GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Paraburkholderia bryophila 376MFSha3.1

Align alanine-glyoxylate transaminase (EC 2.6.1.44); serine-glyoxylate transaminase (EC 2.6.1.45) (characterized)
to candidate H281DRAFT_03566 H281DRAFT_03566 alanine-glyoxylate transaminase / serine-glyoxylate transaminase / serine-pyruvate transaminase

Query= BRENDA::Q56YA5
         (401 letters)



>FitnessBrowser__Burk376:H281DRAFT_03566
          Length = 406

 Score =  350 bits (899), Expect = e-101
 Identities = 178/387 (45%), Positives = 253/387 (65%), Gaps = 7/387 (1%)

Query: 8   GRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPT 67
           GRH L +PGP  +P+ ++RAM+    D+R P    L   +L+ +KKIFKT      ++P 
Sbjct: 10  GRHFLQIPGPSPVPDRILRAMSYPTIDHRGPEFGELGLKVLDGIKKIFKTQHPV-VIYPA 68

Query: 68  TGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVE----SDWGQGANL 123
           +GTGAWE+AL+NTLSPGD ++ F  G F+ LW    + L    + +       W +G   
Sbjct: 69  SGTGAWEAALSNTLSPGDHVLMFETGHFATLWKKMAESLGLKPEFLGLPGIEGWRRGVQP 128

Query: 124 QVLASKLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICAL 183
           Q++ ++L +D  H+IKA+C+VHNET+TGVT+DI+AVR  +D   HPALLLVD +S +   
Sbjct: 129 QMIEARLREDTQHSIKAVCVVHNETSTGVTSDIAAVRRAIDAAGHPALLLVDTISGLACA 188

Query: 184 DFRMDEWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKL 243
           D+R DEWGVDV ++GSQK L LP G+     SPKA+ A+K +K  + F+DW++ ++  K 
Sbjct: 189 DYRHDEWGVDVTVSGSQKGLMLPPGISFNAISPKAVAASKHAKLPRSFWDWSEIVEMNKT 248

Query: 244 GTYWPYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKEEW 303
           G YWPYTP+  LLYGL  AL++I  EGL+N+ ARH RL +ATR AV AWGL+        
Sbjct: 249 G-YWPYTPNTNLLYGLHEALEMILGEGLDNVFARHERLAEATRRAVRAWGLEIQCADPAV 307

Query: 304 ISNTVTAVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCL 363
            S  +T VM+P  +D   + +  ++R+++SLG GL K+ G++FRIGHLG+ N+L LL  L
Sbjct: 308 YSPVLTGVMMPDGVDADAVRKLIYERFDMSLGTGLGKMKGRMFRIGHLGDCNDLMLLATL 367

Query: 364 AGVEMILKDVGYPVVMGSGVAAASTYL 390
           AG EM L+  G P + GSG+ AA  +L
Sbjct: 368 AGCEMGLRLAGVP-LKGSGLPAAMEWL 393


Lambda     K      H
   0.320    0.137    0.419 

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: 506
Number of extensions: 21
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: 401
Length of database: 406
Length adjustment: 31
Effective length of query: 370
Effective length of database: 375
Effective search space:   138750
Effective search space used:   138750
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: 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