Align Tyrosine aminotransferase; TAT; L-tyrosine:2-oxoglutarate aminotransferase; EC 2.6.1.5 (characterized)
to candidate WP_069662075.1 BCR25_RS02850 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q93703 (464 letters) >NCBI__GCF_001730305.1:WP_069662075.1 Length = 405 Score = 154 bits (389), Expect = 5e-42 Identities = 108/371 (29%), Positives = 191/371 (51%), Gaps = 14/371 (3%) Query: 75 KVIKLHLGDPSVGGKLPPSEIAVQAMHESVSSHMFDGYGPAVGALAAREAIVERYSSADN 134 +++KL+ G+P+ G P+E+ V+ M +V + +GY + G +AR+AI E+Y Sbjct: 34 RILKLNTGNPAPFGFDAPNEV-VRDMITNVRNS--EGYSDSKGIFSARKAI-EQYCQVKG 89 Query: 135 V--FTADDVVLASGCSHALQMAIEAVANAGENILVPHPGFPLYSTLCRPHNIVDKPYKID 192 T +D+ +G S + M ++ + N G+ +LVP P +PL++ Y D Sbjct: 90 FPNVTINDIYTGNGVSELITMCMQGLLNNGDEVLVPMPDYPLWTASVSLAGGNPVHYICD 149 Query: 193 MTGEDVRIDLSYMATIIDDNTKAIIVNNPGNPTGGVFTKEHLEEILAFAHQYKLIIIADE 252 E D+ + + + NTKAI++ NP NPTG ++ KE LE+I+ A Q LII +DE Sbjct: 150 EQAE-WNPDIDDIKSKVTSNTKAIVLINPNNPTGALYPKEILEQIVEIARQNDLIIFSDE 208 Query: 253 IYGDLVYNGATFYPLASLSPKVPIITCDGIAKRWMVPGWRLGWLIIHNHFGVLTDVKNGI 312 IY LV +G T P+A+L+P + ++T +G++K V G+R GW+++ + + G+ Sbjct: 209 IYDRLVMDGLTHIPIATLAPDLFVVTLNGLSKSHRVAGFRCGWMVLSGNKKHVKGYIEGL 268 Query: 313 VALSQKIVGPCSLVQGALPKIL--RETPEDYFVYTRNVIETNANIVDSILADVPGMRVVK 370 L+ + L Q + L ++ ++ + V E I ++I ++PG+ VK Sbjct: 269 NMLASMRLCSNVLSQQIIQTALGGYQSVDELLLPGGRVYEQREFIYNAI-NEIPGLSAVK 327 Query: 371 PKGAMYMMVNISRTAYG--SDVSFCQNLIREESVFCLPGQAF--SAPGYFRVVLTCGSED 426 PK A Y+ I + D F + + E + + G F + P +FR+V ED Sbjct: 328 PKAAFYIFPKIDTARFDIYDDEKFVLDFLHEHHILLVHGGGFNWTQPDHFRIVYLPKMED 387 Query: 427 MEEAALRIREF 437 ++ A +++ F Sbjct: 388 LKLTAEKMQRF 398 Lambda K H 0.319 0.136 0.407 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: 415 Number of extensions: 23 Number of successful extensions: 4 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: 464 Length of database: 405 Length adjustment: 32 Effective length of query: 432 Effective length of database: 373 Effective search space: 161136 Effective search space used: 161136 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: 51 (24.3 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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