GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Phyllobacterium brassicacearum STM 196

Align Predicted dapE by GapMind curators (no experimental data)
to candidate WP_106711061.1 CU102_RS09815 amidohydrolase

Query= predicted:L0FXC2
         (397 letters)



>NCBI__GCF_003010955.1:WP_106711061.1
          Length = 387

 Score =  252 bits (643), Expect = 1e-71
 Identities = 150/385 (38%), Positives = 211/385 (54%), Gaps = 12/385 (3%)

Query: 11  ADQLNQTIAI-RRHIHAHPELSFEEHQTCAFVEKHLQEIGITNIQRK-ANTGLVALIEGK 68
           A ++ Q +A  R H+H +PE+ ++ HQT AFV + L+E G   I+     TG+V L+ G+
Sbjct: 7   AHEMQQHVAEWRHHLHENPEILYDVHQTSAFVAEKLREFGCDTIETGIGQTGVVGLVRGR 66

Query: 69  NPSKKVIALRADMDALPIVEQNDVPYKSNKEGVMHACGHDVHTSSLLGAASILHAVKDQF 128
           +    VI  RADMDALPI E +  P+ S   G MHACGHD HT+ LLGAA  L   ++ F
Sbjct: 67  HGEGPVIGFRADMDALPITEASGKPWASKTLGKMHACGHDGHTAMLLGAAQYLAETRN-F 125

Query: 129 EGTVKLIFQPGEEKIPGGASLMIKDKALENPRPSGIVGQHVMPLIDAGKVGFRKGMYMAS 188
            GT+ LIFQP EE    GA  MI D  ++      + G H  P +  G+   RKG  MA+
Sbjct: 126 RGTIVLIFQPAEEG-GAGARAMIDDGLMDRFAIGEVYGMHNAPGLPVGQFATRKGSIMAA 184

Query: 189 ADELYLKVIGKGGHGAMPETLVDPVLIASHIIVALQQVISRNASPKVPSVLSFGRIEALG 248
            +E  + V G+ GH A P T +DPV+I++HII+ALQ ++SR   P    V+S  ++    
Sbjct: 185 TNEFEITVTGRSGHAAKPHTAIDPVVISAHIILALQSIVSRETDPLKALVVSVTQLNGGD 244

Query: 249 ATNVIPNEVNIQGTFRTLDETWRAEAHQKMVKIAEGIAEGMGGSVDFEVRKGYPFLQNAP 308
           ATNVIP+ + + GT RTL    R  A +++ +I E  A   GG  +    +GYP   N  
Sbjct: 245 ATNVIPDVIKLGGTVRTLVPEIREFAQKRLTEIVESTAAVFGGKAEVVYHQGYPVTFNHD 304

Query: 309 ELTDRAYKAAQAYLGEENVE-DLDIWMAAEDFSYYTQEMDGCFYRLGIRNEEKGITSGVH 367
             TD A   AQ  +GE  V   +   M AEDFSY  +   G F  LG      G T G+H
Sbjct: 305 RETDFAIGIAQTIVGEAAVNTTMPPVMGAEDFSYMLESRPGAFVFLG-----NGDTPGLH 359

Query: 368 TPTFDIDESALEVGAGLMAWIAINE 392
              +D ++ A+    G+  W+++ E
Sbjct: 360 NSAYDFNDDAIPY--GISYWVSLAE 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: 402
Number of extensions: 27
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 26 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