Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate GFF2141 HP15_2095 aspartate aminotransferase
Query= curated2:P63499 (429 letters) >FitnessBrowser__Marino:GFF2141 Length = 404 Score = 503 bits (1296), Expect = e-147 Identities = 248/402 (61%), Positives = 309/402 (76%), Gaps = 1/402 (0%) Query: 28 FAQSAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALP 87 + +SAKL +V YEIRG V + A RLE EGHR+LKLNIGNPA F + P+ I +D+I + Sbjct: 4 YYKSAKLDNVCYEIRGVVLREARRLEEEGHRVLKLNIGNPAAFELDVPEEIQQDVIYNMH 63 Query: 88 YAQGYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQV 147 AQGY +S+G+ SAR+AV+ Y G + D+DD++LGNGVSELI MT+QA+L+ GD+V Sbjct: 64 QAQGYVESKGLFSARKAVM-HYCQQRGIDKVDIDDIFLGNGVSELIVMTMQAMLNTGDEV 122 Query: 148 LIPSPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTG 207 LIP+PDYPLWTA+ +L+ G PVHY CDE Q W PDI D+ KIT RT+A+V+INPNNPTG Sbjct: 123 LIPAPDYPLWTAAVTLSSGKPVHYRCDEQQDWFPDIDDIRKKITRRTRAIVLINPNNPTG 182 Query: 208 AVYSCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSKAY 267 AVYS E+L Q+++LARKH L++L+DEIYDKILYD +HIS AS+A D+L T+NGLSK Y Sbjct: 183 AVYSKELLEQVIELARKHNLIILSDEIYDKILYDGTQHISTASLADDVLFFTYNGLSKNY 242 Query: 268 RVAGYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVLP 327 R AGYR+GW+ ++G K A IEGI +L+NMRLC NVPAQ AIQ ALGG+QSI DLV P Sbjct: 243 RAAGYRSGWMIVSGAKHRAKDLIEGIDMLSNMRLCANVPAQLAIQTALGGYQSINDLVAP 302 Query: 328 GGRLLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKIL 387 GGRL EQR+ AW LN+IPGVSCVKP GALY FP+LDP+ + I +DE+LVLDLLL EKIL Sbjct: 303 GGRLYEQRETAWRMLNDIPGVSCVKPQGALYLFPKLDPKHFPIVNDEKLVLDLLLQEKIL 362 Query: 388 VTQGTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFLVSYRQ 429 + QG+ FN HLR+V LP L A+ RLGNFL Y+Q Sbjct: 363 LVQGSAFNIDDRQHLRVVFLPREDTLEDAMGRLGNFLGQYQQ 404 Lambda K H 0.320 0.138 0.419 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: 544 Number of extensions: 27 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: 429 Length of database: 404 Length adjustment: 31 Effective length of query: 398 Effective length of database: 373 Effective search space: 148454 Effective search space used: 148454 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 Aug 03 2021. The underlying query database was built on Aug 03 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