GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Pseudomonas fluorescens FW300-N2C3

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate AO356_17010 AO356_17010 acetylornithine aminotransferase

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_17010
          Length = 391

 Score =  223 bits (568), Expect = 9e-63
 Identities = 142/389 (36%), Positives = 218/389 (56%), Gaps = 16/389 (4%)

Query: 65  AVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD- 123
           A+ +  G    L D  G+E++D + G  + NVGH +P +V+A+  Q A   LH+  L   
Sbjct: 14  ALNFTHGLGTRLWDQDGREYLDAVAGVAVTNVGHSHPRLVAAISEQ-AGLLLHTSNLYSI 72

Query: 124 PLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG--KFTFIATSGAFH 181
             +  LA+ L  L+   ++ +FF NSG E+ E ALKLA+ Y   +G  +   +    AFH
Sbjct: 73  DWQQRLAQKLTQLSG--MERAFFNNSGAEANETALKLARLYGWHKGIEQPLVVVMDNAFH 130

Query: 182 GKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQ 241
           G++LG +SA+   + R  +  L   F  VPFG++ A+       +   + + AV++EPIQ
Sbjct: 131 GRTLGTMSASDGPSVRLGYNRLPGDFIKVPFGDLAALEQIQ---QAHAERIVAVLVEPIQ 187

Query: 242 GEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKA 301
           GE GV L PPGYL A+R+LC     L++LDE+QTG+GRTG+ FA +HE + PD++ LAK 
Sbjct: 188 GESGVQLAPPGYLKALRQLCSRRAWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAKG 247

Query: 302 LGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQ 361
           LG GV PIGA +A  +   +    P  H +TFGGNPLAC      ++++ EQ L   A  
Sbjct: 248 LGNGV-PIGACLARGKAAELF--TPGSHGSTFGGNPLACRVGCTVLDIIEEQALVGNARH 304

Query: 362 KGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNN 421
           +G+ LL   R    E P+ V   RG+G+++ IE    +   +      R   L+   +  
Sbjct: 305 QGEQLLSRLRTELAENPN-VLAIRGQGLMIGIEL--KQPVRDLTLRAARDHGLLI-NVTR 360

Query: 422 AKTIRIEPPLTLTIEQCELVIKAARKALA 450
            +TIR+ PPLT+   + E++++   + LA
Sbjct: 361 GQTIRLLPPLTIDGREVEMIVRGVSRCLA 389


Lambda     K      H
   0.320    0.135    0.393 

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: 417
Number of extensions: 24
Number of successful extensions: 6
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: 459
Length of database: 391
Length adjustment: 32
Effective length of query: 427
Effective length of database: 359
Effective search space:   153293
Effective search space used:   153293
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