Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate RR42_RS05990 RR42_RS05990 aromatic amino acid aminotransferase
Query= reanno::Cup4G11:RR42_RS33490 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS05990 Length = 398 Score = 434 bits (1117), Expect = e-126 Identities = 212/396 (53%), Positives = 276/396 (69%) Query: 1 MFEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADM 60 +F ++ P DPIL LNE+F D R KVNL +G+YF DEG++P+++AV+EAE A + Sbjct: 3 LFSAVEMAPRDPILGLNEAFNADTRATKVNLGVGVYFTDEGKIPLLRAVQEAEKARLTTA 62 Query: 61 GPRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFPD 120 PR YLP+ G AAY AVQ L+FG+ EGR+ T Q LGG+GAL++GADFLKR +PD Sbjct: 63 TPRGYLPIEGIAAYDQAVQTLLFGKESPLITEGRVVTAQALGGTGALKIGADFLKRLYPD 122 Query: 121 AQVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHAC 180 A+V ISDPSWENHR +FE GF V Y YYD A+ GL F M+++L+ +IV+LHAC Sbjct: 123 AKVAISDPSWENHRALFEAAGFPVINYAYYDAASHGLNFAGMVESLKSYAANTIVVLHAC 182 Query: 181 CHNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPCLV 240 CHNPTGVDL+ +QW+Q++ L+K+ L+PF+DMAYQGF G++ D AVR G+P V Sbjct: 183 CHNPTGVDLSAEQWKQVVELIKERNLIPFLDMAYQGFAEGIEPDGAAVRLFAESGLPFFV 242 Query: 241 ANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLTT 300 ++SFSK+FSLYGER G LS+V EE RV+ Q+ +R NYSNPPTHG VVA VL + Sbjct: 243 SSSFSKSFSLYGERVGALSIVTTGKEEAQRVMSQVKRVIRTNYSNPPTHGGTVVATVLNS 302 Query: 301 PALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTADQVDR 360 P LR +WE+EL +RI MR A+ LAA S +QRGMF+Y+GL + QVD Sbjct: 303 PELRAMWEQELGEMRDRIKLMRHALVDKLAAKGVPGDFSFVKSQRGMFSYSGLNSAQVDV 362 Query: 361 LRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASVL 396 LR EHG+Y + +GR+CVA LN RN+ V AIA+VL Sbjct: 363 LRNEHGIYAVGTGRICVAALNSRNIDAVVNAIAAVL 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: 436 Number of extensions: 10 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 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