GapMind for Amino acid biosynthesis

 

Aligments for a candidate for glnA in Pseudomonas fluorescens FW300-N1B4

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate Pf1N1B4_4245 glutamine synthetase family protein

Query= BRENDA::O33342
         (457 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4245 glutamine synthetase
           family protein
          Length = 457

 Score =  379 bits (974), Expect = e-110
 Identities = 204/454 (44%), Positives = 276/454 (60%), Gaps = 5/454 (1%)

Query: 7   PPLAWTELERLVAAGDVDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVD 66
           P L++  L+R  A+G++DTV+V   DMQGRL GKR     F+D        CC+YLLA D
Sbjct: 4   PLLSFDALKRAAASGEIDTVLVCMVDMQGRLVGKRFQVEFFIDS-GHEETHCCNYLLADD 62

Query: 67  VDLNTVPGYAMASWDTGYGDMVMTPDLSTLRLIPWLPGTALVIADLV-WADGSEVAVSPR 125
           +D+  VPGYA ASW  GYGD V+ PD++TLR +PWL  TALV+ D++      ++  SPR
Sbjct: 63  IDMEPVPGYAAASWSKGYGDFVLKPDMATLRRVPWLECTALVLCDVLDHHHRRDLPHSPR 122

Query: 126 SILRRQLDRLKARGLVADVATELEFIVFDQPYRQAWASGYRGLTPASDYNIDYAILASSR 185
           +IL++Q++RL+ RG     A+ELEF +FD+ Y       Y     A  Y  DY IL ++R
Sbjct: 123 AILKKQVERLRERGYTGMFASELEFYLFDESYEAIHERNYHKPKTAGHYIEDYNILQTTR 182

Query: 186 MEPLLRDIRLGMAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQ 245
            EP+LR IR  +   G+  E  KGE   GQ+EI  RY +AL   D+H I K+  KEIA  
Sbjct: 183 EEPVLRAIRKHLQACGIPVENSKGEWGPGQEEINIRYADALTMADHHVIIKHACKEIAQL 242

Query: 246 HGKSLTFMAKYD-EREGNSCHIHVSLRGTDG-SAVFADSNGPHGMSSMFRSFVAGQLATL 303
            GK++TFMAK+  +  G+S H+H SL   +G  ++F D     GMS + RS+VAGQL   
Sbjct: 243 QGKAITFMAKWRYDAAGSSSHVHNSLWDKNGKKSLFFDPKAEFGMSKLMRSWVAGQLKYA 302

Query: 304 REFTLCYAPTINSYKRFADSSFAPTALAWGLDNRTCALRVVGHGQN-IRVECRVPGGDVN 362
            + T   AP INSYKRF   +FAPT   W  DNRT   R+   G   IR+ECR+ G D+N
Sbjct: 303 NDITCFLAPYINSYKRFQAGTFAPTRAVWSRDNRTAGFRLCAEGSKAIRIECRIGGADLN 362

Query: 363 QYLAVAALIAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAF 422
            YLA AALIA GL GI+  L L  P  G+AY    +  +  TL +A    + S+++REAF
Sbjct: 363 PYLAFAALIAAGLAGIDEKLSLTPPFEGDAYVDEHLPEVSKTLREACAALKASSMLREAF 422

Query: 423 GEDVVAHYLNNARVELAAFNAAVTDWERIRGFER 456
           G++V+ HY++ A  E   ++  +TDWE  RGFER
Sbjct: 423 GDEVIDHYVHTAEWEQKEYDRRITDWELQRGFER 456


Lambda     K      H
   0.321    0.137    0.417 

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: 595
Number of extensions: 23
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: 457
Length of database: 457
Length adjustment: 33
Effective length of query: 424
Effective length of database: 424
Effective search space:   179776
Effective search space used:   179776
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 (21.9 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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