Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate GFF3717 PS417_19025 aspartate aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__WCS417:GFF3717 Length = 401 Score = 374 bits (960), Expect = e-108 Identities = 182/392 (46%), Positives = 257/392 (65%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 + R+ I S + A ++ +G+ ++ GEPDFDTP H+ AAS A+H G+T Y Sbjct: 6 SDRVLGIAPSPSIAANALVTELRAQGRDIVNFTVGEPDFDTPAHILAAASQAMHNGDTHY 65 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 T+ GT L++AI K Q++N LAY LDE+ G K ++++A+ A+L+ GDEVI+ TPY Sbjct: 66 TSTTGTLALRQAICLKLQQDNDLAYGLDEVVAGCGGKHVIYHALAATLNRGDEVIVHTPY 125 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 W SY DI + + PV+I D S GF+L+ + LE AIT RT+WV+LNSP+NPSGA Y+ Sbjct: 126 WVSYPDIARLNDATPVIIPGDESLGFKLSPDALEQAITARTKWVILNSPNNPSGAVYNET 185 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 + L +VL RHPHV ++ D++YEH +Y R V +L P LK RTL VNG SK YAMT Sbjct: 186 ELLALAQVLRRHPHVLIMADEIYEHFIYGRARHVPLTRLAPDLKPRTLIVNGASKGYAMT 245 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314 GWR+G+ GP LI A+A + SQ T+CPSS+SQAA+VAA G Q + E +Q+RR Sbjct: 246 GWRLGFGAGPAWLIAAIAKLLSQTTTCPSSLSQAAAVAAFTGDQAPIAAMREEYQQRRAR 305 Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374 ++ L I GL C P+GAFY F+ +G++GK+TP G R+ +DT YLL D +A V Sbjct: 306 MLALLADIPGLSCTPPDGAFYVFANVSGLMGKLTPQGDRLDSDTQLVDYLLRDYGLATVS 365 Query: 375 GSAFGLSPFFRISYATSEAELKEALERIAAAC 406 G+A+G+SP+ R+S+A+S ++E R+ AC Sbjct: 366 GAAYGMSPYVRLSFASSSEVIEEGCRRLKDAC 397 Lambda K H 0.318 0.134 0.393 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: 468 Number of extensions: 18 Number of successful extensions: 1 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: 410 Length of database: 401 Length adjustment: 31 Effective length of query: 379 Effective length of database: 370 Effective search space: 140230 Effective search space used: 140230 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 (21.7 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