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_106711968.1 CU102_RS15250 bifunctional aspartate transaminase/aspartate 4-decarboxylase
Query= SwissProt::Q53IZ1 (531 letters) >NCBI__GCF_003010955.1:WP_106711968.1 Length = 536 Score = 474 bits (1219), Expect = e-138 Identities = 250/530 (47%), Positives = 335/530 (63%), Gaps = 3/530 (0%) Query: 4 DYRSLANLSPFELKDELIKVA---SGKANRLMLNAGRGNPNFLATTPRRAFFRLGLFAAA 60 DYR +SPFE+KD LIK+A S K+ +++LNAGRGNPN++AT PR FF G FA + Sbjct: 5 DYRDYEKMSPFEIKDALIKLAKRSSQKSTQVLLNAGRGNPNWIATKPREGFFLFGQFALS 64 Query: 61 ESELSYSYMTVGVGGLAKLDGIEGRFERFIAEHRDQEGVKFLGKSLSYVRDQLGLDPAAF 120 E+ + T GV G+ + I RF+ ++ +H + EG +FL K + + G D AF Sbjct: 65 EARRALDNPTAGVAGMPQQKDIAERFKVWLEKHAEMEGAEFLSKMVDHAVKAFGFDADAF 124 Query: 121 LHEMVDGILGCNYPVPPRMLTVSEQIVRQYIVREMAGGAVPPESVDLFAVEGGTAAMAYI 180 + E+ D I+G NYPVP RML +EQI +Y++ M G VPP DL+AVEGGTAAM YI Sbjct: 125 VFELTDSIIGDNYPVPDRMLVHAEQIAHRYLMWAMCGDKVPPGKFDLYAVEGGTAAMCYI 184 Query: 181 FESLRISGLLKAGDKVAIGMPVFTPYIEIPELAQYDLKEVPIHADPDNGWQYSDAELDKL 240 F+SL + +LK GD +A+G P+FTPYIEI EL Y K V I A +N +QYSD E+ KL Sbjct: 185 FKSLIANRILKKGDTIALGTPIFTPYIEIAELEDYAFKAVHIKAKQENRFQYSDEEIKKL 244 Query: 241 KDPDVKIFFCVNPSNPPSVKMDQRSLDRVRAIVAEQRPDLLILTDDVYGTFADEFQSLFS 300 +DP +K FF VNP NP S+ +D +L ++ +V ++RPDLL+LTDDVYGTF F+SL + Sbjct: 245 EDPKIKAFFVVNPGNPTSMAIDAPTLKKIVDLVKKKRPDLLLLTDDVYGTFVPGFRSLMA 304 Query: 301 VCPRNTLLVYSFSKYFGATGWRLGVIAAHKDNVFDHALSQLPESAKKALDHRYRSLLPDV 360 P NT+ VYS+SKYFG TGWRLGVIA H+ N+ D +++LP +ALD RY S+ + Sbjct: 305 ELPENTIGVYSYSKYFGCTGWRLGVIAIHEKNILDSTIAKLPAKDLEALDKRYISITLEP 364 Query: 361 RSLKFIDRLVADSRVVALNHTAGLSTPQQVQMVLFSLFALMDEADAYKQALKQLIRRREA 420 R LK IDR+VADSR VALNHTAGLS PQQV M +FS+ LMD Y++A + R Sbjct: 365 RKLKMIDRIVADSRDVALNHTAGLSLPQQVMMTMFSMSELMDTEKLYQKACMDICHSRVD 424 Query: 421 TLYRELGMPPLENPNSVNYYTLIDLQNVTCRLYGEAFSQWAVQQSSTGDMLFRVADETGI 480 +L L + NPN YY ID + R GE +W + D++F++A++ I Sbjct: 425 SLLEGLPLDVQPNPNFAYYYGTIDFEFWLRRYVGEDMVKWLKKNVHPLDLVFKLAEDHAI 484 Query: 481 VLLPGRGFGSDRPSGRASLANLNEYEYAAIGRALRRLADELYEQYKALGK 530 VLL G GF + S R S ANL + Y IGRA+R + + + A K Sbjct: 485 VLLNGGGFDAPNWSVRVSFANLTDDVYDDIGRAVRAVGRSYVDAFNASKK 534 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: 671 Number of extensions: 22 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: 531 Length of database: 536 Length adjustment: 35 Effective length of query: 496 Effective length of database: 501 Effective search space: 248496 Effective search space used: 248496 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