Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate H281DRAFT_04193 H281DRAFT_04193 branched chain amino acid aminotransferase apoenzyme
Query= BRENDA::P54691 (305 letters) >FitnessBrowser__Burk376:H281DRAFT_04193 Length = 307 Score = 184 bits (468), Expect = 2e-51 Identities = 106/301 (35%), Positives = 169/301 (56%), Gaps = 12/301 (3%) Query: 9 YFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAK 68 + + K + + DAKI V TH LHYG F G+R + G +FRL H RL SAK Sbjct: 11 WMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTAD--GGTAIFRLQEHTKRLLNSAK 68 Query: 69 FLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVY--SSGLGIAPRLHNLEKDFLVY- 123 D+ E + + V++N+ + S Y+RP+++ S LG++ + + + + Sbjct: 69 IFQMDVPFDHETLAAAQREVVRENKLE-SCYLRPIIWVGSEKLGVSAKGNTIHVAIAAWP 127 Query: 124 -GLEMGDYLAADGVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAILM 182 G +G+ A G+ + SS+ R +R K S Y+ S LA EA+ G+DEA+L+ Sbjct: 128 WGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALLL 187 Query: 183 NSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPIDKSE 242 + G V E +G N F+V NG++ TP + L+GITRD+++T+A D+GIP ++ I + E Sbjct: 188 DVDGYVSEGSGENFFLVNNGKLYTP-DLSSCLDGITRDTVITLARDMGIPVIEKRITRDE 246 Query: 243 LMIADEVFLSGTAAKITPVKRIENFTLGGDR--PITEKLRSVLTAVTENREPKYQDWVFK 300 + DE F +GTAA++TP++ ++N T+G PITEKL+S + + KY W+ K Sbjct: 247 VYTCDEAFFTGTAAEVTPIRELDNRTIGAGARGPITEKLQSGFFDIVNGKSEKYAHWLTK 306 Query: 301 I 301 I Sbjct: 307 I 307 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: 248 Number of extensions: 14 Number of successful extensions: 5 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: 307 Length adjustment: 27 Effective length of query: 278 Effective length of database: 280 Effective search space: 77840 Effective search space used: 77840 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