GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuA in Burkholderia phytofirmans PsJN

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate BPHYT_RS09955 BPHYT_RS09955 glutamine synthetase

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



>lcl|FitnessBrowser__BFirm:BPHYT_RS09955 BPHYT_RS09955 glutamine
           synthetase
          Length = 445

 Score =  580 bits (1494), Expect = e-170
 Identities = 265/442 (59%), Positives = 343/442 (77%)

Query: 3   DIDDFLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDG 62
           D+ +FL+ +R+ E+E +IPDM G+ARGKI+P++ F S   M +  A+++ TV G++    
Sbjct: 4   DLREFLEHHRIHEVECVIPDMTGVARGKIVPKNLFLSEGKMHMSNALLMITVNGEFANFE 63

Query: 63  TLTGVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYK 122
              G +DPDMVC+PD +T+R++PWA++  A VIHDCV  DG P+ ISPR VLRRVL LY+
Sbjct: 64  RFVGPSDPDMVCIPDPNTVRLVPWAIEQVAVVIHDCVGLDGKPIGISPRAVLRRVLRLYE 123

Query: 123 AKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIY 182
           A+GW+PV+APE+EFYL+  NK+P  PL+PP+GR GR E GRQ++SI+AVNEFDP F+D+ 
Sbjct: 124 ARGWRPVVAPEMEFYLIAQNKNPHEPLRPPLGRAGRHEAGRQSFSIDAVNEFDPFFQDLS 183

Query: 183 EYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMA 242
            +CE+ +L V+TL+HEVGA QMEINF HGD L LAD VFLFKR VRE A RH ++ATFMA
Sbjct: 184 RFCEMTQLGVETLVHEVGAGQMEINFSHGDALDLADRVFLFKRAVRETAFRHGIFATFMA 243

Query: 243 KPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAPYI 302
           KPME EPGSAMH+HQS+VD E+G N+F+ PDG  + LF +YI GLQKY P  MP+FAPY+
Sbjct: 244 KPMEHEPGSAMHIHQSIVDRESGQNIFSLPDGSASPLFFNYIGGLQKYMPQAMPMFAPYV 303

Query: 303 NSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLAA 362
           NSYRRLSRF AAPINV WGYDNRT G R+P+S P  RR+ENR+PGVD NPYLA+AATLA 
Sbjct: 304 NSYRRLSRFTAAPINVRWGYDNRTCGIRVPNSEPDGRRLENRVPGVDVNPYLAMAATLAC 363

Query: 363 GYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLALKE 422
           GYLGM ++ EA+ P++   Y+L Y+LPR LE+ L  +  C  +AEVLG+ FV+AY A+KE
Sbjct: 364 GYLGMVEQQEASAPMIESAYDLEYELPRGLEDALKALSKCTELAEVLGDSFVQAYCAVKE 423

Query: 423 TEYEAFFRVISSWERRHLLLHV 444
            E+E F + I++WER HL L V
Sbjct: 424 KEFETFSQGITAWEREHLQLLV 445


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: 644
Number of extensions: 20
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 444
Length of database: 445
Length adjustment: 32
Effective length of query: 412
Effective length of database: 413
Effective search space:   170156
Effective search space used:   170156
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