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 3607384 Dshi_0798 acetylornithine and succinylornithine aminotransferase (RefSeq)

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Dino:3607384
          Length = 393

 Score =  226 bits (576), Expect = 1e-63
 Identities = 137/382 (35%), Positives = 206/382 (53%), Gaps = 20/382 (5%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD-PLRAMLAKTLA 134
           L++  G+ F+D   G  +  +GH +P +V+A+ +Q A+   H   L   P +  LA+ L 
Sbjct: 24  LIEADGRRFLDLGAGIAVNALGHAHPRLVAALTDQ-AQALWHVSNLYQIPAQQKLAEMLV 82

Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSAT 191
           A T       FF NSGTES E A+K+ + +    G   +   +   G+FHG+S   ++A 
Sbjct: 83  AETFADTV--FFTNSGTESCELAVKMVRKHFHDAGQPERVEILTFEGSFHGRSSAGIAAA 140

Query: 192 AKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPP 251
                 K F PLLPGFRH+PFGN EA+++A+N      D  AA+++EP+QGEGG+   P 
Sbjct: 141 GSEKMTKGFGPLLPGFRHLPFGNHEALQSAVN------DRTAAIMVEPVQGEGGIRALPD 194

Query: 252 GYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGA 311
             L  +R LCD+ G LMILDEVQ G+GRTG++FA E   V PDI+ +AK +GGG  P+GA
Sbjct: 195 ACLKGLRDLCDQHGILMILDEVQCGVGRTGRLFAHEWAGVSPDIMMVAKGIGGG-FPLGA 253

Query: 312 TIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371
            +AT +  S +      H +T+GGNPL CA   A +  +       +  +K  ++     
Sbjct: 254 VLATADAASGM--TAGTHGSTYGGNPLGCAVGCAVLETVCADGFLEEVRRKAGLMRQALE 311

Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPL 431
            L  E+P +  E RG G+++ +  V      +     +   VLV     N   +R+ PPL
Sbjct: 312 GLVAEFPGVFAEVRGAGLMLGL--VCRAPNTDVVQAGYGAEVLVVPAAEN--VVRLLPPL 367

Query: 432 TLTIEQCELVIKAARKALAAMR 453
           T+T  +    +   RKA A ++
Sbjct: 368 TITDAEIREALARLRKAAALVQ 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: 19
Number of successful extensions: 7
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: 393
Length adjustment: 32
Effective length of query: 427
Effective length of database: 361
Effective search space:   154147
Effective search space used:   154147
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