPVVTS 120 Query: 121 ALTHGLSIAADLFVNEGDTLLLPDKYWGNYNFIFGVRRKASIETYPLFQQD-GRFNAAGL 179 +THG+SI +D++VN D +++PD WGNYN IF VR A TY + FN Sbjct: 121 GITHGVSILSDMWVNANDVIVMPDMMWGNYNMIFCVRNSARFVTYKSYDDALTHFNIDDF 180 Query: 180 SELLKKQ---EEKAIVVLNFPNNPTGYTPGEEEASEIVSVILEAAEAGKEIVVLVDDAYY 236 ++++Q +K I +LNFP+NPTGYT EEA+ + ++++ A+ G +V DDAY+ Sbjct: 181 ERVIREQAAHNDKIITILNFPHNPTGYTLSREEATRVAQILIDVAQKGTNVVAACDDAYF 240 Query: 237 NLFYDETAIQESIFSKLAQVHDRVLCVKIDGATKENYAWGFRVGFITYSTKS----EKAL 292 LF++E +ES+F+KLA R+L VK+DG TKE+Y GFR GF TY + ++ Sbjct: 241 GLFFEEETSKESLFAKLAGKASRLLAVKLDGPTKEDYVMGFRTGFTTYGVAADANLDRVY 300 Query: 293 RVLEEKTKGIIRGTISSAPHPSQTFMLRAMQSPEYEKEKSLKYNIMKKRADKVKAVLAEN 352 RVLE+KT G IRG IS+ H SQT ++++M+ Y+ K K++++K RA +K VL + Sbjct: 301 RVLEKKTAGCIRGNISNCSHLSQTILVKSMEDANYKILKQEKFDLLKSRATAIKEVLKDP 360 Query: 353 KHYEDVWTPYPFNSGYFMCVRLKDINAGELRVSLLEKRGIGTISINETDLRIAFSCVEEE 412 K Y + + YPFNSGYF+C+R+K +NA LR LL+ G G ISI E +LR+AFSC+EE+ Sbjct: 361 K-YAEGFDVYPFNSGYFVCIRVKGVNAESLRRHLLDNYGTGLISIGEDNLRVAFSCLEEK 419 Query: 413 HIADLFEEIYQEAKQLQ 429 + LF+ I L+ Sbjct: 420 DVKTLFDIILSGINDLR 436 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: 494 Number of extensions: 14 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: 436 Length of database: 436 Length adjustment: 32 Effective length of query: 404 Effective length of database: 404 Effective search space: 163216 Effective search space used: 163216 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