GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Pseudomonas fluorescens GW456-L13

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate PfGW456L13_1529 Valine--pyruvate aminotransferase (EC 2.6.1.66)

Query= SwissProt::Q2RK33
         (390 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1529
          Length = 390

 Score =  149 bits (375), Expect = 2e-40
 Identities = 114/384 (29%), Positives = 179/384 (46%), Gaps = 10/384 (2%)

Query: 6   RIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRYP 65
           R R + P+    +  +  E +  G D+I L IG+PD  T   +I +    A      RY 
Sbjct: 8   RSRAIEPFHVMALLARANELQAAGHDVIHLEIGEPDFTTAEPII-RAGQAALTAGKTRYT 66

Query: 66  TSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDPG 125
            + G+   R+A++ +YQ+ YG+++DPRR ++T  GS   +   S   VDPG   L+ DPG
Sbjct: 67  AARGIPELREAISGFYQQRYGLNIDPRRILITPGGSG-ALLLASALLVDPGKHWLLADPG 125

Query: 126 YPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVADLK 185
           YP       L  G +  +P+     +    G I       +    +  P NPTG +    
Sbjct: 126 YPCNRHFLRLVEGAAQLVPVGPEVRYQLTPGLIERHWDHDSVGALVASPANPTGTILTRD 185

Query: 186 FFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTGW 245
              ++    +     +  D  Y  +TY G  A S L+   +  V    NS SK + MTGW
Sbjct: 186 ELAKLSVAIKERHGHLVVDEIYHGLTY-GTDAASVLEVDDSAFV---LNSFSKYFGMTGW 241

Query: 246 RLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRV-YQERRDII 304
           RLGW       +  L ++  N+   A    Q+A +A        + E RR  +  RRD +
Sbjct: 242 RLGWLVAPDAAVGELEKLAQNLYISAPSMAQHAALACFEPATISILEERRAEFGRRRDYL 301

Query: 305 VEGFNSLGWHLE-KPKATFYVWAPVPR-GYTSASFAEMVLEKAGVIITPGNGYGNYGEG- 361
           +     LG+ +  +P+  FY++A + + G  + +F +  LE   V  TPG  +G Y  G 
Sbjct: 302 LPALRELGFGIAVEPEGAFYLYADISKFGGDAFAFCKHFLETEHVAFTPGLDFGRYQAGH 361

Query: 362 YFRIALTISKERMQEAIERLRRVL 385
           + R A T + ER+QEA+ER+ R L
Sbjct: 362 HVRFAYTQNLERLQEAVERIARGL 385


Lambda     K      H
   0.320    0.139    0.421 

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: 385
Number of extensions: 24
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: 390
Length of database: 390
Length adjustment: 31
Effective length of query: 359
Effective length of database: 359
Effective search space:   128881
Effective search space used:   128881
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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