GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Dinoroseobacter shibae DFL-12

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 3608039 Dshi_1446 aminotransferase class-III (RefSeq)

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Dino:3608039
          Length = 444

 Score =  185 bits (469), Expect = 3e-51
 Identities = 121/352 (34%), Positives = 183/352 (51%), Gaps = 24/352 (6%)

Query: 70  AGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPL-HSQELLDPLRAM 128
           AG+   ++D  G+ ++D  GG  +  +GH +P V +A+  Q+ K    H+         +
Sbjct: 18  AGAGCYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQIDKIAFAHTGFFTSEPAEV 77

Query: 129 LAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSL 185
           L   L A  P  ++  +  + G+ESVEAALKLA+ +    G   +   IA   ++HG +L
Sbjct: 78  LCDALIAAAPKGIEKVYLLSGGSESVEAALKLARQFFLETGEPRRHRVIARRQSYHGNTL 137

Query: 186 GALSATAKSTFRKPFMPLLP---------GFRHVPFGNIEAM--RTALN----ECKKTGD 230
           GAL+A   +  R+ + PLL           +RH   G  +A   R A +    E ++ G 
Sbjct: 138 GALAAGGNAWRREKYAPLLVETYHIDPCYAYRHQAVGESDAAYGRRAADALRTEIERLGP 197

Query: 231 D-VAAVILEPIQGE-GGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEH 288
           + V A I EP+ G   G + P PGY   +R++CDE+G L+ILDEV  GMGRTG +FACE 
Sbjct: 198 ETVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILDEVMCGMGRTGTLFACEQ 257

Query: 289 ENVQPDILCLAKALGGGVMPIGATIATEEVFSVLF--DNPFLHTTTFGGNPLACAAALAT 346
           + + PDI+ +AK LG G  PIGA +A+  ++  +      F H  T+ G+PLA AAA A 
Sbjct: 258 DGISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGSGSFQHGHTYHGHPLAAAAAGAV 317

Query: 347 INVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDN 398
           +  L      AQ   KG  L         ++   V + RG+G+   IE V++
Sbjct: 318 VETLRAPGTMAQVRAKGATLQSRLEAALGQHSH-VGDIRGRGLFRGIELVED 368


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: 489
Number of extensions: 22
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: 444
Length adjustment: 33
Effective length of query: 426
Effective length of database: 411
Effective search space:   175086
Effective search space used:   175086
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