GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Escherichia coli BW25113

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate 16484 b2379 hypothetical protein (NCBI)

Query= BRENDA::Q2RK33
         (390 letters)



>FitnessBrowser__Keio:16484
          Length = 412

 Score =  342 bits (878), Expect = 9e-99
 Identities = 161/380 (42%), Positives = 244/380 (64%), Gaps = 3/380 (0%)

Query: 6   RIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRYP 65
           RI  LPPY+F    +    AR RG DII   +G+PD  TP H+++KL   A  P+ H Y 
Sbjct: 12  RIDRLPPYVFNITAELKMAARRRGEDIIDFSMGNPDGATPPHIVEKLCTVAQRPDTHGYS 71

Query: 66  TSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDPG 125
           TS G+   R+A++ WYQ  Y V++DP  E +  IGSKEG+AH+ L  +D GD  LVP+P 
Sbjct: 72  TSRGIPRLRRAISRWYQDRYDVEIDPESEAIVTIGSKEGLAHLMLATLDHGDTVLVPNPS 131

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

Query: 186 FFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTGW 245
           FF++VV  A+ YD++V HD AY++I YDG++APS +Q PGA++V +EF ++SK YNM GW
Sbjct: 192 FFEKVVALAKRYDVLVVHDLAYADIVYDGWKAPSIMQVPGARDVAVEFFTLSKSYNMAGW 251

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

Query: 306 EGFNSLGWHLEKPKATFYVWAPVPRGYT---SASFAEMVLEKAGVIITPGNGYGNYGEGY 362
           +G +  GW +E PKA+ YVWA +P  Y    S  FA+ +L +A V ++PG G+G+YG+ +
Sbjct: 312 KGLHEAGWMVEMPKASMYVWAKIPEPYAAMGSLEFAKKLLNEAKVCVSPGIGFGDYGDTH 371

Query: 363 FRIALTISKERMQEAIERLR 382
            R AL  +++R+++AI  ++
Sbjct: 372 VRFALIENRDRIRQAIRGIK 391


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: 500
Number of extensions: 15
Number of successful extensions: 2
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: 412
Length adjustment: 31
Effective length of query: 359
Effective length of database: 381
Effective search space:   136779
Effective search space used:   136779
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