GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Sinorhizobium meliloti 1021

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate SMa1347 SMa1347 dehydrogenase

Query= BRENDA::P9WNX3
         (528 letters)



>FitnessBrowser__Smeli:SMa1347
          Length = 324

 Score =  178 bits (451), Expect = 3e-49
 Identities = 110/300 (36%), Positives = 161/300 (53%), Gaps = 9/300 (3%)

Query: 11  KLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVA 70
           +L P   A L    ++R    PD + LL     A+ ++VR+   +        P L+ V 
Sbjct: 9   RLHPDAEAMLKAASDLRVASAPDPETLLREGEGAEIVIVRAP--IPPAFFGNVPALRAVV 66

Query: 71  RAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTW- 129
           R G GLD +  DAATA GVL+ N P  N  + AEH   + LA  RQ    D  LR   W 
Sbjct: 67  RHGAGLDMIPYDAATAAGVLIANVPAVNAPTVAEHVFMVTLALLRQFRPMDRDLRNMGWS 126

Query: 130 --KRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELL 187
             +  S    ++ G+ +GV+G+G +G+ V  RIA +G  +       SP      G+  L
Sbjct: 127 TGRAHSDRALDLAGRIMGVIGMGNVGKAVF-RIAKYGFQLEIVANSRSPESLPD-GVRFL 184

Query: 188 SLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITG 247
           S+DDLL+ AD + +  P TP+T GL+ +E +A+ KPG I+VN +RG +VD+AAL +A+  
Sbjct: 185 SVDDLLSTADIVVLCCPLTPKTTGLLSRERIARMKPGAILVNVSRGPVVDDAALIEALER 244

Query: 248 GHVRAAGLDVFATEPC-TDSPLFELAQVVVTPHLGASTAEAQDRAGTD-VAESVRLALAG 305
           G +  A LDVF+T+P   + P F    V+VTPHL   + E+  R G    AE++R+   G
Sbjct: 245 GRIGGAALDVFSTQPLPPEHPYFRQDNVIVTPHLAGISEESMMRMGKGAAAEAIRVMEGG 304


Lambda     K      H
   0.317    0.133    0.370 

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: 369
Number of extensions: 19
Number of successful extensions: 5
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: 528
Length of database: 324
Length adjustment: 31
Effective length of query: 497
Effective length of database: 293
Effective search space:   145621
Effective search space used:   145621
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 (21.6 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