GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapL in Sinorhizobium fredii NGR234

Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate WP_164924727.1 NGR_RS30500 M20 family metallopeptidase

Query= SwissProt::O34916
         (374 letters)



>NCBI__GCF_000018545.1:WP_164924727.1
          Length = 398

 Score =  189 bits (481), Expect = 9e-53
 Identities = 116/354 (32%), Positives = 187/354 (52%), Gaps = 13/354 (3%)

Query: 4   EELIAIRRDLHRIPELGFQEFKTQQYLLNVLEQYPQDRIEIEKWRTGLFVKVNGTA--PE 61
           + ++ +R  +HR PEL   E+KTQQ +  +LE++      +    TGL++ + G+A  P+
Sbjct: 16  DAVLELRHAMHREPELSNNEWKTQQRIRGMLERFGLKGATVFH-NTGLYIDIEGSASGPK 74

Query: 62  KMLAYRADIDALSIEE-QTGLPFASEHHGNMHACGHDLHMTIALGII--DHFVHHPVKHD 118
           + +A R DIDAL I+E +  LP+ S   G MHACGHDLH +IA+G+    H + +     
Sbjct: 75  RAVAVRGDIDALPIQETRDDLPYQSHVEGVMHACGHDLHASIAMGVALAFHRMRNNFAGK 134

Query: 119 LLFLFQPAEEG-PGGAEPMLESDVLKKWQPDFITALHIAPELPVGTIATKSGLLFANTSE 177
           L   FQPAEE  P G   +LE  +L+ +  D     H+ P + VG    + G +  ++ +
Sbjct: 135 LRVFFQPAEEAEPLGGRTVLEERLLEGF--DNAVGFHVTPSIQVGKFGAREGAVSKSSDQ 192

Query: 178 LVIDLEGKGGHAAYPHLAEDMVVAASTLVTQLQTIISRNTDPLDSAVITVGTITGGSAQN 237
             + + G   H + PH   D +  A+  V ++Q +ISR     D +VIT+GTI GG A N
Sbjct: 193 FKVTVSGSAAHGSTPHNGIDAITIAAAFVNEVQKVISREVPVDDRSVITIGTIHGGEATN 252

Query: 238 IIAETAHLEGTIRTLSEESMKQVKERIEDVVKGIEIGFRCKGKVTYPSVYHQVYNTSGLT 297
           II     +EGTIRT + E    + +R+ ++ +G+    R K +V   S    V N   + 
Sbjct: 253 IICPKVVMEGTIRTTNPELRPLLSQRVREIAEGVAALHRGKAEVVVTSGEPAVINDPEMV 312

Query: 298 EEFMSFVAEHQLATVIEAKEAMTG-EDFGYMLKKYPGFMFWLGA---DSEHGLH 347
             F   V++   +  +   +A++G +DFG+  +  P   FW G+    +E G+H
Sbjct: 313 RLFRDAVSDMAGSDALTQGKAISGSDDFGFYSQCIPSIYFWFGSGEPGNESGVH 366


Lambda     K      H
   0.319    0.135    0.397 

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: 382
Number of extensions: 18
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: 374
Length of database: 398
Length adjustment: 30
Effective length of query: 344
Effective length of database: 368
Effective search space:   126592
Effective search space used:   126592
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 (21.7 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