GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Desulfovibrio vulgaris Miyazaki F

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate 8499593 DvMF_0361 LL-diaminopimelate aminotransferase (RefSeq)

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__Miya:8499593
          Length = 389

 Score =  172 bits (436), Expect = 2e-47
 Identities = 117/393 (29%), Positives = 186/393 (47%), Gaps = 16/393 (4%)

Query: 4   LADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDR-GET 62
           LAD L+ + P     + +   E+ A+G D+I LG G+PD  TPD I +A   A++R    
Sbjct: 6   LADRLATLPPYLFAGIDKVKAEVAARGVDIISLGIGDPDMPTPDFIIEAMKKAVERPANH 65

Query: 63  KYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGT-GGKQILFNAFMATLNPGDEVVIP 121
           +Y    G+ E R+ +A  + R   +       ++G  G K+ + +  +A +NPGD V++ 
Sbjct: 66  QYPSYVGMLEFRQEVANWYGRRFGVSLDPKTEVIGLIGSKEGIAHFPLAFVNPGDLVLVC 125

Query: 122 APYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAY 181
            P +  Y       GG   F+P  +EN++    + +  A   + K    N P+NP+ A  
Sbjct: 126 TPNYPVYHIATGFVGGEVQFIPLVEENDYLPDLDAIPAATWDRAKMIFVNYPNNPTAATA 185

Query: 182 SHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAY 241
                + L  +  KH +V +  D  Y  + Y +      +    G  + T+  + +SK Y
Sbjct: 186 PRAFYEKLIGICRKH-NVIIAHDTAYTEVYYDENDKPMSILEVEGAKDVTIEFHSLSKTY 244

Query: 242 AMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGR 301
            MTGWR+G A G   L+  +  ++    SG     Q A++ AL    DF    + I++ R
Sbjct: 245 NMTGWRVGMAVGNASLVAGLGKVKENVDSGIFQAVQEASIVALRDGDDFCRELRGIYRKR 304

Query: 302 RDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVA 361
           RD+VV+ LN+  GI+C  P  AFY++       G +A          +FV+ +LE  GV 
Sbjct: 305 RDVVVAALNKV-GIACRVPTAAFYIWAKVPAGYGSSA----------EFVTAVLEKTGVV 353

Query: 362 VVHGSAFGLGPN--FRISYATSEALLEEACRRI 392
           +  G+ FG      FRIS       LEEA  RI
Sbjct: 354 LTPGNGFGTPGEGYFRISLTVDTDRLEEAVSRI 386


Lambda     K      H
   0.318    0.134    0.402 

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: 432
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: 400
Length of database: 389
Length adjustment: 31
Effective length of query: 369
Effective length of database: 358
Effective search space:   132102
Effective search space used:   132102
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 (21.7 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