GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Dyella japonica UNC79MFTsu3.2

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate N515DRAFT_3024 N515DRAFT_3024 L-glutamine synthetase (EC 6.3.1.2)

Query= reanno::BFirm:BPHYT_RS23160
         (444 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3024
          Length = 469

 Score =  122 bits (307), Expect = 2e-32
 Identities = 117/399 (29%), Positives = 175/399 (43%), Gaps = 48/399 (12%)

Query: 66  GVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAIS--PRRVLRRVLELYKA 123
           G+ + DM+ +PD  T  + P++   T  V+H  V    T  A    PR + +R     K+
Sbjct: 60  GINESDMILLPDPDTAYLDPFS-GHTQLVLHCDVLEPSTMQAYGRDPRSIAKRGEAFLKS 118

Query: 124 KGWKPV--IAPELEFYLVDMNKDPDLPLQPPIGR----------------------TG-R 158
            G        PE EF++ D      +  Q  +GR                      TG R
Sbjct: 119 TGIADTAFFGPEPEFFIFD-----SVRWQNDMGRVFYEIGSEEASWSSRYKYEDNNTGHR 173

Query: 159 PETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEVG-AAQMEINFMHGDPLKLA 217
           P      + +  V+    L  D+ +  E     V+   HEV  A Q EI       ++ A
Sbjct: 174 PGVKGGYFPVSPVDSLGDLRADMCKVLESLGQVVEVHHHEVANAGQCEIGVKFNTLVQKA 233

Query: 218 DSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGP-DGKP 276
           D +   K  ++  A ++   ATFM KP+ G+ GS MH+HQSL  +  G NLF G   G  
Sbjct: 234 DELMTMKYVIKNVAHQNGKTATFMPKPIVGDNGSGMHVHQSLAKD--GKNLFAGDLYGGL 291

Query: 277 TSLFTSYIAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPH-SG 335
           +     YI G+ K+  A+        NSY+RL     AP+ +A+   NR+   RIP+ S 
Sbjct: 292 SQTALWYIGGIFKHAKAINAFANSTTNSYKRLVPGFEAPVMLAYSARNRSASCRIPYVSN 351

Query: 336 PAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYELPYQLPRNLEEG 395
           P  RRIE R P    + YL   A + AG  G+  K++   P   D Y+LP +  +N+ + 
Sbjct: 352 PKGRRIEVRFPDPMNSGYLVFTALMMAGLDGIINKIDPGAPADKDLYDLPPEEEKNIPQV 411

Query: 396 L-TLMGACEPIAE---------VLGEKFVKAYLALKETE 424
             +L  A E + +         V  + F+ AY+ALK  E
Sbjct: 412 CSSLDQALEALDKDRDFLKAGGVFTDDFIDAYIALKMQE 450


Lambda     K      H
   0.321    0.138    0.418 

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: 538
Number of extensions: 32
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 444
Length of database: 469
Length adjustment: 33
Effective length of query: 411
Effective length of database: 436
Effective search space:   179196
Effective search space used:   179196
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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