GapMind for catabolism of small carbon sources

 

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

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 3607384 Dshi_0798 acetylornithine and succinylornithine aminotransferase (RefSeq)

Query= BRENDA::O30508
         (406 letters)



>FitnessBrowser__Dino:3607384
          Length = 393

 Score =  327 bits (837), Expect = 5e-94
 Identities = 168/386 (43%), Positives = 239/386 (61%), Gaps = 5/386 (1%)

Query: 17  MVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWH 76
           ++P Y  A    V+GEG+ + +  GR  +D   GIAV +LGHAHP LV ALT+QAQ +WH
Sbjct: 5   ILPTYNRAPLSFVKGEGAWLIEADGRRFLDLGAGIAVNALGHAHPRLVAALTDQAQALWH 64

Query: 77  VSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIA 136
           VSN++      +LA  LV  TFA+ VF  NSG E+ E A K+ R++ +D   P++ EI+ 
Sbjct: 65  VSNLYQIPAQQKLAEMLVAETFADTVFFTNSGTESCELAVKMVRKHFHDAGQPERVEILT 124

Query: 137 ASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEPIQ 196
              SFHGR+   +   G  K + GFGP   G  H+P+ + EAL++A++D+T A+++EP+Q
Sbjct: 125 FEGSFHGRSSAGIAAAGSEKMTKGFGPLLPGFRHLPFGNHEALQSAVNDRTAAIMVEPVQ 184

Query: 197 GEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKS 256
           GEGG+     A L+G R LCD+H  L++ DEVQ G+GR G LFA+   GV PDI+  AK 
Sbjct: 185 GEGGIRALPDACLKGLRDLCDQHGILMILDEVQCGVGRTGRLFAHEWAGVSPDIMMVAKG 244

Query: 257 LGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHE 316
           +GGGFP+GA+L T + A  ++ GTHG+TYGGNPL  AV  A L+ +     L+ V+ K  
Sbjct: 245 IGGGFPLGAVLATADAASGMTAGTHGSTYGGNPLGCAVGCAVLETVCADGFLEEVRRKAG 304

Query: 317 RFKSRLQKIGQEY-GIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDV 375
             +  L+ +  E+ G+F E+RG GL++G       +    DV+ A     V+V+ A+ +V
Sbjct: 305 LMRQALEGLVAEFPGVFAEVRGAGLMLGLVC----RAPNTDVVQAGYGAEVLVVPAAENV 360

Query: 376 VRFAPSLVIDDAEIDEGLERFERAVA 401
           VR  P L I DAEI E L R  +A A
Sbjct: 361 VRLLPPLTITDAEIREALARLRKAAA 386


Lambda     K      H
   0.318    0.135    0.394 

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: 405
Number of extensions: 22
Number of successful extensions: 3
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: 406
Length of database: 393
Length adjustment: 31
Effective length of query: 375
Effective length of database: 362
Effective search space:   135750
Effective search space used:   135750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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