GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuA in Marinobacter adhaerens HP15

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate GFF440 HP15_428 glutamine synthetase, type I

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



>lcl|FitnessBrowser__Marino:GFF440 HP15_428 glutamine synthetase,
           type I
          Length = 467

 Score =  130 bits (326), Expect = 1e-34
 Identities = 120/403 (29%), Positives = 170/403 (42%), Gaps = 52/403 (12%)

Query: 66  GVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTP-VAISPRRVLRRVLELYKAK 124
           G+ + DM+ +PD  T  + P+  + T  +  + V           PR V RR  E  K+ 
Sbjct: 58  GINESDMILMPDDETSVLDPFTEETTVNITCNIVEPSTMQGYERDPRSVARRAEEYLKST 117

Query: 125 GWKP--VIAPELEFYLVDM---NKDPDLPL-----------------QPPIGRTGRPETG 162
           G     +  PE EF++ D    N D    +                 +  IG   RP   
Sbjct: 118 GIADGALFGPEPEFFVFDSVKWNVDMQGAMYHIHSEEAAWVSGEDFDRNNIGH--RPGVK 175

Query: 163 RQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEVGAA-QMEINFMHGDPLKLADSVF 221
              + +  V+    L   +    E   L+++   HEVG A Q EI        K AD V 
Sbjct: 176 GGYFPVPPVDSLHDLRGAMCAAMESMGLDIEVHHHEVGTAGQCEIGVGANTLTKKADEVQ 235

Query: 222 LFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTS-LF 280
           + K  V   A  +   ATFM KP+ G+ GS MH+H SL   + G NLF G      S   
Sbjct: 236 ILKYCVHNVAHAYGKTATFMPKPVVGDNGSGMHVHMSL--SKDGKNLFAGDSYAGLSEAA 293

Query: 281 TSYIAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPH-SGPAAR 339
             YI G+ K+  A+        NSY+RL     AP+ +A+   NR+   RIP+ + P AR
Sbjct: 294 LYYIGGVIKHAKAINAFTNSSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPKAR 353

Query: 340 RIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLM 399
           RIE R P    NPYLA AA + AG  G+  K+   + +  D Y+LP       EE L++ 
Sbjct: 354 RIEVRFPDPSANPYLAFAALMMAGLDGIQNKIHPGDAMDKDLYDLP------KEEALSIP 407

Query: 400 GACEPIAEVLG----------------EKFVKAYLALKETEYE 426
              E ++E L                 E  +  Y+ LK  E E
Sbjct: 408 TVAETLSEALDCLEADHEFLTRGGVFTEDMIAGYVGLKRGEVE 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: 512
Number of extensions: 21
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: 467
Length adjustment: 33
Effective length of query: 411
Effective length of database: 434
Effective search space:   178374
Effective search space used:   178374
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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