Align Bifunctional aspartate aminotransferase and L-aspartate beta-decarboxylase; Aspartate 4-decarboxylase; Asd; AsdP; EC 2.6.1.1; EC 4.1.1.12 (characterized)
to candidate BPHYT_RS03850 BPHYT_RS03850 aspartate aminotransferase
Query= SwissProt::Q53IZ1 (531 letters) >FitnessBrowser__BFirm:BPHYT_RS03850 Length = 554 Score = 617 bits (1592), Expect = 0.0 Identities = 314/526 (59%), Positives = 391/526 (74%), Gaps = 7/526 (1%) Query: 8 LANLSPFELKDELIKVASGKA-----NRLMLNAGRGNPNFLATTPRRAFFRLGLFAAAES 62 +A LSPFELKDELIK A G A N MLNAGRGNPNFLAT PR F++LGLFA ES Sbjct: 18 MAALSPFELKDELIKAAGGAAVERPANASMLNAGRGNPNFLATIPRHGFWQLGLFAMRES 77 Query: 63 ELSYSYMTVGVGGLAKLDGIEGRFERFIAEHRDQEGVKFLGKSLSYVRDQLGLDPAAFLH 122 E S++YM GVGG + +G+E RF+ F+ E++ G+ FL ++SYVRDQLG FL+ Sbjct: 78 ERSFAYMPEGVGGFPRREGLEERFDLFLRENKGVAGIDFLRGAVSYVRDQLGYSAGDFLY 137 Query: 123 EMVDGILGCNYPVPPRMLTVSEQIVRQYIVREMAGGAVPPESVDLFAVEGGTAAMAYIFE 182 EM +GIL NYPVP RML +SE IV QY+ +EM G D+FAVEGGTAAM YIF Sbjct: 138 EMCEGILASNYPVPDRMLKLSELIVGQYLRKEMIGDHPFVGEFDVFAVEGGTAAMTYIFN 197 Query: 183 SLRISGLLKAGDKVAIGMPVFTPYIEIPELAQYDLKEVPIHADPDNGWQYSDAELDKLKD 242 ++R + L+KAGD +A+GMP+FTPYIEIP L Y L V + AD NGWQYS ELDKL+D Sbjct: 198 TMRENHLIKAGDTIALGMPIFTPYIEIPRLNDYRLNVVNLEADVANGWQYSKKELDKLRD 257 Query: 243 PDVKIFFCVNPSNPPSVKMDQRSLDRVRAIVAEQRPDLLILTDDVYGTFADEFQSLFSVC 302 P VK FF VNPSNPPSVKMD SL R A + ++RPDL++LTDDVYGTFAD+F SLF++ Sbjct: 258 PKVKAFFLVNPSNPPSVKMDDESL-RYIADIVKERPDLILLTDDVYGTFADDFVSLFALA 316 Query: 303 PRNTLLVYSFSKYFGATGWRLGVIAAHKDNVFDHALSQLPESAKKALDHRYRSLLPDVRS 362 P+NT+LVYS+SKYFGATGWRLG IA H+DNV D ++ LP+ AKK L RY S+ + Sbjct: 317 PKNTILVYSYSKYFGATGWRLGTIATHRDNVLDKLIADLPKDAKKQLHERYESITTEPDK 376 Query: 363 LKFIDRLVADSRVVALNHTAGLSTPQQVQMVLFSLFALMDEADAYKQALKQLIRRREATL 422 LKFIDRLVADSR VALNHTAGLSTPQQVQMVLFSLF+LMD DAYK ALK+LIR+R+ L Sbjct: 377 LKFIDRLVADSRTVALNHTAGLSTPQQVQMVLFSLFSLMDTPDAYKNALKRLIRKRKQAL 436 Query: 423 YRELGMP-PLENPNSVNYYTLIDLQNVTCRLYGEAFSQWAVQQSSTGDMLFRVADETGIV 481 Y E+G+ ++PN V+YYT++D++ + R++G F W ++ + ++LFR+A E +V Sbjct: 437 YEEVGISFKDDDPNQVDYYTILDVEFLGERMFGREFVDWLLKNTEPSELLFRLAREARVV 496 Query: 482 LLPGRGFGSDRPSGRASLANLNEYEYAAIGRALRRLADELYEQYKA 527 LLPG GFG+ PSGR SLANLNE +Y IGRA+R+L +EL E++ A Sbjct: 497 LLPGLGFGTQHPSGRVSLANLNESDYRQIGRAMRKLIEELVERFNA 542 Lambda K H 0.321 0.138 0.400 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: 811 Number of extensions: 31 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: 531 Length of database: 554 Length adjustment: 35 Effective length of query: 496 Effective length of database: 519 Effective search space: 257424 Effective search space used: 257424 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: 52 (24.6 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