Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate PfGW456L13_1398 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)
Query= reanno::BFirm:BPHYT_RS23155 (482 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1398 Length = 456 Score = 573 bits (1478), Expect = e-168 Identities = 272/452 (60%), Positives = 344/452 (76%), Gaps = 3/452 (0%) Query: 30 RSTAEYRALDAAHHIHPFSDMGSLNRSGSRVIVKAQGVYLWDSEGNKVIDGMAGLWCVNV 89 R T +Y+A DAAHHIH F D +LN G RV+V+ + ++LWD++G + +DGM+GLWC N+ Sbjct: 5 RDTRDYQAADAAHHIHAFVDQKALNDEGPRVMVRGERLHLWDNDGRRYLDGMSGLWCTNL 64 Query: 90 GYGRKELADAAYKQMQELPYYNTFFKTTHPPVIELSALLAELAPEAFNHFFYCNSGSEGN 149 GYGRK+LA AA +Q+++LPYYN FF TTHP VIELS LL L P ++H Y NSGSE N Sbjct: 65 GYGRKDLAAAASRQLEQLPYYNMFFHTTHPQVIELSELLFSLLPAHYSHAIYTNSGSEAN 124 Query: 150 DTVLRIVHQYWATQGKHSKKFVISRKNGYHGSTIAGGTLGGMGYMHEQMPSKVENIVHID 209 + ++R V +YW GK KK +I R NGYHGST+A LGGM +MHE M + +I HID Sbjct: 125 EVLIRTVRRYWQVLGKPEKKIMIGRWNGYHGSTLAATALGGMKFMHE-MGGMIPDIEHID 183 Query: 210 QPYFFGEAQGNLTPEEFALARAQQLEAKILEIGADNVAAFIGEPFQGAGGVIFPASTYWP 269 +PYFF +GNLTP EF L AQQLEAKILE+GAD VA FI EPFQGAGG+IFP +YWP Sbjct: 184 EPYFFAH-EGNLTPAEFGLRAAQQLEAKILELGADKVAGFIAEPFQGAGGMIFPPESYWP 242 Query: 270 EIQRICRKYDILLVADEVIGGFGRTGEWFAHQHFGFEPDLITLAKGLTSGYVPMGAVGLH 329 EIQRICRKYD+LL ADEVIGGFGRTGEWFAH++FGFEPD +++AKGLTSGY+PMG + L Sbjct: 243 EIQRICRKYDVLLCADEVIGGFGRTGEWFAHEYFGFEPDTLSIAKGLTSGYIPMGGLILS 302 Query: 330 DRVAKAIIENGD-FNHGLTYSGHPVAAAVAVANLKLLRDEKIVDRVKNDTGPYFQKQLRE 388 ++A ++E G F HGLTYSGHPVAAAVA+ANLK LRDE +V RVK+D GPY Q+ LRE Sbjct: 303 KKMASVLVEQGGVFAHGLTYSGHPVAAAVAIANLKALRDEGVVTRVKDDIGPYLQQCLRE 362 Query: 389 TFANHPIIGEISGTGLVAGLQLAQDPKARKRFANGGDVGTICRDFCFNGNLIMRATGDRM 448 F HP++G+I GTG+VA LQLA+D +RKRFAN D+ CR F +I+R+T RM Sbjct: 363 VFGKHPLVGDIQGTGMVAALQLAEDKTSRKRFANENDIAWRCRTIGFEEGVIIRSTLGRM 422 Query: 449 LLSPPLVINKLEIDEIVSKAKKAIDATAQQLG 480 +++P L+ ++ EIDE+++K KA+D TAQ+ G Sbjct: 423 IMAPALIASREEIDELIAKTLKAVDRTAQEYG 454 Lambda K H 0.319 0.136 0.408 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: 642 Number of extensions: 26 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: 482 Length of database: 456 Length adjustment: 33 Effective length of query: 449 Effective length of database: 423 Effective search space: 189927 Effective search space used: 189927 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: 51 (24.3 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