GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Synechococcus elongatus PCC 7942

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate Synpcc7942_2156 Synpcc7942_2156 L-glutamine synthetase

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



>FitnessBrowser__SynE:Synpcc7942_2156
          Length = 473

 Score =  140 bits (354), Expect = 7e-38
 Identities = 119/395 (30%), Positives = 186/395 (47%), Gaps = 47/395 (11%)

Query: 67  VTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFD---GTPVAISPRRVLRRVLELYKA 123
           + + DM  VPD +T  + P+  +PT  +I  C  ++    TP    PR + ++ ++  KA
Sbjct: 63  INESDMTMVPDPTTAWIDPFMKEPTLSMI--CTIYEPRTNTPYERCPRAIAQKAVDYLKA 120

Query: 124 KGWKPV--IAPELEFYLVD---MNKDPDLPLQPPIGRTGRPETGRQAYSIEAVN-EFDPL 177
            G        PE EF++ D    ++  +          GR  +GR+    E  N  + P 
Sbjct: 121 SGIGDTAYFGPEAEFFIFDDVRFDQAENKSYYYVDSIEGRWNSGREE---EGGNLGYKPR 177

Query: 178 FEDIY----EYCEVQELEVDTLI-------------HEVGAA-QMEINFMHGDPLKLADS 219
           +++ Y         Q++  + L+             HEV    Q E+ F  G  ++ AD 
Sbjct: 178 YKEGYFPVAPTDTSQDMRSEMLLTMADCGVPIEKHHHEVATGGQCELGFRFGKLIEAADW 237

Query: 220 VFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSL 279
           +  +K  ++    R+    TFM KP+  + GS MH HQS+ ++  G  LF G      S 
Sbjct: 238 LMTYKYVIKNVGRRYGKTITFMPKPLFNDNGSGMHTHQSIWND--GQPLFAGDQYAGLSQ 295

Query: 280 FTS-YIAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSG--P 336
               YI G+ K+ PAL+ +  P  NSY+RL     AP+N+A+   NR+   RIP SG  P
Sbjct: 296 MALWYIGGILKHAPALLALTNPTTNSYKRLVPGFEAPVNLAYSQGNRSASVRIPLSGTNP 355

Query: 337 AARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYEL-PYQL------P 389
            A+R+E R P    NPYLA AA L AG  G+  +++  EPL  D Y+L P +L      P
Sbjct: 356 KAKRLEFRCPDATSNPYLAFAAMLCAGIDGIKNQIDPGEPLDVDIYDLSPEELAKIPSTP 415

Query: 390 RNLEEGLTLMGACEPIAEVLG---EKFVKAYLALK 421
            +L++ L  + A      V G   E F++ ++  K
Sbjct: 416 GSLKDALKALEADHDFLTVGGVFTEDFIQNWIEYK 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: 578
Number of extensions: 30
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: 473
Length adjustment: 33
Effective length of query: 411
Effective length of database: 440
Effective search space:   180840
Effective search space used:   180840
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