GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Pseudomonas putida KT2440

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate PP_0817 PP_0817 aminotransferase

Query= BRENDA::Q2RK33
         (390 letters)



>FitnessBrowser__Putida:PP_0817
          Length = 402

 Score =  342 bits (877), Expect = 1e-98
 Identities = 160/382 (41%), Positives = 248/382 (64%), Gaps = 3/382 (0%)

Query: 6   RIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRYP 65
           RI  LPPY+F    +    AR RG DII L +G+PD  TP H+++KLV  A   + H Y 
Sbjct: 12  RIDRLPPYVFNITAELKMAARRRGEDIIDLSMGNPDGATPPHIVEKLVQVAQREDTHGYS 71

Query: 66  TSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDPG 125
           TS G+   R+A+++WY+  Y VD+DP  E +  IGSKEG+AH+ L  +D GD  LVP+P 
Sbjct: 72  TSRGIPRLRRAISNWYKDRYEVDIDPESEAIVTIGSKEGLAHLMLATLDQGDTVLVPNPS 131

Query: 126 YPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVADLK 185
           YP++  G ++AG +   +PL     F  +L     +   + K+M + +P+NPT    +L 
Sbjct: 132 YPIHIYGAVIAGAQVRSVPLVPGVDFFNELERAIRESIPKPKMMILGFPSNPTAQCVELD 191

Query: 186 FFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTGW 245
           FF+ VV  A+ Y+++V HD AY++I YDG++APS +Q PGAK++ +EF ++SK YNM GW
Sbjct: 192 FFERVVALAKQYNVLVVHDLAYADIVYDGWKAPSIMQVPGAKDIAVEFFTLSKSYNMAGW 251

Query: 246 RLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDIIV 305
           R+G+  G  +++ ALARIKS  D G F  +Q A IAAL G Q+ + ++   Y++RR+++V
Sbjct: 252 RIGFMVGNPELVSALARIKSYHDYGTFTPLQVAAIAALEGDQQCVRDIAEQYRQRRNLLV 311

Query: 306 EGFNSLGWHLEKPKATFYVWAPVPRGYT---SASFAEMVLEKAGVIITPGNGYGNYGEGY 362
           +G + LGW +E PKA+ YVWA +P  Y    S  F++ +L +  V ++PG G+G+YG+ +
Sbjct: 312 KGLHELGWMVENPKASMYVWAKIPPEYAHLGSLEFSKKLLAETKVCVSPGIGFGDYGDDH 371

Query: 363 FRIALTISKERMQEAIERLRRV 384
            R AL  +++R+++AI  +R++
Sbjct: 372 VRFALIENQDRIRQAIRGIRQM 393


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: 496
Number of extensions: 17
Number of successful extensions: 1
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: 402
Length adjustment: 31
Effective length of query: 359
Effective length of database: 371
Effective search space:   133189
Effective search space used:   133189
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