Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate YP_425599.1 Rru_A0508 aminotransferase
Query= BRENDA::F0QW25 (314 letters) >NCBI__GCF_000013085.1:YP_425599.1 Length = 294 Score = 107 bits (268), Expect = 3e-28 Identities = 85/273 (31%), Positives = 128/273 (46%), Gaps = 16/273 (5%) Query: 29 ATIPILTHALHYGTSIFEGIRAYWNSDNNNLYVFRARDHYVRFHDSAKIMSIKVGYSVDE 88 A I TH L +++F+G R Y+ +L H R SA++M ++ + E Sbjct: 27 ALIGPATHGLWMASTVFDGAR-YFEGVAPDLLA-----HCERVIHSARLMGLEPCLTGAE 80 Query: 89 LIDATVE-LLRANDVHED---VYIRPITFVSASTVNLDIRNLDVTTAIITVPFGHYLEPK 144 + D E + R D +ED +YI P+ + + D + + P EP Sbjct: 81 IADFAWEGISRFKDHYEDAGDLYICPMIYGETGFIMPDAESAQFVLCLWETPMP---EPV 137 Query: 145 GIKAKVVSWLRVHNSMFPMKAKVSGIYVNSVIAIIDAKVSGFDEAILLNRDGYVAEGSGE 204 G A + + R M P +AK S +Y N A+ AK GF+ A++L+ G VAE S Sbjct: 138 GFSACLTPFRRPARDMAPTEAKASCLYPNVGRAVRAAKERGFETAVMLDPAGNVAEFSYT 197 Query: 205 NIFIIKDGILYTPPVYDSILEGITRDTVITIARDLGLTVTEKRITREELYTADEVFFTGT 264 N+F K + TP + L G+TR +I + RD G+ V E+ + E+ ADEVF TG Sbjct: 198 NLFFAKGSQVITPAPNGTFLNGLTRQRIIRLLRDDGVDVVERAVDFAEVLDADEVFATGN 257 Query: 265 AAEVTPVVNIDGRVIGNGEPGPIALKVRSYYMD 297 +V V I+ R EPGP K R+ Y + Sbjct: 258 YFKVGTCVKIEDRTF---EPGPYYRKARALYWE 287 Lambda K H 0.321 0.139 0.409 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: 215 Number of extensions: 12 Number of successful extensions: 1 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: 314 Length of database: 294 Length adjustment: 27 Effective length of query: 287 Effective length of database: 267 Effective search space: 76629 Effective search space used: 76629 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: 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