GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Caulobacter crescentus NA1000

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate CCNA_01345 CCNA_01345 short chain dehydrogenase

Query= BRENDA::Q1J2J0
         (255 letters)



>FitnessBrowser__Caulo:CCNA_01345
          Length = 260

 Score =  167 bits (423), Expect = 2e-46
 Identities = 101/254 (39%), Positives = 146/254 (57%), Gaps = 14/254 (5%)

Query: 13  LFRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIA-----DLNPDVGEGAARELDGTFE 67
           LF L GR A+VTGG++G+G +IAR LA+ GA V +      +L+  V    A        
Sbjct: 8   LFDLTGRVAIVTGGSRGLGLQIARALAEYGAAVALVARKQGELDAAVAALTAEGRTAVGL 67

Query: 68  RLNVTDADAVADLARRLPD----VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFW 123
             ++  A +  DL  R+ +    +D+LVNNAG    APAED P + W  V+ +N+ G+F 
Sbjct: 68  VADLGQAGSAQDLTARVLERFGRIDILVNNAGAAWGAPAEDYPLEGWNKVMDLNVTGLFL 127

Query: 124 CCREFGR-TMLARGRGAIVSTASMSGLISNHPQPQA--AYNASKAAVIHLTRSLAGEWAS 180
             +   R   L +G+GA+V+ AS+ GL  +H       AYN +K AVI++TR+LA EW  
Sbjct: 128 LTQAVAREAFLKQGKGAVVNVASIEGLQGHHHSQLGTIAYNTAKGAVINMTRALAAEWGP 187

Query: 181 RGVRVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASF 240
           R +RVNAVAPGY  + +T   L   +  +  L++TPLG+L    ++    L LASDA   
Sbjct: 188 RNIRVNAVAPGYFPSKMTMTTL--GQHGDDMLRQTPLGKLGGDTDLMGPALLLASDAGGH 245

Query: 241 VTGHTLVVDGGYTV 254
           +TG  +VVDGG T+
Sbjct: 246 ITGQIIVVDGGMTI 259


Lambda     K      H
   0.319    0.134    0.408 

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: 210
Number of extensions: 12
Number of successful extensions: 5
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: 255
Length of database: 260
Length adjustment: 24
Effective length of query: 231
Effective length of database: 236
Effective search space:    54516
Effective search space used:    54516
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: 47 (22.7 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