GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Pseudomonas fluorescens FW300-N2E2

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate Pf6N2E2_5686 glutamine synthetase family protein

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5686
          Length = 447

 Score =  344 bits (883), Expect = 3e-99
 Identities = 179/434 (41%), Positives = 250/434 (57%), Gaps = 12/434 (2%)

Query: 13  VTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDGTLTGVTDPDM 72
           + EIE + PD+ G+ RGK++    F  G  ++L + V++Q + G YP      G  D D+
Sbjct: 16  IDEIECVTPDLNGVPRGKVMTAEGFLEGRRLQLARGVLLQCIMGGYPPS-RFYGSDDGDL 74

Query: 73  VCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYKAKGWKPVIAP 132
             V D   I  +PW+  P A  I D     G    +S R  L+ V+  Y A G  PV+A 
Sbjct: 75  ALVADPKQIHRLPWSQQPRALAICDADELTGESSRLSTRGQLKAVVARYAALGLAPVVAT 134

Query: 133 ELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEV 192
           ELEF++   N DP  P QPP+G  GR E G  A+S+ + N   P F ++Y       L  
Sbjct: 135 ELEFFVFAPNPDPTQPFQPPMGLDGRREDGHSAFSVSSNNGLRPFFSEVYACMAALGLPR 194

Query: 193 DTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSA 252
           DT +HE+G +Q EIN +HGDPL LAD  FLFK  ++E AL+H +    MAKP+   PGS+
Sbjct: 195 DTFMHEMGVSQFEINLLHGDPLLLADQTFLFKHLLKEVALKHGLTVVCMAKPLAHTPGSS 254

Query: 253 MHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAPYINSYRRLSRFM 312
           MH+HQS+V+E +G N+F+   G+PT+ F  +I G Q        +FAP +NSY+RL    
Sbjct: 255 MHIHQSVVEEGSGRNVFSDEAGEPTAAFRHFIGGQQACLADFTALFAPNVNSYQRLCHPF 314

Query: 313 AAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLE 372
           A+P N  W +DNR+ G RIP S P ARR+ENR+PG D NPYLAIAA+LAAG  G+  +LE
Sbjct: 315 ASPNNACWSHDNRSAGLRIPASSPVARRVENRLPGADANPYLAIAASLAAGLYGIEHRLE 374

Query: 373 ATEPLLSDGYELPYQLPRNLEEGLTLMGACEPI------AEVLGEKFVKAYLALKETEYE 426
            +  +  +     +++P NL    TL  A E +       E+ G +F++ Y+A K  E  
Sbjct: 375 PSAAIQGE-----FEVPDNLSLPCTLHAALERLKRSHLAKELFGTEFIEGYIASKTLELT 429

Query: 427 AFFRVISSWERRHL 440
           +FF  I+ WERR L
Sbjct: 430 SFFDEITPWERRVL 443


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: 592
Number of extensions: 23
Number of successful extensions: 3
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: 447
Length adjustment: 32
Effective length of query: 412
Effective length of database: 415
Effective search space:   170980
Effective search space used:   170980
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