GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Dyella japonica UNC79MFTsu3.2

Align homoserine dehydrogenase; EC 1.1.1.3 (characterized)
to candidate N515DRAFT_0577 N515DRAFT_0577 homoserine dehydrogenase

Query= CharProtDB::CH_122339
         (368 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0577
          Length = 382

 Score =  218 bits (554), Expect = 3e-61
 Identities = 151/373 (40%), Positives = 212/373 (56%), Gaps = 37/373 (9%)

Query: 7   LGVIGVGGVGTAFLNQLARLPNAPKLILLARSSQTLLSPTPSYSPTIPAAEWKTA---VE 63
           +G+IG G VG+A L QL             R++QT LS +         A  K      +
Sbjct: 32  VGLIGPGRVGSALLTQL-------------RAAQTRLSESGLELKLCGVAASKRMWLDCD 78

Query: 64  TPSLTK----SGALTPDEI---ATYLASAPGR-SILVDNTSDPALASNYPVFLRKGISVV 115
            P L +    +    P ++   A ++    GR ++L+D +++  +A++Y  +L +G+ VV
Sbjct: 79  DPDLNRRCDRAQIWRPADLRQFARHVLGDDGRHALLIDCSANDEVAAHYAGWLAEGVHVV 138

Query: 116 TPNKKGFSSDLSLWKEIFAAAAEGKALVYHESTVGAGLPVISTLKDLVNTGDEVTRIEGV 175
           TPNK   S  L  W+ I AA+  G    Y E+TV AGLPV+ TL+DL++TGDE+  ++G+
Sbjct: 139 TPNKLAGSGPLERWQAIRAASHAGARFRY-EATVCAGLPVVQTLRDLLDTGDELLAVDGM 197

Query: 176 FSGTLSFLFNTFAPASGSSSAKWSEVVSQAKELGYTEPDPRDDLNGMDVARKLTILARIA 235
           FSGTL++L N            +S +V +A  LGYTEPDPRDDL+G+DVARKL ILAR A
Sbjct: 198 FSGTLAWLCNRH-----DGGRPFSALVREAHALGYTEPDPRDDLSGLDVARKLVILAREA 252

Query: 236 GLDVQSPDSFPIESLIPAELTSLPSSADGIAQFMARLPEFDSQMAAIKEGAEKAGKVVRY 295
           G  + S D   ++SL+PAEL +L + A     FMARL E D+ MAA    A   G V+R+
Sbjct: 253 GWAL-SLDDVDVQSLVPAELAALDADA-----FMARLDELDAPMAAQLAIARAEGGVLRH 306

Query: 296 VGSVDVAKKEVRVGLQQFDKDSAIAGLKGSDNIISFYTRRYGSNPLIVQGAGAGGDVTAM 355
           V S+D       V L         A  + +DN++ F TRRY  NPL+VQG GAG +VTA 
Sbjct: 307 VASLD-RDGRASVKLAVLPASHPFAHTRLTDNVVQFTTRRYHDNPLLVQGPGAGPEVTAA 365

Query: 356 GVTADLLKVIERL 368
           GV  DLL++ E L
Sbjct: 366 GVFGDLLRIAESL 378


Lambda     K      H
   0.314    0.132    0.368 

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: 330
Number of extensions: 18
Number of successful extensions: 6
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: 368
Length of database: 382
Length adjustment: 30
Effective length of query: 338
Effective length of database: 352
Effective search space:   118976
Effective search space used:   118976
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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