Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate GFF1262 Psest_1295 Aspartate/tyrosine/aromatic aminotransferase
Query= reanno::Cup4G11:RR42_RS33490 (400 letters) >FitnessBrowser__psRCH2:GFF1262 Length = 398 Score = 423 bits (1088), Expect = e-123 Identities = 208/396 (52%), Positives = 274/396 (69%) Query: 1 MFEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADM 60 +F ++ P DPIL LNE+F D R +KVNL +G+Y+++EGR+P+++AV EAE A +A Sbjct: 3 LFSAVEMAPRDPILGLNEAFNADTRPNKVNLGVGVYYNEEGRIPLLRAVVEAEHARIAAN 62 Query: 61 GPRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFPD 120 PR YLP+ G AAY AVQ L+FG AEGR+ T Q LGG+GAL+VGADFLKR PD Sbjct: 63 APRGYLPIEGIAAYDAAVQKLLFGNDSSLIAEGRVVTTQALGGTGALKVGADFLKRLLPD 122 Query: 121 AQVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHAC 180 A V IS+PSWENHR +FE GF V Y YYD + G+ +L L+ +P RSIV+LHAC Sbjct: 123 AVVAISNPSWENHRALFESAGFPVQNYSYYDASNHGIDRAGLLQDLKNLPPRSIVVLHAC 182 Query: 181 CHNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPCLV 240 CHNPTGVDLN + W+Q++ +L+ + +PF+D+AYQGFG +++DA AVR G+ V Sbjct: 183 CHNPTGVDLNLEDWKQILEVLRAQDHVPFIDIAYQGFGDSIEEDAAAVRLFAESGMTFFV 242 Query: 241 ANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLTT 300 ++SFSK+FSLYGER G LS+V S EE+ RVL Q+ +R NYSNPPTHGA +VA VL + Sbjct: 243 SSSFSKSFSLYGERVGALSMVTQSREESARVLSQVKRVIRTNYSNPPTHGATIVASVLNS 302 Query: 301 PALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTADQVDR 360 P LR +WE EL RI ++R ++ + L A + S QRGMF+Y+GLTA+QV+R Sbjct: 303 PELRAMWEAELGEMRSRIRELRLSMVEQLTAKGAKTDFSFVAAQRGMFSYSGLTAEQVER 362 Query: 361 LRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASVL 396 LR E GVY + +GR+C A LN N+ V AI VL Sbjct: 363 LRVEFGVYAISTGRICAAALNRSNIGHVTDAIVQVL 398 Lambda K H 0.323 0.137 0.417 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: 424 Number of extensions: 17 Number of successful extensions: 1 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: 400 Length of database: 398 Length adjustment: 31 Effective length of query: 369 Effective length of database: 367 Effective search space: 135423 Effective search space used: 135423 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: 50 (23.9 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