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 WP_106711050.1 CU102_RS09420 bifunctional aspartate transaminase/aspartate 4-decarboxylase
Query= SwissProt::Q53IZ1 (531 letters) >NCBI__GCF_003010955.1:WP_106711050.1 Length = 531 Score = 756 bits (1953), Expect = 0.0 Identities = 372/523 (71%), Positives = 437/523 (83%) Query: 4 DYRSLANLSPFELKDELIKVASGKANRLMLNAGRGNPNFLATTPRRAFFRLGLFAAAESE 63 DY A LSPFELKD LI+VAS + NRL+LNAGRGNPNFLAT PRRAFFRLGLFAAAE+E Sbjct: 5 DYSQYAKLSPFELKDALIQVASSRENRLILNAGRGNPNFLATLPRRAFFRLGLFAAAEAE 64 Query: 64 LSYSYMTVGVGGLAKLDGIEGRFERFIAEHRDQEGVKFLGKSLSYVRDQLGLDPAAFLHE 123 LS+SYM GVGGL KL GIEGRFERF++EHRDQ G FLG++LSYVRDQLGL + FLHE Sbjct: 65 LSFSYMENGVGGLPKLAGIEGRFERFVSEHRDQPGGVFLGRALSYVRDQLGLSASDFLHE 124 Query: 124 MVDGILGCNYPVPPRMLTVSEQIVRQYIVREMAGGAVPPESVDLFAVEGGTAAMAYIFES 183 V+GILG NYPVPPRML VSE+IV+ YIV+EM GG + +DLFAVEGGTAAM YIF S Sbjct: 125 AVEGILGSNYPVPPRMLRVSEEIVKHYIVKEMIGGYLTSSEIDLFAVEGGTAAMTYIFNS 184 Query: 184 LRISGLLKAGDKVAIGMPVFTPYIEIPELAQYDLKEVPIHADPDNGWQYSDAELDKLKDP 243 L+ + L+ GDKVAIGMP FTPYIEIPEL Y LK+V I+ADP GWQY DAELDKL D Sbjct: 185 LKQNKLIAPGDKVAIGMPAFTPYIEIPELNDYRLKQVHINADPAAGWQYPDAELDKLLDK 244 Query: 244 DVKIFFCVNPSNPPSVKMDQRSLDRVRAIVAEQRPDLLILTDDVYGTFADEFQSLFSVCP 303 D+KIFFC+NPSNPPSVKMD RSL+R+ IVAE+RPDL+ILTDDVYGTFAD+F+SLF+ CP Sbjct: 245 DIKIFFCINPSNPPSVKMDDRSLERITKIVAEKRPDLMILTDDVYGTFADDFKSLFATCP 304 Query: 304 RNTLLVYSFSKYFGATGWRLGVIAAHKDNVFDHALSQLPESAKKALDHRYRSLLPDVRSL 363 NTLLVYSFSKYFGATGWRLGVIAA ++NVFD L L +S +K LD RY +L+PDV L Sbjct: 305 ANTLLVYSFSKYFGATGWRLGVIAAQRENVFDAKLKDLSKSDRKELDERYSTLVPDVSKL 364 Query: 364 KFIDRLVADSRVVALNHTAGLSTPQQVQMVLFSLFALMDEADAYKQALKQLIRRREATLY 423 KF+DRLVADSR VALNHTAGLSTPQQVQMVLFSLFALMDEAD YK LK+LIRRREA L+ Sbjct: 365 KFLDRLVADSRTVALNHTAGLSTPQQVQMVLFSLFALMDEADGYKAELKKLIRRREAALF 424 Query: 424 RELGMPPLENPNSVNYYTLIDLQNVTCRLYGEAFSQWAVQQSSTGDMLFRVADETGIVLL 483 RELG+PP + N V+YYTL+DL+ ++ RLYG+AF+ W + + ++LFR+A++TGIV+L Sbjct: 425 RELGLPPQNDTNEVDYYTLLDLEAISRRLYGDAFADWVKKNVAPTELLFRIANDTGIVML 484 Query: 484 PGRGFGSDRPSGRASLANLNEYEYAAIGRALRRLADELYEQYK 526 PG GFG+ +P+GR SLANLNE+EYA IGR+LR +AD++Y +K Sbjct: 485 PGSGFGTLQPAGRVSLANLNEFEYANIGRSLRTMADQVYADFK 527 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: 841 Number of extensions: 26 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: 531 Length of database: 531 Length adjustment: 35 Effective length of query: 496 Effective length of database: 496 Effective search space: 246016 Effective search space used: 246016 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 Jul 26 2024. The underlying query database was built on Jul 25 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