GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Pseudomonas fluorescens FW300-N2E3

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate AO353_03235 AO353_03235 glutamate-pyruvate aminotransferase

Query= BRENDA::Q2RK33
         (390 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03235
          Length = 401

 Score =  349 bits (896), Expect = e-101
 Identities = 162/380 (42%), Positives = 247/380 (65%), Gaps = 3/380 (0%)

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

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

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

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

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

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

Query: 363 FRIALTISKERMQEAIERLR 382
            R AL  +++R+++A+  +R
Sbjct: 372 VRFALIENQDRIRQAVRGIR 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: 488
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: 401
Length adjustment: 31
Effective length of query: 359
Effective length of database: 370
Effective search space:   132830
Effective search space used:   132830
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