GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argJ in Novosphingobium barchaimii LL02

Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_059149857.1 V474_RS01890 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ

Query= BRENDA::Q92MJ1
         (413 letters)



>NCBI__GCF_001046635.1:WP_059149857.1
          Length = 408

 Score =  369 bits (948), Expect = e-107
 Identities = 210/413 (50%), Positives = 268/413 (64%), Gaps = 5/413 (1%)

Query: 1   MSGSVSPLAPKTFAEMPALRGVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCP 60
           M+  VSPLA   F  +PA+ GV      AG K   R D+  + F+   +VAGVFT++ C 
Sbjct: 1   MAYPVSPLA-SPFPALPAIAGVTPHVVRAGYKDWGRCDLTYVTFEAGTAVAGVFTKNLCC 59

Query: 61  SAPVDHCRQNLPGGIARAVVVNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFLAS 120
           S+ V+  R N+  G ARA+VVN+GN+NAFTG +GREA     +  A  +G    +VF++S
Sbjct: 60  SSEVELGRDNIVQGRARALVVNAGNSNAFTGYRGREAVEQIMDQVAAHIGAPREQVFVSS 119

Query: 121 TGVIGEPLDATKFAGVLDKLAASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVKVAIN 180
           TGVIG PL   K    ++K A +A    W +AA  I TTDT+ K A  +A IG  KV I+
Sbjct: 120 TGVIGVPLPKDKAREGVEK-ALTAQPCTWEDAANTIATTDTFAKGAAATAMIGDTKVTIS 178

Query: 181 GIAKGAGMIAPDMATMLSFVVTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSDTLML 240
            I KG+GMIAPDMATML ++ TDA + PA LQA L A    TF+ +TVDSDTSTSDT++ 
Sbjct: 179 AIIKGSGMIAPDMATMLGYLFTDAAVEPAFLQACLSAANLRTFSCITVDSDTSTSDTVLA 238

Query: 241 FATGAAAGDGQAKVEDAADPRLDGFRAALDDLLRDLALQVVRDGEGARKMVEVTVEGAEN 300
           FATG A   G A +          F AA+ D+ R LA  VVRDGEGA+K + V V GA +
Sbjct: 239 FATGKA---GNAPLTSFQSDGAHAFAAAVHDVCRQLAHLVVRDGEGAQKFIAVAVTGAVS 295

Query: 301 DAAAKRIALSIANSPLVKTAVAGEDANWGRVVMAVGKSGEMAERDRLAIWFGDIRVAVEG 360
           D +A+++ ++IANSPLVKTA+AGEDANWGRVVMAVGK+GE A+RD+L+I FG    A EG
Sbjct: 296 DESARKVGMAIANSPLVKTAIAGEDANWGRVVMAVGKAGEPADRDKLSIGFGGTWAAREG 355

Query: 361 ERDPAYSEAAATAVMQGETIPIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413
                Y EA   A ++G  I I VD+GLG G ATV+TCDLT  Y+ IN DYRS
Sbjct: 356 VPLADYDEAPVAAHLKGHDISIEVDLGLGDGSATVWTCDLTHGYISINADYRS 408


Lambda     K      H
   0.316    0.130    0.365 

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: 393
Number of extensions: 9
Number of successful extensions: 3
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: 413
Length of database: 408
Length adjustment: 31
Effective length of query: 382
Effective length of database: 377
Effective search space:   144014
Effective search space used:   144014
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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