GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Marivita geojedonensis DPG-138

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 WP_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q9X103
         (369 letters)



>NCBI__GCF_002115805.1:WP_085637757.1
          Length = 365

 Score =  333 bits (855), Expect = 3e-96
 Identities = 181/357 (50%), Positives = 247/357 (69%), Gaps = 3/357 (0%)

Query: 8   LENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDG 67
           ++N+ K Y    + +K+ N+ +E  +F+VL+GPSGCGK+T L  IAGLE IT G I I G
Sbjct: 7   IKNLYKSYGTTEI-LKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSINIGG 65

Query: 68  KVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIE 127
           K +  V PKDRDIAMVFQ+YALYP MTV +N+ FG+K+R   +   DR++ + A+ L IE
Sbjct: 66  KDMTHVSPKDRDIAMVFQSYALYPTMTVAKNITFGMKVRGVDQATQDRKLAQVAQQLQIE 125

Query: 128 NLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQ 187
            LL+R+P QLSGGQRQRVA+GRA+VR+PK+FLFDEPLSNLDAKLRV+MR+E+K LHH L 
Sbjct: 126 PLLNRRPGQLSGGQRQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHHNLG 185

Query: 188 ATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFVNA 247
           A+++YVTHDQ+EAMT+A KIVVMK G IQQIG+P EIYN PAN+FVA F+GSP MN + A
Sbjct: 186 ASMVYVTHDQIEAMTLATKIVVMKGGVIQQIGSPAEIYNRPANLFVADFMGSPAMNLIPA 245

Query: 248 RVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPSPENTI 307
           +  R + G  I+ +  K   P    D     + +++I G+RPEDI D     A + +   
Sbjct: 246 KAHRADEGTRIEITR-KSGEPIVLTDTKNRDLPEDVILGVRPEDIADPDLRGAEAAQ-AA 303

Query: 308 TGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMTRMHAFDKET 364
             ++D+VEP G++T   +++G   + A ++  T AK  Q   L  D+ ++  F  ET
Sbjct: 304 ECLIDMVEPAGADTFAVMQLGGKHVTARLHAETTAKPGQPKRLSFDLGKVSYFAPET 360


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: 354
Number of extensions: 21
Number of successful extensions: 3
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: 365
Length adjustment: 30
Effective length of query: 339
Effective length of database: 335
Effective search space:   113565
Effective search space used:   113565
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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