Align Putative aspartate aminotransferase YhdR; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_035235354.1 Q366_RS00510 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O07587 (393 letters) >NCBI__GCF_000745975.1:WP_035235354.1 Length = 391 Score = 299 bits (766), Expect = 8e-86 Identities = 149/370 (40%), Positives = 235/370 (63%), Gaps = 4/370 (1%) Query: 14 LNKGSWIRKLFDEGARLKKEFGEDQVFDFSLGNPIVEPPEAFKRALIEEAEKG--SHGYI 71 + S IRK+F+EG R++++FG D VFDFSLGNP V PP K +++ SHGY+ Sbjct: 11 VKSASMIRKMFEEGIRMREQFGADNVFDFSLGNPDVPPPPVVKETVLDLVNDAATSHGYM 70 Query: 72 QNQGLLAAREKVAQFLGSRFEADFSAERIVMTVGAGGALNVALKSIVNPGEEVIILAPYF 131 N G R+ +A +L ++ +++ ++M+VGA GALN LK++VNPGEE+++ APYF Sbjct: 71 PNAGYPWVRQAIADYLNAQCGVGMTSDLVIMSVGAAGALNDTLKALVNPGEEILVPAPYF 130 Query: 132 AEYKLYIENYGGKAVSCPLTSRFEIDIEAVRQSITPQTKGLILNTPHNPTGTVLSQKNID 191 Y Y G + F +D+ A+ +I T+ +++N+P+NPTG V +++ +D Sbjct: 131 VGYNQYAFIVGASLKTVSARPDFHLDLGAIEAAINKNTRVMLINSPNNPTGVVYTRQELD 190 Query: 192 DLGALLKEIEEKSGQTIYVLFDEPYSQLIYDEELANPFQSYHRVILASSFSKDLGIAGER 251 +LG LL++ + G+ IY+L DEPY ++ YD ++ F Y I+ +S+SK+L +AGER Sbjct: 191 ELGQLLEKKSREFGKRIYLLSDEPYRKIAYDVDVPWMFGVYDHTIVLTSYSKELSLAGER 250 Query: 252 LGYIGLDSRMPDADLLINAFVYCNRTLGFVNAPVMMQRAVARMDDLRVDASAYKERRDLM 311 +GY+ + DA+L+ A N T+ FVNAP + Q+ V ++ + VD Y++RRD++ Sbjct: 251 VGYLAVHPGAEDAELIAVAAGVAN-TMMFVNAPALFQQVVGKLQGVCVDIDIYRKRRDMI 309 Query: 312 VDILKEAGFEFEMPKGGFFVFPKSPIEDEVAFCVHAAQKYKLLIVPSSGFGMSGHFRLSF 371 + L AG+EF +P+G F++FPK+PIE++V F +K +L VP SGFG GH RLS+ Sbjct: 310 CEGLAAAGYEFNIPEGAFYLFPKTPIENDVEF-AGLLKKENILAVPGSGFGGPGHIRLSY 368 Query: 372 SVPIEQIKNS 381 +VP + I NS Sbjct: 369 AVPEQAIVNS 378 Lambda K H 0.320 0.139 0.396 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: 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: 393 Length of database: 391 Length adjustment: 31 Effective length of query: 362 Effective length of database: 360 Effective search space: 130320 Effective search space used: 130320 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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