Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate 201550 SO2406 aspartate aminotransferase (NCBI ptt file)
Query= CharProtDB::CH_004054 (397 letters) >FitnessBrowser__MR1:201550 Length = 396 Score = 317 bits (812), Expect = 4e-91 Identities = 159/397 (40%), Positives = 237/397 (59%), Gaps = 1/397 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MF + A DPIL L+ +++ED KV+L +G+Y + G P L V +AE + + Sbjct: 1 MFNSLIAMPADPILGLLTQYREDTHPQKVDLGVGVYKDPAGNTPILNCVKKAE-KFRLET 59 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 +Y+ G + + L FG+DH + R+ T+ T GG+GAL+V DF+KR P Sbjct: 60 ETTKVYIGPTGSPQFNTLMTELAFGSDHSAIIANRIRTVSTPGGTGALRVAGDFIKRCNP 119 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 + +WVSDPTW NH +F AG V TYP+YD + ++F+++LA L + +VLLH Sbjct: 120 NAVLWVSDPTWANHTGLFEAAGITVKTYPYYDYDSKSLKFDEMLAALSQVSPDDVVLLHA 179 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNP+G DLT DQWD V+ + K + P +D+AYQGFG G++ DAY +R +A+A + Sbjct: 180 CCHNPSGMDLTTDQWDKVVTLTKEQGFTPLIDMAYQGFGDGVDIDAYGVRKMAAAVDNMI 239 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 + +S SK F LY ER+G SV+ +DA A L VR YS PP GA +V +L Sbjct: 240 LCSSCSKNFGLYRERIGSCSVVAKDANTANIAQSVLLYVVRCLYSMPPAHGAAIVETILG 299 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 + L WL E++ MR RI R LV+ L R+F ++ Q+GMFS+ G++ QV Sbjct: 300 SKELTQEWLDELKVMRDRINGNRAILVEKLKANGVARDFSFIARQKGMFSFLGVNPEQVA 359 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 RL++EF +Y++ S R+ +AG++ NV +A++ A V+ Sbjct: 360 RLQKEFSIYMVGSSRISIAGISEDNVDYLAQSIAKVL 396 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: 381 Number of extensions: 13 Number of successful extensions: 2 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: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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 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