GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Klebsiella michiganensis M5al

Align Probable succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18 (uncharacterized)
to candidate BWI76_RS10270 BWI76_RS10270 acetylornithine deacetylase

Query= curated2:Q8CQC2
         (405 letters)



>FitnessBrowser__Koxy:BWI76_RS10270
          Length = 391

 Score =  133 bits (334), Expect = 1e-35
 Identities = 110/399 (27%), Positives = 170/399 (42%), Gaps = 36/399 (9%)

Query: 13  LADIVKIQTEND--HEIEVCEYLKDLLSQYDIDSKIVKVNDSRANLVAEIGSG-APVLAI 69
           LA +V I TEN   HE E  E L+  L     D    +    R N++A + +G     A 
Sbjct: 15  LATLVAINTENPPGHEREAAECLEGWLLTAGFDLSFSEYAPGRTNVIAVLHNGPGQCFAF 74

Query: 70  SGHMDVVDAGDHDDWTFPPFELTDKDGKLFGRGTTDMKGGLMAMVIAMIELKQSNALKQG 129
           + H+D V AG    WT  PF L ++ G+L+GRG  D KG L+AMV A+  L  +     G
Sbjct: 75  NTHIDTVPAGS--GWTSDPFTLAERGGRLYGRGACDAKGPLVAMVEALRLLAATRQRWSG 132

Query: 130 TIRLLATTGEETEQYGAQLLADEGYLDDVSGLIIGEPTSNIAYYAHKGSMSCVVTAKGKA 189
           T+  + T  EE    GA+    +     +   +IGEPTSN  + AHKGS+   V  KG  
Sbjct: 133 TLMGVFTADEEVASEGAKFYVRDNP-PAIDFAVIGEPTSNATFSAHKGSLRPRVRVKGVT 191

Query: 190 AHSSMPHLGTNAVDILVDFVNEMKQEYKNIKEHDKVHELDAVPMIEKHLHRKIGEEESHI 249
           AHS  P LG NA+             Y++ +          + +IE+  H+++      +
Sbjct: 192 AHSGTPELGVNAI-------------YQSAR---------LLGLIEEAHHQQVRCRCHDL 229

Query: 250 YSGFVMLNSVFNGGKQVNSVPHKATAKYNVRTVPEYDSTFVKDLFEKVIRHVG-----EN 304
                +  +  +GG   N VP       + R VP  D   VK   ++++ H       E 
Sbjct: 230 VGNASLTVTRIHGGHADNVVPDSCELLLDRRMVPGEDEAVVKAELQQLLDHAHAHAGVEA 289

Query: 305 YLTVDIPSSHDPVASDRDNPLIQNITRIAPNYVHEDIVVSALIGTTDASSFLGTNENNVD 364
            +    P++     +D    +++        +   +       G  D   F       V 
Sbjct: 290 EIIAWQPTTGGATQTDSSEAIVEQSLAACRRHGQSEPGPFGFQGGCDLVHFRSLGAKGV- 348

Query: 365 FAVFGPGESIMAHQVDEFIRKDMYLSYIDVYKDVFKAYL 403
             V GPG   +AH+ DEF+  D +++   +Y D+  A L
Sbjct: 349 --VIGPGSLAVAHKPDEFVPVDEFIAAAYIYLDIALAML 385


Lambda     K      H
   0.316    0.134    0.380 

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: 380
Number of extensions: 21
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 405
Length of database: 391
Length adjustment: 31
Effective length of query: 374
Effective length of database: 360
Effective search space:   134640
Effective search space used:   134640
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 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