GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Xenophilus azovorans DSM 13620

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_038207325.1 Q392_RS12390 NAD(P)-dependent oxidoreductase

Query= BRENDA::P9WNX3
         (528 letters)



>NCBI__GCF_000745855.1:WP_038207325.1
          Length = 312

 Score =  187 bits (476), Expect = 4e-52
 Identities = 114/308 (37%), Positives = 170/308 (55%), Gaps = 10/308 (3%)

Query: 1   MSLPVVLIADKLAPSTVAALGDQVEVRWVD----GPDRDKLLAAVPEADALLVRSATTVD 56
           MS  +VL    L P+    L  + E+ + D     P +        +  AL VR    +D
Sbjct: 1   MSARIVLTLPAL-PAAAQTLLARHELHFADPREAAPGQLADFVRARDPHALFVRFGR-ID 58

Query: 57  AEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQ 116
           A+VL AAP L+++AR G GLD +D++ A ARG+ V   P +N  + AEHALALLLA ++ 
Sbjct: 59  AQVLEAAPSLRVIARHGSGLDTIDLECARARGIAVSATPGANAVAVAEHALALLLACAKG 118

Query: 117 IPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSP 176
           +   DA +    W +++  G ++  +T+G++GLG +G  +A+   A G  V+A       
Sbjct: 119 VARLDARMHAGHWDKAAHQGMQLASRTLGIIGLGPVGLRMARLAGAIGMRVIA---ATRT 175

Query: 177 ARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLV 236
            RA    + L++LDDL    D IS+H      T G+++   LA+ + GV++VN  RGGL+
Sbjct: 176 PRAVPRHVRLVALDDLWPACDAISLHCALNAATQGIVNAGMLARCRHGVLLVNTGRGGLI 235

Query: 237 DEAALADAITGGHVRAAGLDVFATEPC-TDSPLFELAQVVVTPHLGASTAEAQDRAGTDV 295
           D+AAL  A+  G V AAGLD F  EP   D+P   LA  V+TPH+GA+T +A + A    
Sbjct: 236 DDAALVAALRSGQVCAAGLDTFTREPAGPDNPYAGLANAVLTPHVGAATPQAFESAAVQA 295

Query: 296 AESVRLAL 303
           A  +   L
Sbjct: 296 ARQLLAGL 303


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: 18
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: 528
Length of database: 312
Length adjustment: 31
Effective length of query: 497
Effective length of database: 281
Effective search space:   139657
Effective search space used:   139657
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 Jul 25 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