Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate GFF3088 PGA1_c31390 putative aromatic-L-amino-acid decarboxylase
Query= BRENDA::H7CE71 (509 letters) >FitnessBrowser__Phaeo:GFF3088 Length = 470 Score = 307 bits (786), Expect = 6e-88 Identities = 165/483 (34%), Positives = 261/483 (54%), Gaps = 22/483 (4%) Query: 26 EFRKQGHMVIDFIADYYQNIEKYPVLSRVEPGYLKKCLPESAPYDPEPISTILKDVQDHI 85 +F G + D+ DY+Q + PV +R EPG + LP + P E + I D + + Sbjct: 5 DFSYWGRKIADWTQDYHQTVGDRPVRARTEPGDVLNALPATPPETGEDMEAIFADFETVV 64 Query: 86 VPGLTHWQSPNFFAYFSSTASTAGFLGEILTTGFNVVGFNWVSSPAATELENIVMDWLGD 145 +PG+THWQ P FFAYF+S A+ L E LT+ W +SPAATE+E +MDWL Sbjct: 65 MPGITHWQHPRFFAYFTSNAAAPSVLAEFLTSAIAPQCMLWQTSPAATEMETRMMDWLRQ 124 Query: 146 MLQLPKSFHFSGNGGGVLHGSTCEAIVCTMVAARDQMLRRIGSEN----LGKLVVYGSDQ 201 L LP+ F GV+ S A + ++ R++ L G+E L +Y S + Sbjct: 125 ALDLPEEFQ------GVIQDSASSATLAAVLTMREKALNWQGNEQGLFAQKTLRIYCSSE 178 Query: 202 THSTLQKATQIVGINTENFRAIKTTKSTGFALSPEMLRLTISSDLEKGLVPLFLCATIGT 261 H+++ +A + GI +N + K + PE L I +D+ G P + +G Sbjct: 179 VHTSVDRAIWVAGIGQQNLVRVPI-KGDWRGMDPEALDAAIEADIAVGHQPAGVILCVGG 237 Query: 262 TATTAIDPLEALCHVAKEYGVWVHVDAAYAGSACICPEFRHFINGVEGANSFSFNPHKWL 321 T A DP++ + VA++YG++ HVDAA+AGSA ICPE+R + G+E A+S FNPHKWL Sbjct: 238 TGVGATDPVDQVLDVAEKYGLYTHVDAAWAGSAMICPEYRDYWPGIERADSIVFNPHKWL 297 Query: 322 FTGMDCCCLWVKNPSVLASSLSTNPEFLRNKASDSKQVVDYKDWQIALSRRFRALKLWLV 381 DC ++K+P L +L+ +PE+L+ D +++Y +W + L RRFRALK+W + Sbjct: 298 GVQFDCSAHFLKDPDDLVRTLAISPEYLKTHGKDG--IINYSEWSVPLGRRFRALKIWFL 355 Query: 382 LRSYGVANLRNFIRIHVNMAKTFEGLVRMDKRFEILVPRNFSLVCFRISPSALISSNEDD 441 +R+YG+ LR +R HV ++ ++ + FEI+ P +SL FR P+ Sbjct: 356 IRTYGLEGLRQRLRNHVTWSQQLHDRLKSEPDFEIVTPPMWSLWSFRYQPNGAAD----- 410 Query: 442 EIGMVNEVNCKLLEAINASGKAYMTHAVVGGLYVLRCAVGATLSEEKHIVEAWKVVQDHA 501 ++++N +L+ AIN G+ Y+T V G V+R G + E ++ A V+ + A Sbjct: 411 ----LDDLNLRLVNAINDDGRIYLTQTRVDGALVIRFQAGQFETTEADVMMAHDVITEIA 466 Query: 502 KAI 504 + + Sbjct: 467 RTL 469 Lambda K H 0.321 0.135 0.416 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: 588 Number of extensions: 21 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: 509 Length of database: 470 Length adjustment: 34 Effective length of query: 475 Effective length of database: 436 Effective search space: 207100 Effective search space used: 207100 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 (21.9 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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