GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Phyllobacterium brassicacearum STM 196

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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