GapMind for catabolism of small carbon sources

 

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

Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate 3608723 Dshi_2115 sarcosine oxidase, alpha subunit family (RefSeq)

Query= curated2:Q67N36
         (375 letters)



>FitnessBrowser__Dino:3608723
          Length = 1000

 Score =  149 bits (375), Expect = 4e-40
 Identities = 122/400 (30%), Positives = 189/400 (47%), Gaps = 49/400 (12%)

Query: 3   ESLKRTPLYELHLKLGARMVPFG----GWEMPV----QYSSVIEEHRAVREAAGLFDVSH 54
           E  ++TP+     + GA   P       W  P      + +V  E ++ RE+ G+FD S 
Sbjct: 607 EVTRKTPIDPWAEEHGAAFEPVALWRRAWYFPQAGEDMHKAVARECKSTRESVGMFDAST 666

Query: 55  MGEFEVRGPQALDLIQLVSTNDAAKLAVGRVQYALMCYENGTVVDDILIYRLDEHRYWLV 114
           +G+ EV GP A++ +  + TN   KL VGR +Y L+  E+G + DD +I R+ +  + + 
Sbjct: 667 LGKIEVSGPDAVEFMNRMYTNPWTKLGVGRCRYGLLLGEDGFIRDDGVIGRMRDDLFHVT 726

Query: 115 VNAG------NTQKDW---EWINTARERAGLHNLELIDRSAEIALLALQGPKAEEILQPL 165
              G      N  +D+   EW            + L   + E A +AL GP A ++L P 
Sbjct: 727 TTTGGAARVLNMMEDYLQTEWPEL--------KVWLTSTTEEWATIALNGPNARKLLAPF 778

Query: 166 ATGVVLS-QLEPFSLAKNVTVSGVPTLVLSRTGYTGEDGFEIYVKAEDVAALWEALLEAG 224
             G  +S    P       TV+G P+  L R  +TGE GFEI V A    ALWE L EAG
Sbjct: 779 VEGADISADAFPHMSVVECTVAGFPSR-LFRISFTGELGFEINVPARHGKALWEKLWEAG 837

Query: 225 DEQGLLPCGLGARDTLRFEAKLPLYGHEISDQHNPLEAGLGFAVKLKKGVDFIGRDALAR 284
            +  + P G      LR E    + G +      P +AG+G+A+  K   DF+G+ +L R
Sbjct: 838 QQYDICPYGTETMHVLRAEKGYIIVGQDTDGTVTPQDAGIGWAIG-KAKPDFVGKRSLQR 896

Query: 285 IKEQGPTRK-LVGI-------------EMIDRGVPRQGYPVAVGGEVVGEVTTGSFSPTL 330
                P RK LVG+             +++D   P+Q  P+    +++G VT+  +S TL
Sbjct: 897 PDIVAPGRKQLVGLLTEDPKTVLAEGAQIVDD--PKQAKPM----KMIGHVTSSYWSETL 950

Query: 331 EKNIALAYVPVAHSAVGTEVEVIIR-GRALKARVVETPFY 369
            ++IA+A V      + + + +    G A+ A+V  T FY
Sbjct: 951 GRSIAMAVVEGGFDRMDSTLHIPTESGDAVPAKVTGTVFY 990


Lambda     K      H
   0.319    0.137    0.402 

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: 820
Number of extensions: 46
Number of successful extensions: 2
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: 375
Length of database: 1000
Length adjustment: 37
Effective length of query: 338
Effective length of database: 963
Effective search space:   325494
Effective search space used:   325494
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 (21.7 bits)
S2: 53 (25.0 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