GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Pseudomonas fluorescens FW300-N1B4

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate Pf1N1B4_572 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)

Query= BRENDA::D3GE78
         (556 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_572
          Length = 341

 Score =  151 bits (381), Expect = 4e-41
 Identities = 106/344 (30%), Positives = 175/344 (50%), Gaps = 11/344 (3%)

Query: 211 ISHRNYVANMLQYCHTASLHPDYKARLERSRWLCFLPMYHAMAQNIF-IAAALYRATPVY 269
           ++HRN VANMLQ       + +    +     +  LP+YH  A     +A  L     + 
Sbjct: 2   LTHRNLVANMLQCKALMGSNLNEGCEI----LITPLPLYHIYAFTFHCMAMMLIGNHNIL 57

Query: 270 IMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGREV 329
           I +  D   M++   +++ + F+ +  + VAL  + A  + D SS+++  SG   L    
Sbjct: 58  ISNPRDLTAMVKELSKWKFSGFVGLNTLFVALCNNEAFRKLDFSSLKITLSGGMALQLAA 117

Query: 330 CEEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEISTSASVGELNANCEAKIMFDGVEV 389
            E  +++       I +G+GMTE T  V   NP++     ++G    +   K++ D    
Sbjct: 118 AERWKEV---AGCPICEGYGMTE-TSPVATVNPSQNIQIGTIGIPVPSTLCKVIDDAGVE 173

Query: 390 KERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMKEL 449
           +   + GEL V+ P VMKGYW+ + AT E    +GWL TGDIA +  DG   +VDR K++
Sbjct: 174 QPLGAIGELCVKGPQVMKGYWQRQDATDEILDSEGWLKTGDIALIQPDGYMRIVDRKKDM 233

Query: 450 IKVKGNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSATANEIAHY 508
           I V G  V P ELE +L   P +   A IGV    + E  + ++V +PG + T +++  +
Sbjct: 234 ILVSGFNVYPNELEDVLATLPGVLQCAAIGVPDEKSGEAIKIFIVAKPGVTLTKDQVMEH 293

Query: 509 LDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQAKEELRV 552
           +   V+ +K +   V F +A+P    GKILR +LR++  ++L V
Sbjct: 294 MRANVTGYK-VPKAVEFRDALPTTNVGKILRRELRDEELKKLGV 336


Lambda     K      H
   0.319    0.134    0.403 

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: 394
Number of extensions: 21
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: 556
Length of database: 341
Length adjustment: 32
Effective length of query: 524
Effective length of database: 309
Effective search space:   161916
Effective search space used:   161916
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 (21.7 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