GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Phyllobacterium brassicacearum STM 196

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_106709221.1 CU102_RS01735 aminotransferase

Query= BRENDA::O69689
         (435 letters)



>NCBI__GCF_003010955.1:WP_106709221.1
          Length = 432

 Score =  447 bits (1149), Expect = e-130
 Identities = 214/416 (51%), Positives = 291/416 (69%), Gaps = 2/416 (0%)

Query: 6   LSPQELAALHARHQQDYAALQGMKLALDLTRGKPSAEQLDLSNQLLSLPGD-DYRDPEGT 64
           LS ++L AL  R   +Y A +   L +D+TRGKPS EQLDL+N +L+LPG+ D+    G 
Sbjct: 7   LSAEDLRALRNRVLGEYEAFRARGLQIDMTRGKPSPEQLDLANGMLALPGNGDHFTEAGE 66

Query: 65  DTRNYGGQHGLPGLRAIFAELLGIAVPNLIAGNNSSLELMHDIVAFSMLYGGVDSPRPWI 124
           D RNYGG  GLP +RA+FA ++G     ++ G+NSSL LMHD + +S+  G  +   PW 
Sbjct: 67  DARNYGGLQGLPEVRALFAPMMGAPAERVVVGDNSSLALMHDCLVWSLFKGVSNEMEPWS 126

Query: 125 QEQDGIKFLCPVPGYDRHFAITETMGIEMIPIPMLQDGPDVDLIEELVAVDPAIKGMWTV 184
           Q+     F+CPVPGYDRHFAI E  GI M+P+P+   GPD+D++EEL A DP +KGMW V
Sbjct: 127 QQSGTPAFICPVPGYDRHFAICEEYGIRMLPVPLTGHGPDMDIVEELAA-DPDVKGMWCV 185

Query: 185 PVFGNPSGVTYSWETVRRLVQMRTAAPDFRLFWDNAYAVHTLTLDFPRQVDVLGLAAKAG 244
           P + NPSG  YS E + RL  MRT APDFRLFWDNAYAVH LT       ++L L A+AG
Sbjct: 186 PKYSNPSGEIYSTEVIERLAAMRTGAPDFRLFWDNAYAVHHLTPQRHEIANILELCAQAG 245

Query: 245 NPNRPYVFASTSKITFAGGGVSFFGGSLGNIAWYLQYAGKKSIGPDKVNQLRHLRFFGDA 304
           NP+R +VFASTSK+T AG G++ F  S  N+ WYL  AGK++IGPDK+NQ+RH+RF  + 
Sbjct: 246 NPDRAFVFASTSKVTLAGAGLALFASSAANVKWYLARAGKRTIGPDKLNQIRHVRFLKNI 305

Query: 305 DGVRLHMLRHQQILAPKFALVAEVLDQRLSESKIASWTEPKGGYFISLDVLPGTARRTVA 364
           +G+  HM  H+ ++APKF  V + LD+RLS + IA WT+P+GGYFI +D + GTA+  V 
Sbjct: 306 EGLHEHMEAHRALIAPKFDAVIDALDKRLSGTGIAHWTKPEGGYFICVDGMEGTAKHVVD 365

Query: 365 LAKDVGIAVTEAGASFPYRKDPDDKNIRIAPSFPSVPDLRNAVDGLATCALLAATE 420
           LA+  G+ +T AGA+ PY +DP D+ +R+AP++PS+ +++ A +G+A C LLAA E
Sbjct: 366 LARQAGVVLTPAGATSPYGRDPHDRTLRLAPTYPSLREVQQASEGIALCILLAALE 421


Lambda     K      H
   0.320    0.138    0.415 

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: 577
Number of extensions: 24
Number of successful extensions: 3
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: 435
Length of database: 432
Length adjustment: 32
Effective length of query: 403
Effective length of database: 400
Effective search space:   161200
Effective search space used:   161200
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: 51 (24.3 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