GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Paraburkholderia bryophila 376MFSha3.1

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate H281DRAFT_03566 H281DRAFT_03566 alanine-glyoxylate transaminase / serine-glyoxylate transaminase / serine-pyruvate transaminase

Query= BRENDA::P74281
         (384 letters)



>FitnessBrowser__Burk376:H281DRAFT_03566
          Length = 406

 Score =  254 bits (649), Expect = 3e-72
 Identities = 145/381 (38%), Positives = 223/381 (58%), Gaps = 9/381 (2%)

Query: 4   KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSG 63
           +  L IPGP+PVP+++L AM+   I HR  +F ++  ++   +K + +T++ V++   SG
Sbjct: 11  RHFLQIPGPSPVPDRILRAMSYPTIDHRGPEFGELGLKVLDGIKKIFKTQHPVVIYPASG 70

Query: 64  TGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAE----WGKALDPND 119
           TGA EA++ N LSPGD VL+   G F   W K+A++ GL  E +       W + + P  
Sbjct: 71  TGAWEAALSNTLSPGDHVLMFETGHFATLWKKMAESLGLKPEFLGLPGIEGWRRGVQPQM 130

Query: 120 FKTLLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGG-ALMIVDAVTSLGATPV 178
            +  L  D+  +IKA+ + H+ETSTGV +D+AA+  A  A G  AL++VD ++ L     
Sbjct: 131 IEARLREDTQHSIKAVCVVHNETSTGVTSDIAAVRRAIDAAGHPALLLVDTISGLACADY 190

Query: 179 AIDDLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDS 238
             D+ G+DV  SGSQKG M+PPG+ F ++S KA  A + A +PR + D  +  +      
Sbjct: 191 RHDEWGVDVTVSGSQKGLMLPPGISFNAISPKAVAASKHAKLPRSFWDWSEIVEMNKTGY 250

Query: 239 SPFTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAA-SN 297
            P+TP  NL+YGL  +L+M+  EGLD +F RH+R   ATR A++A  L +   D A  S 
Sbjct: 251 WPYTPNTNLLYGLHEALEMILGEGLDNVFARHERLAEATRRAVRAWGLEIQCADPAVYSP 310

Query: 298 AITAV-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGAL 356
            +T V  P GV+A+ +R  + ++FD+++  G   +KG++FRIGHLG   D  +L+ +   
Sbjct: 311 VLTGVMMPDGVDADAVRKLIYERFDMSLGTGLGKMKGRMFRIGHLGDCNDLMLLATLAGC 370

Query: 357 EATLIELGYEGVTPGSGVAAA 377
           E  L   G      GSG+ AA
Sbjct: 371 EMGLRLAGVP--LKGSGLPAA 389


Lambda     K      H
   0.317    0.134    0.386 

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: 372
Number of extensions: 13
Number of successful extensions: 4
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: 384
Length of database: 406
Length adjustment: 31
Effective length of query: 353
Effective length of database: 375
Effective search space:   132375
Effective search space used:   132375
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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