GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Shewanella loihica PV-4

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__PV4:5208351
          Length = 342

 Score =  190 bits (482), Expect = 6e-53
 Identities = 113/302 (37%), Positives = 173/302 (57%), Gaps = 25/302 (8%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           M+ + +E V   +     ++  +L    GE    +GPSGCGKTT L+ IAGL+ IS+G I
Sbjct: 1   MSTLTIEQVHSDYQGQTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRI 60

Query: 61  YIGDRLVND----VPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKE 116
            I  RL++     VP + R++ M+FQ+YAL+PH+ V EN+ FG++     K     R+ E
Sbjct: 61  SINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVK--GLDKAARQARLGE 118

Query: 117 AARILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEI 176
              ++K+E L  R P ELSGGQ+QRV++ RA+  EP++ L+DEP SN+DAK+R EM  EI
Sbjct: 119 MLALVKLEGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVEI 178

Query: 177 AKLQRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGS 236
            ++ ++ GV+ ++VTH + EA     ++ + KDG I Q  +  +LY  P +++VA F+G 
Sbjct: 179 REILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFLG- 237

Query: 237 PSMNFVRAGVEVQGEKVYLVAPGFRIRANAVLG-----SALKPYAGKEVWLGVRPEHLGL 291
             +N++   V+             R R   +LG     S L   AG    L +RPE L +
Sbjct: 238 -QVNYLSCEVK------------DRARLQTLLGEVQSSSDLPKAAGYRGELLLRPEQLQM 284

Query: 292 KG 293
            G
Sbjct: 285 AG 286


Lambda     K      H
   0.320    0.139    0.400 

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: 316
Number of extensions: 16
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: 376
Length of database: 342
Length adjustment: 29
Effective length of query: 347
Effective length of database: 313
Effective search space:   108611
Effective search space used:   108611
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.

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