GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Paraburkholderia bryophila 376MFSha3.1

Align Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 (characterized)
to candidate H281DRAFT_05713 H281DRAFT_05713 anthranilate phosphoribosyltransferase

Query= SwissProt::P00904
         (531 letters)



>FitnessBrowser__Burk376:H281DRAFT_05713
          Length = 343

 Score =  222 bits (565), Expect = 2e-62
 Identities = 129/331 (38%), Positives = 184/331 (55%), Gaps = 2/331 (0%)

Query: 199 TLQPILEKLYQAQTLSQQESHQLFSAVVRGELKPEQLAAALVSMKIRGEHPNEIAGAATA 258
           T Q  L++  + + +   E   L   ++RGEL P   AA +  ++++ E   EI  AAT 
Sbjct: 4   TPQEALQRTIEHREIFHDEMLHLMRLIMRGELSPVMAAAIITGLRVKKETIGEITAAATV 63

Query: 259 LLENAAPFPRPDYL-FADIVGTGGDGSNSINISTASAFVAAACGLKVAKHGNRSVSSKSG 317
           + E A      D   F DIVGTGGDGS++ NISTA+ FV+AA G KVAKHGNR VSSKSG
Sbjct: 64  MREFARHVEVQDNSNFVDIVGTGGDGSHTFNISTATMFVSAAAGAKVAKHGNRGVSSKSG 123

Query: 318 SSDLLAAFGINLDMNADKSRQALDELGVCFLFAPKYHTGFRHAMPVRQQLKTRTLFNVLG 377
           S+D+L A G+N+D+  ++   ++ E G+ F+FAP +H   ++  PVR++L  RT+FN+LG
Sbjct: 124 SADVLEALGVNIDLQPEQVAASIAETGMGFMFAPNHHPAMKNIAPVRRELGVRTIFNILG 183

Query: 378 PLINPAHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVHS-GGMDEVSLHAPTIVAELH 436
           PL NPA  P  L+GV+  +LV      ++ LG +   VV+   GMDEVSL A T V EL 
Sbjct: 184 PLTNPAGAPNQLMGVFHADLVGIQVRVMQRLGAKHVLVVYGMDGMDEVSLGAATQVGELR 243

Query: 437 DGEIKSYQLTAEDFGLTPYHQEQLAGGTPEENRDILTRLLQGKGDAAHEAAVAANVAMLM 496
           DGE++ Y++  EDFG+       L      E++ +L   L  K   A E         L 
Sbjct: 244 DGEVREYEIHPEDFGMQMVSNRTLKVADATESKAMLLEALDNKPGVAREIVTLNAGTALY 303

Query: 497 RLHGHEDLQANAQTVLEVLRSGSAYDRVTAL 527
             +    +    +   E + SG A  +V  L
Sbjct: 304 SANVASSIANGIELAREAIASGKARAKVDEL 334


Lambda     K      H
   0.318    0.134    0.388 

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: 435
Number of extensions: 18
Number of successful extensions: 3
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: 531
Length of database: 343
Length adjustment: 32
Effective length of query: 499
Effective length of database: 311
Effective search space:   155189
Effective search space used:   155189
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: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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