GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_1321 Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component

Query= TCDB::Q9X103
         (369 letters)



>FitnessBrowser__Korea:Ga0059261_1321
          Length = 238

 Score =  111 bits (278), Expect = 2e-29
 Identities = 71/219 (32%), Positives = 111/219 (50%), Gaps = 10/219 (4%)

Query: 8   LENVTKVYENKVVA---VKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIY 64
           L N+TKV+     A   +K  +L + +++FV ++GPSG GK+TT+ ++  L+  T G+  
Sbjct: 10  LRNITKVFGEGATAFQALKGVDLDIAERDFVAVMGPSGSGKSTTMNILGCLDVPTSGEFL 69

Query: 65  IDGKVVNDVEPKDRDIA------MVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVR 118
             G  +  ++   R +        VFQ + L       EN+   L  R   K        
Sbjct: 70  FKGVYIETLDRDQRALVRRKYLGFVFQGFNLLSRTNALENVELPLLYRGEDKKVRHELGM 129

Query: 119 EAAKILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSE 178
            A + +G+ +  D  P +LSGGQ QRVA+ RAIV +P V L DEP  NLD+   V++   
Sbjct: 130 AALEKVGLADWWDHTPAELSGGQPQRVAIARAIVTSPAVLLADEPTGNLDSARSVEIMEL 189

Query: 179 LKKLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQ 217
           L  L+     T++ VTH+  +    A  IV  KDG +++
Sbjct: 190 LTSLNKDSGITVLMVTHEP-DMAAFARTIVHFKDGLVER 227


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: 168
Number of extensions: 5
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: 369
Length of database: 238
Length adjustment: 26
Effective length of query: 343
Effective length of database: 212
Effective search space:    72716
Effective search space used:    72716
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:

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