Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate GFF1734 Psest_1772 Aspartate/tyrosine/aromatic aminotransferase
Query= curated2:O67781 (394 letters) >FitnessBrowser__psRCH2:GFF1734 Length = 403 Score = 157 bits (396), Expect = 7e-43 Identities = 115/354 (32%), Positives = 177/354 (50%), Gaps = 17/354 (4%) Query: 24 AKELRAKGVDVIGFGAGEP---DFDTPDFIKEACIRALREGKTKYAPSAGIPELREAIAE 80 AK L +G ++ G P F+ P+ I + IR L + Y+ S G+ R+AI + Sbjct: 24 AKRLEEEGHRILKLNIGNPAPFGFEAPEEILQDVIRNLPTAQG-YSDSKGLFSARKAIMQ 82 Query: 81 KLLKENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSPYWVTYPEQIRFFGGVP 140 ++ +I + G ++ + A+L+ GDEVL+P+P + + + GG P Sbjct: 83 YYQQKQVEGVSIEDIYLGNGVSELIVMSMQALLNNGDEVLIPAPDYPLWTAAVSLAGGKP 142 Query: 141 VEVPLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEEEELKKIAEFCVERGIF 200 V ++ + L D+K K+T TKA+V+ +PNNPTGAVY +E L+ + E + + Sbjct: 143 VHYLCDEQANWWPDLADIKAKITPNTKALVLINPNNPTGAVYPKEVLEGMVELARQHKLV 202 Query: 201 IISDECYEYFVYGDAKFVSPASFSDEVKNITFTVNAFSKSYSMTGWRIGYVAC------P 254 + SDE Y+ +Y DA +S AS + +V +TF N SKSY + G+R G+VA Sbjct: 203 LFSDEIYDKILYDDAVHISTASLAPDVLCLTF--NGLSKSYRVAGFRSGWVAISGPKHKA 260 Query: 255 EEYAKVIASL-NSQSVSNVTTFAQYGALEALKNPKS-KDFVNEMRNAFERRRDTAVEELS 312 + Y + + L N + +NV AQ+ AL +S D V E+R T E L+ Sbjct: 261 QSYIEGLDILANMRLCANVP--AQHAIQTALGGYQSINDLVLPPGRLLEQRNRT-WELLN 317 Query: 313 KIPGMDVVKPEGAFYIFPDFSAYAEKLGGDVKLSEFLLEKAKVAVVPGSAFGAP 366 IPG+ VKP GA Y FP + D K LL K+ +V G+AF P Sbjct: 318 DIPGISCVKPMGALYAFPRIDPKICPIHNDEKFVLDLLLSEKLLIVQGTAFNWP 371 Lambda K H 0.317 0.135 0.383 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: 349 Number of extensions: 16 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: 394 Length of database: 403 Length adjustment: 31 Effective length of query: 363 Effective length of database: 372 Effective search space: 135036 Effective search space used: 135036 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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