GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Sphingobium czechense LL01

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_066600058.1 V473_RS02290 aspartate aminotransferase family protein

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_001046645.1:WP_066600058.1
          Length = 398

 Score =  200 bits (508), Expect = 8e-56
 Identities = 129/382 (33%), Positives = 193/382 (50%), Gaps = 20/382 (5%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD-PLRAMLAKTLA 134
           L+  +G+ ++D   G  +  +GH +P +V A+ +Q A   +H   L   PL    A+ L 
Sbjct: 25  LIGERGERYLDFASGIAVNLLGHGHPRLVKAIADQAATL-MHVSNLYGMPLGEQFAQKL- 82

Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSAT 191
            +        FF NSG E+VE A+K A+ Y    G   +   I+   AFHG++LG +SAT
Sbjct: 83  -VDNSFADTVFFTNSGAEAVECAIKTARRYHYANGQAHRHKIISFDNAFHGRTLGTISAT 141

Query: 192 AKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPP 251
           ++   R  F PLLPGF  VPF +++A    ++      D+ A  +LEP+QGEGGV     
Sbjct: 142 SQPKMRDGFEPLLPGFTVVPFNDLDAALAQID------DNTAGFLLEPVQGEGGVTPSTQ 195

Query: 252 GYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGA 311
            +L  +R+ CD  G L+ILDEVQ G  RTG  FA E   V PDI+ +AK +G G  P+GA
Sbjct: 196 AFLKGLREACDAHGLLLILDEVQCGYARTGTFFAHEQYGVTPDIMAVAKGIGAG-FPLGA 254

Query: 312 TIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371
            +ATEE    +      H +T+GGNPLA A  +A +  +L      +    G  L     
Sbjct: 255 CLATEEAAKGMVFG--THGSTYGGNPLAMAVGIAVLEEVLADGFLDRVTAMGARLRSALE 312

Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPL 431
           QL   +  + ++ RG G+++ ++  D      F   +     L+A +      +RI PPL
Sbjct: 313 QLIPNHDGMFEDVRGMGLMLGVKLKDAHDARAFVGHLRDHHGLLAVSAGQ-NVLRILPPL 371

Query: 432 TLT---IEQCELVIKAARKALA 450
            +    I +C   I A  +  A
Sbjct: 372 VIEESHIAECIEKISAGARTFA 393


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: 440
Number of extensions: 20
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: 398
Length adjustment: 32
Effective length of query: 427
Effective length of database: 366
Effective search space:   156282
Effective search space used:   156282
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 24 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