GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas simiae WCS417

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF1577 PS417_08025 acetylornithine aminotransferase

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__WCS417:GFF1577
          Length = 389

 Score =  209 bits (532), Expect = 1e-58
 Identities = 136/389 (34%), Positives = 202/389 (51%), Gaps = 35/389 (8%)

Query: 30  RAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIE 89
           R   + +WD +GREY+D   G+AV N GH HP+++AA+ EQ G L HT   + + +    
Sbjct: 19  RGLGTRLWDQQGREYLDAVAGVAVTNVGHSHPRLVAAISEQAGLLLHTS-NLYSIDWQQR 77

Query: 90  LAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATGRAG-----VIAFTGAYHGRTM 144
           LA+ + +    D   +     SG+EA E A+K+AR    + G     V+    A+HGRT+
Sbjct: 78  LAQRLTQLSGLD---RAFFNNSGAEANETALKLARLHGWKKGIEAPLVVVMENAFHGRTL 134

Query: 145 MTLGLT-GKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAA 203
            TL  + G  V    G   +PG   +               +A++E I K  A    I A
Sbjct: 135 GTLAASDGPSV--RLGFQQLPGDFLKV----------RFGDLAALEAITK--AFGPRITA 180

Query: 204 IIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPD 263
           +++EP+QGE G       ++Q LR  C + G L++ DE+QTG GRTGT+FA +  GIVPD
Sbjct: 181 VLLEPIQGESGVLPAPSGYLQALRDHCTRQGWLMMLDEIQTGIGRTGTWFAFQHEGIVPD 240

Query: 264 LTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKLLE 323
           + T AK +G G PI     +A +     PG  G T+ G+P+AC     VL + EE+ LL+
Sbjct: 241 VMTLAKGLGNGVPIGACLARAAVAQLFTPGSHGSTFGGNPLACRVGCTVLDIIEEQGLLQ 300

Query: 324 RSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRARE 383
            +   GERL A LR    +H  +  +RG G M+ IEL        P  +L  +    A+E
Sbjct: 301 NAAQQGERLLARLRVELNEHAQVVAIRGQGLMIGIEL------ASPCRDLAQR---AAQE 351

Query: 384 KGLILLSCGTYYNVIRFLMPVTIPDAQLE 412
            GL++    T   +IR L P+T+   ++E
Sbjct: 352 HGLLINV--TRGKIIRLLPPLTLDTQEVE 378


Lambda     K      H
   0.319    0.137    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: 374
Number of extensions: 20
Number of successful extensions: 4
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: 426
Length of database: 389
Length adjustment: 31
Effective length of query: 395
Effective length of database: 358
Effective search space:   141410
Effective search space used:   141410
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: 50 (23.9 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