GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Herbaspirillum seropedicae SmR1

Align Predicted dapE by GapMind curators (no experimental data)
to candidate HSERO_RS04135 HSERO_RS04135 amidohydrolase

Query= predicted:L0FXC2
         (397 letters)



>FitnessBrowser__HerbieS:HSERO_RS04135
          Length = 402

 Score =  255 bits (652), Expect = 1e-72
 Identities = 153/398 (38%), Positives = 221/398 (55%), Gaps = 15/398 (3%)

Query: 1   MLKDTIKKLAADQLNQTIAIRRHIHAHPELSFEEHQTCAFVEKHLQEIGITNIQRKANTG 60
           ++ D IK+L  +     ++IRRH+HAHPEL FEE +T +FV   L+  G+T  +     G
Sbjct: 3   IVNDGIKELPKEM--DLVSIRRHLHAHPELRFEEKRTASFVADMLRSYGLTVAENIGGYG 60

Query: 61  LVALIEGKNPSKKVIALRADMDALPIVEQNDVPYKSNKEGVMHACGHDVHTSSLLGAASI 120
           +VA +  K  S + IALRADMDALP+ EQND  + S   G MHACGHD HT+ LLGAA  
Sbjct: 61  VVATLR-KGKSTRAIALRADMDALPMSEQNDFSHISTCAGKMHACGHDGHTTMLLGAARR 119

Query: 121 LHAVKDQFEGTVKLIFQPGEEKIPGGASLMIKDKALENPRPSGIVGQHVMPLIDAGKVGF 180
           L   + +F+GTV  +FQP EE    GA LMI+D   E      I G H  P + AG  G 
Sbjct: 120 LSR-EVEFDGTVHFVFQPAEEG-GAGARLMIEDGLFERFPADAIFGVHNWPGLPAGSFGL 177

Query: 181 RKGMYMASADELYLKVIGKGGHGAMPETLVDPVLIASHIIVALQQVISRNASPKVPSVLS 240
           R G  MAS++     + G+G HGA P   +DPVL A+ + +A Q +++RN +P   +V+S
Sbjct: 178 RPGPLMASSNTFSATLFGRGAHGAQPHRSIDPVLAAAQLTLAWQSIVTRNINPNHRAVIS 237

Query: 241 FGRIEALGATNVIPNEVNIQGTFRTLDETWRAEAHQKMVKIAEGIAEGMGGSVDFEVRKG 300
             ++    A NVIP +  + GT R+ D         +M  IAE I +     V F   + 
Sbjct: 238 VTQLHTGTADNVIPEQATLSGTVRSFDAETLDLIEHRMAAIAEAIGQMFDLRVQFHFERL 297

Query: 301 YPFLQNAPELTDRAYKAAQAYLGEENVE-DLDIWMAAEDFSYYTQEMDGCFYRLGIRNEE 359
           YP + N PE T +A +A  A +G E V+ D +   A+EDF++Y Q   GC+  LG     
Sbjct: 298 YPAVVNHPEATQQAMQAMMAAVGAEQVDGDTEPAFASEDFAFYLQHKPGCYAFLGNGVIA 357

Query: 360 KGITSG-------VHTPTFDIDESALEVGAGLMAWIAI 390
            G  +G       +H+P +D ++  ++  AG+  W+++
Sbjct: 358 DGKQAGSQATSRELHSPFYDFNDDIID--AGVAYWVSL 393


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: 365
Number of extensions: 17
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: 402
Length adjustment: 31
Effective length of query: 366
Effective length of database: 371
Effective search space:   135786
Effective search space used:   135786
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.

Links

Downloads

Related tools

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