GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS09955
          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.

Links

Downloads

Related tools

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