Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate 3606714 Dshi_0145 Aspartate transaminase (RefSeq)
Query= CharProtDB::CH_004054 (397 letters) >FitnessBrowser__Dino:3606714 Length = 392 Score = 226 bits (577), Expect = 7e-64 Identities = 146/398 (36%), Positives = 204/398 (51%), Gaps = 9/398 (2%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MF + A DPIL LM F+ DPR KV+L IG++ + +G P AV AE RL + Sbjct: 1 MFAHLRPQADDPILVLMRAFQADPRPGKVDLGIGVWRDAEGRTPVFGAVKTAEERL-WRT 59 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 Y+ G + A+ LL G+ + + R T T GG+ A++ + P Sbjct: 60 QDTKSYVSFAGDPAFHAAVGDLLLGS----VTRPRAVTATT-GGTSAVQTLLALSQVARP 114 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 + VW+ TW NH + G + + G+ LL L A +V+LH Sbjct: 115 AAQVWIPAETWPNHRVLAEHLGLATRAFTYLAPEGTGIDREVLLRDLAQAQAGDVVILHA 174 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLP-A 239 CCHNPTG D + +++ L +P +D AY GFGA E DA +R +AS LP A Sbjct: 175 CCHNPTGIDPDPELQAEIVDSLARTGAVPLVDCAYLGFGAVPEADAAFLRRLAS--LPEA 232 Query: 240 LVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVL 299 +++ S SK F LY ERVG V+ E V QL R NYS PP+ GA+VV +L Sbjct: 233 MLAFSGSKSFGLYRERVGLALVLLEQPGVVEAVQSQLTRLNRVNYSFPPDHGARVVTEIL 292 Query: 300 NDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQV 359 D AL+ +W AE+ +RT + A RQ L K L + FD L Q GMF+ L +V Sbjct: 293 ADPALRTAWEAELAAIRTALSANRQALAKALRARLQSDRFDGLAAQSGMFAMLPLGKERV 352 Query: 360 DRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 R+RE+F VY + +GR+ +AG+ RVA+A AAV+ Sbjct: 353 MRMREDFAVYAVGTGRVNLAGVTPRTTDRVAEAIAAVL 390 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: 387 Number of extensions: 23 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: 392 Length adjustment: 31 Effective length of query: 366 Effective length of database: 361 Effective search space: 132126 Effective search space used: 132126 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