Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012384514.1 BIND_RS07730 D-amino-acid transaminase
Query= BRENDA::E6TUA8 (302 letters) >NCBI__GCF_000019845.1:WP_012384514.1 Length = 286 Score = 149 bits (375), Expect = 1e-40 Identities = 90/278 (32%), Positives = 155/278 (55%), Gaps = 9/278 (3%) Query: 3 SQWIFSNGKFVTKQEAVISVYDHGFLYGDGVFEGIRVYDGNIFKLTEHLKRLYESAQSIM 62 S+ + NG+++ ++EA +SV D G+L+GDGV+E + ++ G + H +RL S + Sbjct: 2 SRIFYLNGRYLPREEAHVSVEDRGYLFGDGVYEVLEIHRGALIDEDRHWQRLDRSLSELR 61 Query: 63 LEIPYSKEDFQQIIVDTVRKNQLESGYIRVVVSRGPG-NLGLDPSRCSAPHVIVIAEELA 121 + P + F +++ + +N++E+G++ + ++RG + P++ P ++V A + Sbjct: 62 ISWPIGQAAFGRVLREVKARNKVENGFLYIQITRGAAPREHVFPAQNVRPSLLVSARPVD 121 Query: 122 LFPKELY-ELGLTVASVASRR-NRPDVLSPQIKSLNYLNNILVKLEANQAGAHEALMLND 179 E + G+ V S+ R R D IK++N L N+L K A + GA EA + ++ Sbjct: 122 PRKGEAQAQKGIGVISLPDLRWKRVD-----IKTINLLPNVLAKQAAKEEGATEAWLFDE 176 Query: 180 QGYVTEGSADNIFIV-KNNTIITPPVYLGALEGITRNAIIDLAKECGYEMKETPFTRHDV 238 +G VTEG+A N +I+ +N TI T PV L GITR +ID+ GY +KE F+ + Sbjct: 177 EGLVTEGAASNAWIIDENRTIHTHPVDHSILRGITRTTLIDIIAAKGYALKERRFSLAEA 236 Query: 239 YVADEVFLTGTAAEVIAVVEVDKRMISDGKPGKVTNHL 276 A E F+TG + V+ VV +D + I +G PG + L Sbjct: 237 RAAREAFITGALSLVMPVVRIDGKPIGEGVPGPIATEL 274 Lambda K H 0.318 0.136 0.385 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: 172 Number of extensions: 4 Number of successful extensions: 3 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: 302 Length of database: 286 Length adjustment: 26 Effective length of query: 276 Effective length of database: 260 Effective search space: 71760 Effective search space used: 71760 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: 48 (23.1 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