Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_050465852.1 AKL27_RS26210 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_001189915.1:WP_050465852.1 Length = 403 Score = 404 bits (1037), Expect = e-117 Identities = 199/389 (51%), Positives = 263/389 (67%), Gaps = 6/389 (1%) Query: 11 DPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARL--NAQPHGASLYLP 68 DPIL + E + K+NL +G+YY++ G +P LQ V +AEA L + +PH YLP Sbjct: 19 DPILGITEAYNRSTHPAKINLGVGVYYDDQGKVPLLQCVRQAEADLLQHPKPH---TYLP 75 Query: 69 MEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFPESGVWVSD 128 +EGL Y +A+ LF +QRV T+QT GG+GALKVGADFL+R+FP++ VW+SD Sbjct: 76 IEGLAAYNNAVRRQLFDGTR-AFDEQRVITLQTAGGTGALKVGADFLQRFFPDAQVWISD 134 Query: 129 PTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHPCCHNPTGA 188 P+WENH A+F AGF V+ YP+YD A N + F +LATL+ +PA IVLLH CCHNPTG Sbjct: 135 PSWENHAALFEAAGFTVNAYPYYDAARNDLNFPAMLATLEQIPAGDIVLLHACCHNPTGL 194 Query: 189 DLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPALVSNSFSKI 248 DL + QW V+EI+ R LIPFLD+AYQGFG + ED ++ A +GL VS++FSK Sbjct: 195 DLDDSQWQQVLEIITRRRLIPFLDMAYQGFGGSLAEDGKVVQRFADSGLTVFVSSTFSKS 254 Query: 249 FSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLNDEALKASW 308 FSLY ER+G LSV+ + A R+L QLK T+R NYSSPP GA +VAAVL + L+A W Sbjct: 255 FSLYSERIGALSVVSASPDEAARLLSQLKRTIRTNYSSPPGHGAAIVAAVLGSDQLRALW 314 Query: 309 LAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVDRLREEFGV 368 E+ +MR RI MRQ+L L +P R+F +L Q G+FSYTGL QV RLREEF + Sbjct: 315 EQELAQMRERITGMRQQLRARLQQHLPARDFSFLTRQAGLFSYTGLQPEQVTRLREEFEI 374 Query: 369 YLIASGRMCVAGLNTANVQRVAKAFAAVM 397 + + +GR+CVA +N+ N+ +A A A VM Sbjct: 375 HTLGTGRICVAAVNSGNLDTIATALARVM 403 Lambda K H 0.320 0.135 0.401 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: 417 Number of extensions: 17 Number of successful extensions: 3 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: 397 Length of database: 403 Length adjustment: 31 Effective length of query: 366 Effective length of database: 372 Effective search space: 136152 Effective search space used: 136152 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: 50 (23.9 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