GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Dechlorosoma suillum PS

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Dsui_3250 Dsui_3250 acetylornithine/succinylornithine aminotransferase

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__PS:Dsui_3250
          Length = 390

 Score =  207 bits (527), Expect = 5e-58
 Identities = 143/406 (35%), Positives = 204/406 (50%), Gaps = 37/406 (9%)

Query: 25  PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84
           PV     E + ++D +G+ Y+D   GIAV   GH HPK++ A+  Q  ++ HT       
Sbjct: 12  PVAFSHGEGNRIYDTDGKCYLDALSGIAVNTLGHNHPKLVNAIASQAARVLHTSNLYR-- 69

Query: 85  EPYIELAEEIAKRVPG-DFPKKTLLVTSGSEAVENAVKIARAATGRAGV-----IAFTGA 138
              I L EE+A R+ G    ++     SG EA E A+K+AR    + GV     I    A
Sbjct: 70  ---IPLQEELADRLAGLSRMEEVFFCNSGCEANEAAIKLARFFGHQKGVDAPVIIVMEKA 126

Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQP 198
           +HGRT+ TL  TG      AG   +  G  R          ++ D+I +   +  N    
Sbjct: 127 FHGRTLATLSATGNRKA-QAGFEPLVSGFVRV-------PYNDLDAIRAAAELNPN---- 174

Query: 199 QDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQL 258
             + A+++E VQGEGG +V    F + LR+LCD+   LL+ DEVQ G GRTGT+F  +  
Sbjct: 175 --VVAVLLEMVQGEGGIHVADPEFQRGLRSLCDEKDWLLMCDEVQCGMGRTGTWFGFQHA 232

Query: 259 GIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEE 318
           GI+PD+ T AK +G G PI       +      PG  G T+ G+P+ACAAAL  +   EE
Sbjct: 233 GILPDVATLAKGLGSGVPIGACMTAGKAAGLFKPGNHGSTFGGNPLACAAALTTIACIEE 292

Query: 319 EKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIV 378
           EKL E + A GE ++ GL E  A    + ++RG G M+ IEL       +P  ELV+K  
Sbjct: 293 EKLRENAVAQGEAIRRGLSEALAGVGGLVEIRGKGLMLGIEL------DRPCGELVAK-- 344

Query: 379 VRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDE 424
               E GL++    T   V+R L  +T   A  ++ +  LA    E
Sbjct: 345 --GLEAGLLINV--TAEKVVRLLPALTFSAADTQELVQRLAALIKE 386


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: 429
Number of extensions: 26
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: 390
Length adjustment: 31
Effective length of query: 395
Effective length of database: 359
Effective search space:   141805
Effective search space used:   141805
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.

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