GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Azospirillum sp. B510

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_012977261.1 AZL_RS25275 acetylglutamate kinase

Query= BRENDA::A0A0H2X8L7
         (447 letters)



>NCBI__GCF_000010725.1:WP_012977261.1
          Length = 448

 Score =  570 bits (1468), Expect = e-167
 Identities = 298/448 (66%), Positives = 348/448 (77%), Gaps = 8/448 (1%)

Query: 1   MSLPAQPHKQTRQTIVRLLSSMASAKEISQYLKRFSQLDAKRFAVVKVGGAVLRD--DLE 58
           M+LP     +TRQTIVRLLS +AS KEI+QYLKRFSQLDAKRFAVV +  A+LRD  + E
Sbjct: 1   MTLPVL-QSETRQTIVRLLSILASTKEINQYLKRFSQLDAKRFAVVNINDAILRDGVEAE 59

Query: 59  ALTSSLSFLQEVGLTPIVLHGAGPQLDAELSAAGIEKQTVNGLRVTSPHALAIVRKVFQA 118
           A+ SSLSFLQ VGLTPIVL G  P    E  A+G+++++ +G    +P   A   + FQA
Sbjct: 60  AVASSLSFLQAVGLTPIVLLGTAPGSREEPPASGVDEESGDGPDREAPAGPAFPYETFQA 119

Query: 119 SNLKLVEALQQNGARATSITGGVFEAEYLNRDTYGLVGEVKAVNLAPIEASLQAGSIPVI 178
            N  LVE L++ G RATSITGGVFEA +L R+  G +G V+AV LAP+EASL AGSIPVI
Sbjct: 120 LNRSLVERLRRKGVRATSITGGVFEAGHLGREVRGSLGTVRAVRLAPVEASLHAGSIPVI 179

Query: 179 TSLGETPSGQILNVNADFAANELVQELQPYKIIFLTGTGGLLDAEGKLIDSINLSTEYDH 238
           +SLGET  GQ L +  D A N LV+ LQP+KIIFLTG GGLLDA G++ID+INLSTEYDH
Sbjct: 180 SSLGETAGGQSLGIECDRATNALVRLLQPFKIIFLTGAGGLLDANGRVIDAINLSTEYDH 239

Query: 239 LMQQPWINGGMRVKIEQIKDLLDRLPLESSVSITRPADLAKELFTHKGSGTLVRRGERVL 298
             +   +   +   +EQ+KDLLDRLP ESS+SIT PA+LA ELFTHKGSGTLVRRGERV 
Sbjct: 240 FDRDSCLRSAITFTVEQMKDLLDRLPPESSISITNPANLANELFTHKGSGTLVRRGERVS 299

Query: 299 RATSWDELDLPRLTSLIESSFGRTLVPDYFSNTKLLRAYVSENYRAAVILTDEGMLGASA 358
           RAT WDELDL RL  LIESSFGR LV DYF  T+LLRAYVSENYRAAVILT+E       
Sbjct: 300 RATCWDELDLTRLRMLIESSFGRRLVEDYFQRTRLLRAYVSENYRAAVILTEE-----DG 354

Query: 359 LIYLDKFAVLDDAQGEGLGRAVWNVMREETPQLFWRSRHNNQVNIFYYAESDGCIKQEKW 418
           + YLDKFAVLD+AQGEGLGRAVW VMR+ETPQLFWRSRH NQ+NIFYYA+SDGC KQEKW
Sbjct: 355 VPYLDKFAVLDEAQGEGLGRAVWKVMRKETPQLFWRSRHKNQINIFYYAQSDGCFKQEKW 414

Query: 419 KVFWYGLENFEQIQHCVAHCATRQPTLL 446
           KVFW GL++F QI+ CVAHCA R+PTL+
Sbjct: 415 KVFWCGLDDFSQIEKCVAHCAVRRPTLI 442


Lambda     K      H
   0.318    0.134    0.383 

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: 600
Number of extensions: 16
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: 447
Length of database: 448
Length adjustment: 33
Effective length of query: 414
Effective length of database: 415
Effective search space:   171810
Effective search space used:   171810
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Jul 25 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