GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK1 in Desulfovibrio vulgaris Hildenborough

Align MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate 206675 DVU1236 amino acid ABC transporter, ATP-binding protein

Query= TCDB::Q9X103
         (369 letters)



>lcl|MicrobesOnline__882:206675 DVU1236 amino acid ABC transporter,
           ATP-binding protein
          Length = 247

 Score =  156 bits (395), Expect = 5e-43
 Identities = 88/237 (37%), Positives = 143/237 (60%), Gaps = 7/237 (2%)

Query: 6   VVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYI 65
           + + NV K +  ++ A+ + +L V+  E VV++GPSG GK+T LR I  LE +  G I +
Sbjct: 9   ISIRNVWKFF-GELTALHDVSLDVQAGEKVVIIGPSGSGKSTLLRSINRLENVDKGSIIV 67

Query: 66  DGKVV----NDVEPKDRDIAMVFQNYALYPHMTVYENMAFG-LKLRKYPKDEIDRRVREA 120
           DGK +    +D+    +D+ MVFQ++ L+PH TV +N+    ++LRK P+DE + R  + 
Sbjct: 68  DGKDIRAEDSDINVIRQDLGMVFQSFNLFPHKTVLQNLTMAPMRLRKVPRDEAESRALDL 127

Query: 121 AKILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELK 180
            K +GI +  +  P  LSGGQ+QRVA+ RA+  NPK+ LFDEP S LD ++  ++   + 
Sbjct: 128 LKKVGISDKANVYPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMIGEVLDVMV 187

Query: 181 KLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFI 237
            L  +   T++ VTH+   A  +AD+I+ M  G+I + GTP   + +P +  +  F+
Sbjct: 188 TL-AKEGMTMVCVTHEMGFAREVADRIIFMDHGQILEQGTPQHFFEAPEHPRLQKFL 243


Lambda     K      H
   0.319    0.138    0.387 

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: 220
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: 369
Length of database: 247
Length adjustment: 27
Effective length of query: 342
Effective length of database: 220
Effective search space:    75240
Effective search space used:    75240
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: 48 (23.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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