GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Dyella japonica UNC79MFTsu3.2

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1751
          Length = 467

 Score =  187 bits (474), Expect = 8e-52
 Identities = 133/405 (32%), Positives = 213/405 (52%), Gaps = 40/405 (9%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQL--AKQPLHSQELLDPLRAMLAKTL 133
           LVD  G+ ++D +  +     GH NP + +A++ QL   +  + +    +P    LA+ L
Sbjct: 58  LVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTLEHVIFAGFTHEPA-IELAERL 116

Query: 134 AALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSA 190
           A +TP  L+  F  ++G+ ++E ALK++  Y   +G   K  FIA +G++HG++LGALS 
Sbjct: 117 AQITPAGLERVFLADNGSAAIEVALKMSFHYWLNQGAGQKTRFIALTGSYHGETLGALSV 176

Query: 191 TAKSTFRKPFMPLL---------PGFRHVPFGNIEAMRTA-LNECK----KTGDDVAAVI 236
           +  + +RK + PLL           +   P  + EA     L E +    +   +  AVI
Sbjct: 177 SDVALYRKTYAPLLLTPVLAPSPDAYEAEPGESAEACAARRLGELRVLLEQHAHETCAVI 236

Query: 237 LEP-IQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDI 295
           +EP +Q  GG+ +  P YLT +R LCDEFG   I DE+  G GRTG +FACE   V PD 
Sbjct: 237 VEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEIAVGFGRTGTLFACEQAGVSPDF 296

Query: 296 LCLAKALGGGVMPIGATIATEEVFSVLF-----DNPFLHTTTFGGNPLACAAALATINVL 350
           +CL+K L GG +P+ A + T  V+   +        FLH+ ++ GNPLAC AALAT+++ 
Sbjct: 297 MCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFLHSHSYTGNPLACRAALATLDIF 356

Query: 351 LEQNLPAQAEQKGDMLLDGFRQLA--REYPDLVQEARGKGMLMAIEFV-DNEIGYNFASE 407
            ++ +    E+  ++     R+LA  RE+P  V + R  GM+ A+E V D      + SE
Sbjct: 357 RDEPV---LERNRELAAHLARRLAPLREHPQ-VADVRQTGMIAAVELVRDKATRAPYPSE 412

Query: 408 MFR-QRVLVAGTLNNA------KTIRIEPPLTLTIEQCELVIKAA 445
             R  RV + G  + A        +   PP  ++ ++ + ++  A
Sbjct: 413 ERRGLRVYLHGLEHGALLRPLGNVVYFMPPYVVSTDELDHLVDVA 457


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: 505
Number of extensions: 37
Number of successful extensions: 5
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: 467
Length adjustment: 33
Effective length of query: 426
Effective length of database: 434
Effective search space:   184884
Effective search space used:   184884
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