GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Sphingomonas koreensis DSMZ 15582

Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Ga0059261_1288 Ga0059261_1288 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::Q82IK5
         (364 letters)



>FitnessBrowser__Korea:Ga0059261_1288
          Length = 401

 Score =  147 bits (371), Expect = 5e-40
 Identities = 119/384 (30%), Positives = 179/384 (46%), Gaps = 35/384 (9%)

Query: 7   RLPTFPWDKLEPYKARAAAHPDGIVDLSVGTPVDPVPELIQKALVAAADSP---GYPTVW 63
           RLP +   ++   +A A A  + I+DL +G P  P P+ +   L   A  P   GY    
Sbjct: 10  RLPPYVIAEVNGMRAAARAAGEDIIDLGMGNPDLPPPQHVIDKLCEVAQKPSAHGYSQSK 69

Query: 64  GTPELRDALTGWVERRLGARGVTHHHVLPIVGSKELVAWLPTQLGLGPGDKVAHPRLAYP 123
           G P LR A   +  RR G        V+  +GSKE +A L T +   PGD +  P  +YP
Sbjct: 70  GIPGLRRAQANYYGRRFGVDVDPESEVVVTMGSKEGLASLATAI-TAPGDVILAPNPSYP 128

Query: 124 TYEVGARLARAD-HVVYDDPTELDPTGLK-----------LLWLNSPSNPTGKVLSKAEL 171
            +  G  +A A    V   P E     L+           +L +N PSNPT + +  A  
Sbjct: 129 IHTFGFIIAGATIRAVPTTPDEHYFESLERAMNFTVPRPSILVVNYPSNPTAETVDLAFY 188

Query: 172 TRIVAWAREHGILVFSDECYLELGWEADP-VSVLHPDVCGGSYEGIVSVHSLSKRSNLAG 230
            R+VAWA+E+ + + SD  Y EL ++  P VS+L      G+ +  +   SLSK  ++AG
Sbjct: 189 ERLVAWAKENKVWIISDLAYSELYYDGKPTVSILQ---VKGAKDVAIEFTSLSKTYSMAG 245

Query: 231 YRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAAL-GDDAHVREQRERYAARRTAL 289
           +R  F  G+  ++  + +++ +       P QAA  AAL G    V   R+ Y  RR  L
Sbjct: 246 WRIGFAVGNKQLIAAMTRVKSYLDYGAFTPVQAAACAALNGPQDIVEANRQLYHKRRDVL 305

Query: 290 RDALLSHGFRIEHSEASLYLWATRGESCWDTVAHLADL----------GILVAPGDFYGS 339
            ++    G+ I    AS++ WA    +    +AHL  L           + VAPG  YG 
Sbjct: 306 VESFGRAGWDIPAPPASMFAWAPLPPA----LAHLGSLEFSKQLLSHAKVAVAPGVGYGE 361

Query: 340 AGEQFVRVALTATDERVAAAVRRL 363
            GE FVR+A+   ++R+  A R +
Sbjct: 362 NGEGFVRIAMVENEQRLRQAARNV 385


Lambda     K      H
   0.319    0.135    0.420 

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: 405
Number of extensions: 20
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: 364
Length of database: 401
Length adjustment: 30
Effective length of query: 334
Effective length of database: 371
Effective search space:   123914
Effective search space used:   123914
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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