GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Dechlorosoma suillum PS

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Dsui_3250 Dsui_3250 acetylornithine/succinylornithine aminotransferase

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>FitnessBrowser__PS:Dsui_3250
          Length = 390

 Score =  278 bits (710), Expect = 3e-79
 Identities = 165/392 (42%), Positives = 219/392 (55%), Gaps = 11/392 (2%)

Query: 14  MMPVYA--PAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKF 71
           +M  YA  P AF    GEG+R++D  GK Y+D   GIAVN LGH HP+LV A+  QA + 
Sbjct: 4   LMNTYARLPVAFS--HGEGNRIYDTDGKCYLDALSGIAVNTLGHNHPKLVNAIASQAARV 61

Query: 72  WHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGI 131
            HT N Y       LA +L   +  + VFFCNSG EANEAA+KLAR + H + G +   I
Sbjct: 62  LHTSNLYRIPLQEELADRLAGLSRMEEVFFCNSGCEANEAAIKLARFFGHQK-GVDAPVI 120

Query: 132 VAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKAL--IDDNTCAVIV 189
           +  + AFHGRTL T+SA G       F PL        YNDLD+ +A   ++ N  AV++
Sbjct: 121 IVMEKAFHGRTLATLSATGNRKAQAGFEPLVSGFVRVPYNDLDAIRAAAELNPNVVAVLL 180

Query: 190 EPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLS 249
           E +QGEGG+  AD +F RGLR LCD  + LL+ DEVQ G+GRTG  + + H G+ PD+ +
Sbjct: 181 EMVQGEGGIHVADPEFQRGLRSLCDEKDWLLMCDEVQCGMGRTGTWFGFQHAGILPDVAT 240

Query: 250 TAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVK 309
            AK LG G PIGA + + + A +   G HG+T+GGNPLACA A    A I   ++     
Sbjct: 241 LAKGLGSGVPIGACMTAGKAAGLFKPGNHGSTFGGNPLACAAALTTIACIEEEKLRENAV 300

Query: 310 QRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMILIAG 369
            + +     L+   A  G   EIRG GL++G  L D   G+  A   +  E GL+I +  
Sbjct: 301 AQGEAIRRGLSEALAGVGGLVEIRGKGLMLGIEL-DRPCGELVA---KGLEAGLLINVTA 356

Query: 370 ANVVRFAPALIISEDEVNSGLDRFELACKRFL 401
             VVR  PAL  S  +    + R     K FL
Sbjct: 357 EKVVRLLPALTFSAADTQELVQRLAALIKEFL 388


Lambda     K      H
   0.321    0.137    0.412 

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: 420
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: 406
Length of database: 390
Length adjustment: 31
Effective length of query: 375
Effective length of database: 359
Effective search space:   134625
Effective search space used:   134625
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