Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate N515DRAFT_2186 N515DRAFT_2186 alanine-synthesizing transaminase
Query= curated2:P63499 (429 letters) >FitnessBrowser__Dyella79:N515DRAFT_2186 Length = 410 Score = 320 bits (819), Expect = 7e-92 Identities = 173/394 (43%), Positives = 239/394 (60%), Gaps = 1/394 (0%) Query: 31 SAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALPYAQ 90 SA L +V YEIRG + + + LEA G I+KLNIGNP +GFE P + I L ++ Sbjct: 5 SAHLAEVRYEIRGALTRRSRELEAAGLPIIKLNIGNPGRYGFETPPHLRDAIAAHLRDSE 64 Query: 91 GYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQVLIP 150 Y QG+ AR + + + G +V+ +++GNGVSELI ++L+ALL GD+VL+P Sbjct: 65 AYGHEQGLEEARETIAAQ-QRARGARGVEVERIFVGNGVSELIDLSLRALLQPGDEVLLP 123 Query: 151 SPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTGAVY 210 SPDYPLW+A+T L G P +Y C G PD ++E+ +T RT+A+V+INPNNPTGAVY Sbjct: 124 SPDYPLWSAATILNDGQPRYYRCLAENGHLPDPDEIEALVTARTRAIVLINPNNPTGAVY 183 Query: 211 SCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSKAYRVA 270 E+L ++V +A +H LLLL DEIYD+ILYD A+ + LA++A D+ C++F GLSK +R Sbjct: 184 PRELLERIVRIAERHHLLLLTDEIYDEILYDGAQFVPLATVAGDVPCVSFGGLSKVHRAC 243 Query: 271 GYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVLPGGR 330 GYR GW++++G + + + LLA +RLC NV AQ A++ AL +I L PGGR Sbjct: 244 GYRVGWMSLSGDPVRTHDYRDALQLLAALRLCANVTAQWAVRPALESKPTIGALTSPGGR 303 Query: 331 LLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKILVTQ 390 L E R + + + P GALYAFPR+ + DD L LL E +LV Sbjct: 304 LHEARRMILEGVANSEFLDLATPGGALYAFPRVRADRVPRFDDNAFALRLLEEESVLVVP 363 Query: 391 GTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFL 424 G+ FN P HLRL LP L R+ L Sbjct: 364 GSSFNVPDSRHLRLTLLPPPEQLREVFVRIERVL 397 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: 527 Number of extensions: 29 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: 410 Length adjustment: 32 Effective length of query: 397 Effective length of database: 378 Effective search space: 150066 Effective search space used: 150066 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