GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Pseudomonas stutzeri RCH2

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate GFF3858 Psest_3928 glutamine synthetase, type I

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



>FitnessBrowser__psRCH2:GFF3858
          Length = 468

 Score =  120 bits (301), Expect = 9e-32
 Identities = 119/407 (29%), Positives = 165/407 (40%), Gaps = 64/407 (15%)

Query: 66  GVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAIS-----PRRVLRRVLEL 120
           G+   DM+ +P   T  + P+  +PT  ++ D V     P  +      PR + +R  E 
Sbjct: 59  GIEASDMILMPVDETAVLDPFTEEPTLILVCDIVE----PSTMQGYDRDPRSIAKRAEEF 114

Query: 121 YKAKGWKPVI--APELEFYLVDMNK---------------------DPDLPLQPPIGRTG 157
            K  G    +   PE EF++ D  K                     D D+      G  G
Sbjct: 115 LKTTGIGDTVFVGPEPEFFIFDQVKFKSDISGSMFKIYSEQGSWMTDQDVEG----GNKG 170

Query: 158 -RPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEVGAA-QMEINFMHGDPLK 215
            RP      + +   +    +   +    E   L V+   HEV  A Q EI       + 
Sbjct: 171 HRPAVKGGYFPVPPCDHDHEIRTAMCNAMEDMGLVVEVHHHEVATAGQNEIGVKFNTLVA 230

Query: 216 LADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGK 275
            AD V   K  V   A  +   ATFM KP+ G+ GS MH+H S+   + G N F G    
Sbjct: 231 KADEVQTLKYCVHNVADAYGKTATFMPKPLYGDNGSGMHVHMSI--SKDGKNTFAGEGYA 288

Query: 276 PTSLFTSY-IAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPH- 333
             S    Y I G+ K+  AL     P  NSY+RL     AP+ +A+   NR+   RIP+ 
Sbjct: 289 GLSETALYFIGGIIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYV 348

Query: 334 SGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYELPYQLPRNLE 393
           S P ARRIE R P    NPYL  AA L AG  G+  K+   +    + Y+LP       E
Sbjct: 349 SSPKARRIEARFPDPAANPYLCFAALLMAGLDGIQNKIHPGDAADKNLYDLP------PE 402

Query: 394 EGLTLMGACEPIAEVLGE----------------KFVKAYLALKETE 424
           EG  +   C  + E L E                +F+ AY+ LK  E
Sbjct: 403 EGKLIPQVCGSLKEALEELDKGRAFLTKGGVFSDEFIDAYIELKSEE 449


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: 509
Number of extensions: 29
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: 468
Length adjustment: 33
Effective length of query: 411
Effective length of database: 435
Effective search space:   178785
Effective search space used:   178785
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