GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Escherichia coli BW25113

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 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)

Query= TCDB::Q9X103
         (369 letters)



>FitnessBrowser__Keio:17511
          Length = 356

 Score =  344 bits (883), Expect = 2e-99
 Identities = 184/366 (50%), Positives = 252/366 (68%), Gaps = 10/366 (2%)

Query: 3   MAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62
           MA + L+ VTK ++ K   +K   L V D EF+V++GPSGCGK+T LRM+AGLE +T+G 
Sbjct: 1   MAGLKLQAVTKSWDGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGD 60

Query: 63  IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122
           I+I+ + V ++EPKDR IAMVFQNYALYPHM+V ENMA+GLK+R   K +I  RV+EAA+
Sbjct: 61  IWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAAR 120

Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182
           IL ++ LL R+PR+LSGGQRQRVA+GRAIVR+P VFLFDEPLSNLDAKLRVQMR EL++L
Sbjct: 121 ILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQL 180

Query: 183 HHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPM 242
           H RL+ T +YVTHDQVEAMT+A +++VM  G  +QIGTP E+Y  PA++FVA FIGSP M
Sbjct: 181 HRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPAM 240

Query: 243 NFVNARVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPS 302
           N +  R V  EG  +    G ++ +   +      Y  +++  GIRPE I     AL+  
Sbjct: 241 NLLTGR-VNNEGTHFELDGGIELPLNGGYR----QYAGRKMTLGIRPEHI-----ALSSQ 290

Query: 303 PENTITGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMTRMHAFDK 362
            E  +  V+D +E LG++ + H + G+  +V  +  + +      + L L   ++H FD 
Sbjct: 291 AEGGVPMVMDTLEILGADNLAHGRWGEQKLVVRLAHQERPTAGSTLWLHLAENQLHLFDG 350

Query: 363 ETEKAI 368
           ET + +
Sbjct: 351 ETGQRV 356


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: 348
Number of extensions: 17
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: 356
Length adjustment: 29
Effective length of query: 340
Effective length of database: 327
Effective search space:   111180
Effective search space used:   111180
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 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