GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF440
          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:

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