GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Sinorhizobium meliloti 1021

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate SMa1836 SMa1836 acetylornithine deacetylase

Query= curated2:A0L3N2
         (380 letters)



>FitnessBrowser__Smeli:SMa1836
          Length = 374

 Score = 96.3 bits (238), Expect = 1e-24
 Identities = 96/331 (29%), Positives = 148/331 (44%), Gaps = 33/331 (9%)

Query: 45  GHVENFYARLGSK-GRNFTFAGHTDVVGAGDTSRWSSDPFAATLEEGYITGRGAVDMKGG 103
           G   N +A +G K  R +  +GH DVV A +T  W+SDPF   +E   + GRG  DMKG 
Sbjct: 47  GDRSNIFATIGPKEARGYIISGHMDVVPAAETG-WTSDPFRLRVEADRLYGRGTTDMKGF 105

Query: 104 LACMVAATARFLAARPHFAQQHSLSFLITGDEEGDALDGTLKVLQWLESQQEKMDYCLVG 163
           LA ++AA  + LAA P    +  L   ++ DEE         + +  E  ++ +   ++G
Sbjct: 106 LAAVLAAVPK-LAAMP---LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLG-AIIG 160

Query: 164 EPTSAAQLGDCIKNGRRGSVNGRLTIRGVQGHVAYPHLVDNPIHRAAPVL----AAISSM 219
           EPT    +        +G    RLT+RG  GH + P    N IH  A VL    A    +
Sbjct: 161 EPTGMRAI-----RAHKGKAAARLTVRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRL 215

Query: 220 TFDQGDRFFQP--TSLQFTAVQSGGSATNVVPGELTAGFNIRFSAMHTPESLEARIRQVL 277
                +  F+P  +SLQ   V+ GG A N++P      F  R  +   P  L A +R+  
Sbjct: 216 VGGPFEHVFEPPYSSLQIGTVK-GGQAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTA 274

Query: 278 D-----GAEVDYDLQMMTSGLPFITEGGPLVEAVKATVAQVTGLEPQLSTGGGTSDARFI 332
           +     G EV++  ++       +    PL     A + ++TG E   +   GT +A   
Sbjct: 275 EALTTLGFEVEWQ-ELSAYPALSLEPDAPLA----ALLEELTGREALPAVSYGT-EAGLF 328

Query: 333 SRHCVQTVEFGL--VGSTMHKVDERVPVADL 361
            R  +  +  G   +G   HK DE + + +L
Sbjct: 329 QRAGIDAIICGPGDIGRA-HKPDEYILIDEL 358


Lambda     K      H
   0.320    0.136    0.404 

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: 359
Number of extensions: 22
Number of successful extensions: 4
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: 380
Length of database: 374
Length adjustment: 30
Effective length of query: 350
Effective length of database: 344
Effective search space:   120400
Effective search space used:   120400
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 (21.8 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