Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate PP_4692 PP_4692 putative aspartate/tyrosine/aromatic aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >FitnessBrowser__Putida:PP_4692 Length = 390 Score = 158 bits (399), Expect = 3e-43 Identities = 115/382 (30%), Positives = 180/382 (47%), Gaps = 27/382 (7%) Query: 17 SVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYVLSNGILECRQAV 76 ++LA A +L+A G +IHL +G+PDF T +V A + AL GH Y + G+ R+A+ Sbjct: 19 ALLARANELQAAGHDVIHLEIGEPDFTTAAPIVAAGQAALAAGHTRYTAARGLPALREAI 78 Query: 77 TRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYESMINYT-- 134 + Y +IDPER+LI PGG + A +PG + P +P + Sbjct: 79 AGFYGQRYGLNIDPERILITPGGSGALLLASSLLVDPGKHWLLADPGYPCNRHFLRLVEG 138 Query: 135 GSTPVP------YDLTED-KDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSAIDV 187 G+ VP Y LT D + +D + + +L+ +P NPTG+ + + A+ Sbjct: 139 GAQLVPVGPDVNYQLTADLVERYWDKDTVGALVA---------SPANPTGTVLGREALAC 189 Query: 188 LAEGL-KKHPHVAILSDEIYSRQIYDGKEMPTFFNYPDLQDRLIVLDGWSKAYAMTGWRM 246 LA ++H H+ + DEIY Y G + P+ ++ D VL+ +SK + MTGWR+ Sbjct: 190 LARTTHERHGHLVV--DEIYHGLTY-GMDAPSVL---EVDDSAFVLNSFSKYFGMTGWRL 243 Query: 247 GWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAI-HEMMVKFDQRRKLIHE 305 GW V P + + KL N + +Q A +A AI E +F +RR + Sbjct: 244 GWLVAPPGAVADLEKLAQNLYISAPSMAQHAALACFQPEALAIFEERRAEFARRRDYLLP 303 Query: 306 GLNSLPGVECSLPGGAFYAFPKVIGTGMNGSEFAKKCMHEAGVAIVPGTAFGK-TCQDYV 364 L L P GAFY + + G + F + + VA PG FG+ +V Sbjct: 304 ALRELGFRIAVEPQGAFYLYADISAFGGDAFAFCRHFLETQHVAFTPGLDFGRHLAGHHV 363 Query: 365 RFSYAASQDNISNALENIKKML 386 RF+Y S + A++ I + L Sbjct: 364 RFAYTQSLPRLEEAVQRIARGL 385 Lambda K H 0.319 0.137 0.414 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: 22 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: 387 Length of database: 390 Length adjustment: 30 Effective length of query: 357 Effective length of database: 360 Effective search space: 128520 Effective search space used: 128520 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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