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_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.

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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