GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapL in Dinoroseobacter shibae DFL-12

Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate 3607752 Dshi_1161 amidohydrolase (RefSeq)

Query= SwissProt::D5E0A1
         (375 letters)



>FitnessBrowser__Dino:3607752
          Length = 386

 Score =  218 bits (555), Expect = 2e-61
 Identities = 128/364 (35%), Positives = 180/364 (49%), Gaps = 3/364 (0%)

Query: 10  RRELHKIPELGFQEVKTQRFLLDYINTLPQERLEVKTWKTGLFVKVHGTNPTKTIGYRAD 69
           R+ LH+ PELGF+  KT R+L+  +     + +  +   +G+   + G  P   IG RAD
Sbjct: 18  RQALHRAPELGFECHKTARYLIARLRAFGVDEVHDRIATSGVVALIRGGGPGPVIGLRAD 77

Query: 70  IDGLPITEETNYSFQSQHEGLMHACGHDMHMAIGLGVLTYFAQ-HEIKDNVLFIFQPAEE 128
           +D LPI EET  ++ S+ EG+MHACGHD HM + LG   Y A+       V  IFQPAEE
Sbjct: 78  MDALPIVEETGVAYASETEGVMHACGHDGHMVMLLGAARYLAETRNFAGTVAIIFQPAEE 137

Query: 129 GPGGAQPMLQSDIMKEWLPDFIFALHVAPEYPVGSIALKEGLLFANTSELFIDLKGKGGH 188
             GGAQ M    +M+ +  + ++ALH AP    G      G + A      I +KG+GGH
Sbjct: 138 HGGGAQVMCDEGLMERFGIEHVYALHNAPGIAEGHFLTTRGPIMAAVDTFHIHIKGRGGH 197

Query: 189 AAYPHTTNDMVVAACQLVSQLQTIVARNVDPLDSAVITVGKIQGGTVQNIIAERARIEGT 248
           AA PH T D ++AA  +   LQTIV+RN    D  V++V +I  GT  N++ + A I GT
Sbjct: 198 AAMPHETADPIMAAVGIAQALQTIVSRNHIATDELVLSVTQIHTGTADNVVPDTAYICGT 257

Query: 249 IRTLSPESMTRVKERIEAIVKGVEVGYQCETAIDYGCMYHQVYNHHEVTREFMEFAKEQT 308
           +R+  P     V  R+E IV G    +     +DY   Y    N  +        A +  
Sbjct: 258 VRSFDPAVQAMVMRRMEQIVAGQAASFDVMAELDYEKGYPPTVNTADEVALAARAASDVV 317

Query: 309 DVDVIECKEA--MTGEDFGYMLKDIPGFMFWLGVQSEYGLHHAKLQPHEGAIDIAISLIT 366
               ++      M  EDF YML+  PG   +LG     GLHH     ++    I  S   
Sbjct: 318 GDRAVDTASGRQMGAEDFAYMLQARPGAYLFLGQGEGAGLHHPAYDFNDRIAPIGASFFA 377

Query: 367 KYFE 370
           +  E
Sbjct: 378 RLVE 381


Lambda     K      H
   0.320    0.137    0.410 

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: 387
Number of extensions: 20
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: 375
Length of database: 386
Length adjustment: 30
Effective length of query: 345
Effective length of database: 356
Effective search space:   122820
Effective search space used:   122820
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