Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate GFF3889 PS417_19910 aromatic amino acid aminotransferase
Query= CharProtDB::CH_004054 (397 letters) >FitnessBrowser__WCS417:GFF3889 Length = 397 Score = 324 bits (831), Expect = 2e-93 Identities = 175/395 (44%), Positives = 241/395 (61%), Gaps = 2/395 (0%) Query: 2 FQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQPH 61 F + GDPIL LM+ + +D +K +L +G+Y ++ G+ P +V AE RL Sbjct: 3 FDAIGRVPGDPILGLMDLYAQDTNPNKFDLGVGVYKDDQGLTPIPHSVKLAEQRL-VDTQ 61 Query: 62 GASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFPE 121 Y+ G + I+ L+ GAD +++++R QT GG+GAL++ ADF+ P Sbjct: 62 TTKTYIGGHGNAAFGKLISELVLGADSTLIRERRAGATQTPGGTGALRLSADFIAHNLPG 121 Query: 122 SGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHPC 181 GVW+S+PTW H IFA AG VS YP Y A N + +LATL T+P +VLLH C Sbjct: 122 RGVWLSNPTWPIHETIFAKAGIPVSHYP-YVGADNRLDVAAMLATLSTVPKGDVVLLHAC 180 Query: 182 CHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPALV 241 CHNPTG DL+ D W V++I++ R+L+P +D AYQGFG G+E+DA+A+R A+ LV Sbjct: 181 CHNPTGFDLSQDDWRQVLQIVRERQLLPLIDFAYQGFGDGLEQDAWAVRLFAAELPEVLV 240 Query: 242 SNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLND 301 ++S SK F LY +RVG L V DAE V QL T R +S+PP+ GA VVA +L D Sbjct: 241 TSSCSKNFGLYSDRVGALIVCAADAEKLTDVRSQLANTARNLWSTPPDHGAAVVATILGD 300 Query: 302 EALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVDR 361 LK W EVE MR+RI +R LV+ L+ F ++ QRGMFSYTGLSA QV + Sbjct: 301 AELKKRWSDEVEAMRSRIAHLRSGLVEALAPHGLSARFAHIGAQRGMFSYTGLSAEQVKQ 360 Query: 362 LREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAV 396 LRE+ VY+++SGR VAG++ + +AKA A V Sbjct: 361 LREKHSVYMVSSGRANVAGIDATRLTLLAKAIADV 395 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: 389 Number of extensions: 14 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: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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 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