GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Sinorhizobium fredii NGR234

Align Predicted dapE by GapMind curators (no experimental data)
to candidate WP_012709239.1 NGR_RS24810 M20 aminoacylase family protein

Query= predicted:L0FXC2
         (397 letters)



>NCBI__GCF_000018545.1:WP_012709239.1
          Length = 387

 Score =  243 bits (621), Expect = 5e-69
 Identities = 151/385 (39%), Positives = 198/385 (51%), Gaps = 11/385 (2%)

Query: 10  AADQLNQTIAIRRHIHAHPELSFEEHQTCAFVEKHLQEIGITNIQRK-ANTGLVALIEGK 68
           AA+  N+    RRH+H +PEL F    T AFVEK L+E G+  I      TG+V LI G 
Sbjct: 7   AAELQNEVTEWRRHLHMNPELLFAVENTAAFVEKKLREFGVDEIVTGLGRTGVVGLIRGN 66

Query: 69  NPSKKVIALRADMDALPIVEQNDVPYKSNKEGVMHACGHDVHTSSLLGAASILHAVKDQF 128
             + + I LRADMDALPI E +   + S   G MHACGHD HT+ LLGAA  L   ++ F
Sbjct: 67  LGAGRTIGLRADMDALPITETSGKAWSSTTPGKMHACGHDGHTAMLLGAAKYLAETRN-F 125

Query: 129 EGTVKLIFQPGEEKIPGGASLMIKDKALENPRPSGIVGQHVMPLIDAGKVGFRKGMYMAS 188
            G V +IFQP EE   GG + M+KD  +E      + G H MP +  G  G R G  MAS
Sbjct: 126 SGNVAVIFQPAEEG-GGGGNEMVKDGMMERFAIEEVYGMHNMPGMPVGHFGSRVGPIMAS 184

Query: 189 ADELYLKVIGKGGHGAMPETLVDPVLIASHIIVALQQVISRNASPKVPSVLSFGRIEALG 248
            DE  + V G+GGH A P   +DP+ I + I+ ALQ + SR   P    V+S  +  A  
Sbjct: 185 TDEFTITVKGRGGHAAQPHKTIDPIAIGAQIVNALQTIASRTVDPLASIVVSVTKFNAGF 244

Query: 249 ATNVIPNEVNIQGTFRTLDETWRAEAHQKMVKIAEGIAEGMGGSVDFEVRKGYPFLQNAP 308
           A NVIP +  + GT R L    R     ++ +IAE IA   G +VD    + YP   N  
Sbjct: 245 AHNVIPEQAVLAGTVRALTPQVRDTGEARIRQIAESIAGAYGATVDVWYGRNYPVTVNHA 304

Query: 309 ELTDRAYKAAQAYLGEENVE-DLDIWMAAEDFSYYTQEMDGCFYRLGIRNEEKGITSGVH 367
             T  A   A    GE NV   LD  M  EDFSY      G F  +G      G ++G+H
Sbjct: 305 TETGHALAVAATVAGEGNVNAALDPMMGGEDFSYMLLARPGAFVFIG-----NGESAGLH 359

Query: 368 TPTFDIDESALEVGAGLMAWIAINE 392
            P +D ++    +  G+  W+ + E
Sbjct: 360 HPAYDFNDDV--IPHGISYWVKLTE 382


Lambda     K      H
   0.317    0.134    0.387 

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: 400
Number of extensions: 26
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: 397
Length of database: 387
Length adjustment: 31
Effective length of query: 366
Effective length of database: 356
Effective search space:   130296
Effective search space used:   130296
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