GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Thiothrix lacustris DSM 21227

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_211248857.1 Q394_RS0118475 glucose 1-dehydrogenase

Query= SwissProt::Q92EU6
         (254 letters)



>NCBI__GCF_000621325.1:WP_211248857.1
          Length = 255

 Score =  129 bits (325), Expect = 4e-35
 Identities = 90/248 (36%), Positives = 136/248 (54%), Gaps = 8/248 (3%)

Query: 11  NITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIK-EDVKDVAAQINPSRTLALQV-- 67
           N+  KV V+TGA+SGIG+A A  F  +G  +VL   + E+ + VAA I  +   A+ V  
Sbjct: 8   NLAGKVVVITGASSGIGEAAAHAFGREGCKLVLGARRAEEGEAVAAAIRATGGEAVFVCT 67

Query: 68  DITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKA--EDLPEEYWDKTMELNLKGSFL 125
           D+ ++ +I ++V      +  +D+L N+AG   +  A  E    EY D TM  N++    
Sbjct: 68  DVLQEADIARLVQTALDTFGGLDVLFNNAGTEGVSSAFTEQSTAEY-DFTMNTNVRSVLW 126

Query: 126 MAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINV 185
             Q   R M  + GG I+N AS  + +       Y ASKAA+V MT+V A+E+    I +
Sbjct: 127 GMQHAIRAM-QSAGGAIINNASIVAHVGFANTALYSASKAAVVGMTRVAAVEYFKQGIRI 185

Query: 186 NAISPTVILTELGKKAWAGQVGED-MKKLIPAGRFGYPEEVAACALFLVSDAASLITGEN 244
           NA+ P +  T + ++   G+  ++      PAGR G PEE+AA  +FL S  AS I+G+ 
Sbjct: 186 NAVCPGITYTPMSQRLLGGEDEQNAFMATTPAGRTGQPEEIAAAVVFLASGNASYISGQC 245

Query: 245 LIIDGGYT 252
           L +DGGYT
Sbjct: 246 LNVDGGYT 253


Lambda     K      H
   0.316    0.133    0.369 

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: 145
Number of extensions: 9
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: 254
Length of database: 255
Length adjustment: 24
Effective length of query: 230
Effective length of database: 231
Effective search space:    53130
Effective search space used:    53130
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 (21.6 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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