GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Dyella japonica UNC79MFTsu3.2

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate N515DRAFT_1006 N515DRAFT_1006 3-oxoacyl-[acyl-carrier protein] reductase

Query= BRENDA::B8H1Z0
         (248 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1006
          Length = 248

 Score =  105 bits (263), Expect = 7e-28
 Identities = 79/248 (31%), Positives = 124/248 (50%), Gaps = 11/248 (4%)

Query: 9   LKGKRVVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRA-----LEAELAGSPIPPV 63
           LKGK  ++TG   GIGAG+    A +GA V+ ++ A   + A        +  G  +   
Sbjct: 4   LKGKVALVTGASKGIGAGIAKALAAEGAAVV-VNYASSKAGADAVVDAITKAGGKAVAVK 62

Query: 64  YKRCDLMNLEAIK-AVFAEIGDVDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFC 122
                  + +AI  A   E G +D+LVNN+G  +   L  +T  ++ ++ NVN+  +L  
Sbjct: 63  GDVAQAADAQAIADAAVKEFGRLDILVNNSGVYEFAPLEQITEDHFHKQFNVNVLGLLLT 122

Query: 123 TQAVAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVT 182
           TQA A  M +  GG++IN GS+   +      +Y   K  ++ +T  L+RELGP  IRV 
Sbjct: 123 TQAAAKHMGE--GGSIINIGSLVTRIVPPGGSVYTATKGAVDAITGVLSRELGPRKIRVN 180

Query: 183 CVVPGNVKTK-RQEKWYTPEGEAQIVAAQCLKGRI-VPENVAALVLFLASDDASLCTGHE 240
            + PG V+T+      +      Q   A    GRI  P+++A + +FLASDD+   TG +
Sbjct: 181 ALNPGMVETEGTVTAGFIGSDFHQEAIAHTPLGRIGQPQDIATIAVFLASDDSYWLTGEK 240

Query: 241 YWIDAGWR 248
            +   G R
Sbjct: 241 LYAAGGAR 248


Lambda     K      H
   0.319    0.137    0.416 

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: 155
Number of extensions: 10
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: 248
Length of database: 248
Length adjustment: 24
Effective length of query: 224
Effective length of database: 224
Effective search space:    50176
Effective search space used:    50176
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: 46 (22.3 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