Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate N515DRAFT_0573 N515DRAFT_0573 branched-chain amino acid aminotransferase
Query= BRENDA::P54691 (305 letters) >FitnessBrowser__Dyella79:N515DRAFT_0573 Length = 313 Score = 169 bits (428), Expect = 8e-47 Identities = 102/302 (33%), Positives = 160/302 (52%), Gaps = 14/302 (4%) Query: 6 PIAYFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSK 65 P + + P+ +A + V+THALHYG++ F G R P+ P FRL H RL + Sbjct: 4 PFLWHNGQIKPWTEATVHVSTHALHYGSSVFEGERVYATPQGPA---YFRLADHTRRLFE 60 Query: 66 SAKFLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVY--SSGLGIAPRLHNLEKDFL 121 SA+ ++ S ++I ++ ++ N+ S Y+RP+V+ + GLG+ + D Sbjct: 61 SARVYEIEVGYSEDEINAACMEVIRANRMG-SAYVRPIVFRGAGGLGVLAK-PGAPVDVA 118 Query: 122 VYGLEMGDYLA---ADGVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDE 178 + +E G YL G +SSW R + P K Y++S L EA G+ E Sbjct: 119 IMAMEWGAYLGDAREQGADVCVSSWQRPAPNTVPSWAKAGGNYLSSQLIGLEARRGGYAE 178 Query: 179 AILMNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPI 238 I + G + E G NVF+V+NG+++TP IL GITRD+++T+A DLGI +R + Sbjct: 179 GIALGHNGLLSEGAGENVFVVKNGKLLTPPTSAGILAGITRDTVMTLAEDLGIKVEERDL 238 Query: 239 DKSELMIADEVFLSGTAAKITPVKRIENFTLGGDR--PITEKLRSVLTAVTENREPKYQD 296 + L ADEVF++GTAA+ITPV+ ++ +G R PIT L+ + + R Sbjct: 239 PREALYTADEVFMTGTAAEITPVRSVDRKPVGTGRPGPITRALQDAFFGLFDGRTDDRWG 298 Query: 297 WV 298 W+ Sbjct: 299 WL 300 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: 232 Number of extensions: 14 Number of successful extensions: 2 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: 313 Length adjustment: 27 Effective length of query: 278 Effective length of database: 286 Effective search space: 79508 Effective search space used: 79508 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 09 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