Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_010935819.1 DET_RS00045 branched-chain amino acid transaminase
Query= BRENDA::P54691 (305 letters) >NCBI__GCF_000011905.1:WP_010935819.1 Length = 306 Score = 223 bits (568), Expect = 4e-63 Identities = 118/295 (40%), Positives = 177/295 (60%), Gaps = 6/295 (2%) Query: 8 AYFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSA 67 AYF+ + +P EDAKI V THALHYGT F G+RG + E + +FRL H RL A Sbjct: 6 AYFKKQIIPLEDAKIGVMTHALHYGTGVFEGIRGNWNNEKK-QMYIFRLKEHYTRLLTGA 64 Query: 68 KFLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVYSSGLGIAPRLHNLEKDFLVYGL 125 K L ++ + +++ ++ +D +KK + YIRPL Y S RLHNL+ D L+ + Sbjct: 65 KVLKMNLPYTVDELCKITIDLIKKCGFKEDIYIRPLAYKSSETFGVRLHNLDCDLLIVAI 124 Query: 126 EMGDYLAADGVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAILMNSQ 185 G Y+ D C +S+W+R +D P + K + Y+ +A KTEAVE+GFDE I++ Sbjct: 125 PWGRYIDKDTCHCCVSTWHRPDDNVMPPQLKSTGIYLNNAFTKTEAVENGFDEGIMLTPD 184 Query: 186 GKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIA-ADLGIPTCQRPIDKSELM 244 G V E +G N+F+VR G+++TP IL+GITR+S++ +A +LG+ +R ID+ EL Sbjct: 185 GHVSEGSGENLFIVRKGKLITPPICDSILDGITRNSVMELAEKELGLEVLERSIDRVELY 244 Query: 245 IADEVFLSGTAAKITPVKRIENFTLGGDR--PITEKLRSVLTAVTENREPKYQDW 297 IA+E FL+GTAA +TPV +++ +G P+T KL+ + + KY W Sbjct: 245 IAEECFLTGTAAHLTPVSEVDHRKVGNGEIGPVTAKLKDLYFEAIKGNIAKYSSW 299 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: 262 Number of extensions: 13 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: 305 Length of database: 306 Length adjustment: 27 Effective length of query: 278 Effective length of database: 279 Effective search space: 77562 Effective search space used: 77562 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