Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Dsui_2030 Dsui_2030 branched-chain amino acid aminotransferase, group I
Query= BRENDA::P54691 (305 letters) >FitnessBrowser__PS:Dsui_2030 Length = 308 Score = 163 bits (413), Expect = 4e-45 Identities = 102/298 (34%), Positives = 159/298 (53%), Gaps = 13/298 (4%) Query: 9 YFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAK 68 + + ++P+ DAK+ V +H LHYG F G+R P P +FRL+ H RL+ SA Sbjct: 11 WLDGHWLPWRDAKVHVLSHTLHYGYGCFEGIRAYATPRGPA---IFRLEEHLRRLADSAH 67 Query: 69 FLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVYSSGLGIAPRLHNLEKDFLVYGLE 126 L D+ S ++ +V + V +N D S YIRPLV+ + + +V Sbjct: 68 ILAIDLPWSRAELAQVCREAVSRNGLD-SAYIRPLVFLGPEKVGVDPAGAQTHVMVAAWP 126 Query: 127 MGDYLAAD----GVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAILM 182 G YL D G+ RISS+ R R K + Y S LA EA G+DEA+L+ Sbjct: 127 WGAYLGGDALEQGIRVRISSYARHHPNVQMCRAKAISTYSNSILAVREARRDGYDEALLL 186 Query: 183 NSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPIDKSE 242 +++G V E +G N+F+VR+G+++ P L+GITR SI +A + G+ + I + E Sbjct: 187 DTEGYVAEGSGENLFLVRDGELLEP-ETTSALDGITRRSIHVLAREAGLTLRAKRITRDE 245 Query: 243 LMIADEVFLSGTAAKITPVKRIENFTLGGDR--PITEKLRSVLTAVTENREPKYQDWV 298 + ADEVFL+GTAA++TPV ++ ++G + P+T L+ A + + DW+ Sbjct: 246 VYCADEVFLTGTAAEVTPVVEVDRRSIGTGQPGPVTRLLQQRYFACVRGEDEAHADWL 303 Lambda K H 0.320 0.138 0.406 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: 237 Number of extensions: 7 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: 305 Length of database: 308 Length adjustment: 27 Effective length of query: 278 Effective length of database: 281 Effective search space: 78118 Effective search space used: 78118 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 Aug 03 2021. The underlying query database was built on Aug 03 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