GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysY in Pedobacter sp. GW460-11-11-14-LB5

Align Putative [LysW]-L-2-aminoadipate 6-phosphate reductase; EC 1.2.1.- (uncharacterized)
to candidate CA265_RS18540 CA265_RS18540 N-acetyl-gamma-glutamyl-phosphate reductase

Query= curated2:B9KZP8
         (352 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS18540 CA265_RS18540
           N-acetyl-gamma-glutamyl-phosphate reductase
          Length = 326

 Score =  179 bits (453), Expect = 1e-49
 Identities = 126/355 (35%), Positives = 185/355 (52%), Gaps = 45/355 (12%)

Query: 1   MVVSVAILGGSGYTGGELLRLLLSHPEVEVKQVTSRSRAGKFVHTVHPNLRKRTALKFVP 60
           M +   I+GG+GYTGGE+LR+L++HP VE+  V S S AG  +  VH +L   T LKFV 
Sbjct: 1   MKIKAGIIGGAGYTGGEMLRILVNHPNVEIAFVNSTSNAGNLISDVHTDLIGDTDLKFV- 59

Query: 61  PEALEPVDLLFACLPHGETA------PIVDRLLELAPIVIDLSADFRLRDPAAYEQWYHW 114
            +  + +D+LF C+ HG+        PI D +      +IDLS DFRL   A++      
Sbjct: 60  SDIPQDIDVLFLCVGHGDAKKFLTANPIKDNIK-----IIDLSQDFRLHANASFS----- 109

Query: 115 THPRPDLLAQAVYGLPELHREEIRNARYIACPGCNSTTVILGLAPLFRAGLIDLDLPVTV 174
                      VYGLPEL+R++I+ A+ IA PGC +T + LGL PL   GLI  +  V +
Sbjct: 110 -------TKDFVYGLPELNRDKIKAAKNIANPGCFATCIQLGLLPLAAKGLIQNE--VHI 160

Query: 175 ECKVGSSGAGGEAGPASHHPERSGVIRPFKPGGHRHTAEVLQELTVCGRTPSLGLSVTSV 234
               GS+GAG      SH   R+  +  +K   H+H  E+ + L      PS+  ++  +
Sbjct: 161 NATTGSTGAGQSLSTTSHFSWRNNNLSIYKAFEHQHLNEISESLLQL--QPSISEALNFI 218

Query: 235 EA----VRGILATAHLFPKQPLTDRDLWQVYRAAYGQEPFIRLVKEASGIHRYPEPKILA 290
                  RGILA  +L  +  L+  +   +Y A Y   PF  + ++   +      K + 
Sbjct: 219 PQRGAFTRGILAAMYL--ESDLSLEEAQNIYEAYYSAHPFTHVSRKNIDL------KQVV 270

Query: 291 GSNYCDIGWELDELPGGRQRLVVMSAIDNLMKGAAGQAVQAMNIRLGFPETLGLE 345
            +N   +  E     GG  +L ++S IDNL+KGA+GQAVQ MN+  G  ET GL+
Sbjct: 271 NTNKALVHLEKH---GG--KLFIISIIDNLLKGASGQAVQNMNLMFGLDETAGLK 320


Lambda     K      H
   0.321    0.140    0.431 

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: 270
Number of extensions: 12
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: 352
Length of database: 326
Length adjustment: 28
Effective length of query: 324
Effective length of database: 298
Effective search space:    96552
Effective search space used:    96552
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: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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