GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4245
          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.

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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