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_106710957.1 CU102_RS10055 amidohydrolase

Query= predicted:L0FXC2
         (397 letters)



>NCBI__GCF_003010955.1:WP_106710957.1
          Length = 389

 Score =  246 bits (629), Expect = 6e-70
 Identities = 140/375 (37%), Positives = 204/375 (54%), Gaps = 9/375 (2%)

Query: 21  RRHIHAHPELSFEEHQTCAFVEKHLQEIGITNIQRK-ANTGLVALIEGKNPSKKVIALRA 79
           RRH+HA+PEL F+ H+T  FV   L + G   ++     TG+V +I G++     + LR+
Sbjct: 18  RRHLHANPELMFDVHETARFVTDKLHQFGCDIVETGIGRTGVVGVIRGRHGEGPTVGLRS 77

Query: 80  DMDALPIVEQNDVPYKSNKEGVMHACGHDVHTSSLLGAASILHAVKDQFEGTVKLIFQPG 139
           DMDALP+ E    P+ S+  G MHACGHD HT+ LLGAA  L   ++ F+G++ +IFQP 
Sbjct: 78  DMDALPLTEITGKPWASHAAGKMHACGHDGHTAMLLGAAQYLAETRN-FKGSIAVIFQPA 136

Query: 140 EEKIPGGASLMIKDKALENPRPSGIVGQHVMPLIDAGKVGFRKGMYMASADELYLKVIGK 199
           EE   GG   M+KD  +E    S + G H +P +  G+   RKG  MA+ DE  + + G+
Sbjct: 137 EEG-GGGGREMVKDGMMERFSISEVYGMHNVPGLPVGEFAIRKGPIMAATDEFTITIEGR 195

Query: 200 GGHGAMPETLVDPVLIASHIIVALQQVISRNASPKVPSVLSFGRIEALGATNVIPNEVNI 259
           GGH A P   +DPV+I S ++ ALQ ++SR   P    VLS  +  A  A N+IP    +
Sbjct: 196 GGHAAQPHRTIDPVVIGSQLVNALQTIVSRGTDPLDSVVLSVTQFHAGDAHNIIPQRAEL 255

Query: 260 QGTFRTLDETWRAEAHQKMVKIAEGIAEGMGGSVDFEVRKGYPFLQNAPELTDRAYKAAQ 319
            GT RTL    R  A +++ ++AEG+A  +G S +    + YP   N    T+ A + A+
Sbjct: 256 AGTVRTLRPEMRDFAERRLTEVAEGVANALGASANVHYARNYPVTFNHERETEFAAQTAR 315

Query: 320 AYLGEENVE-DLDIWMAAEDFSYYTQEMDGCFYRLGIRNEEKGITSGVHTPTFDIDESAL 378
              G   V  D+   MA EDFSY  +   G F  +G      G ++ +H P +D ++ A+
Sbjct: 316 NVAGGGAVNTDVAPMMAGEDFSYMLEARPGAFIFIG-----NGDSASLHNPAYDFNDDAI 370

Query: 379 EVGAGLMAWIAINEL 393
             G      IA N L
Sbjct: 371 VYGISYWVQIAENAL 385


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: 406
Number of extensions: 23
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: 389
Length adjustment: 31
Effective length of query: 366
Effective length of database: 358
Effective search space:   131028
Effective search space used:   131028
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