GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Dechlorosoma suillum PS

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 Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  212 bits (539), Expect = 1e-59
 Identities = 123/333 (36%), Positives = 188/333 (56%), Gaps = 32/333 (9%)

Query: 4   VRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIG 63
           + + ++ KRFG  VA+ D +L    GE V  +GPSGCGKTT LR+IAG+E   EG +   
Sbjct: 3   IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62

Query: 64  DRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLR----RYPKDEIDRRVKEAAR 119
                 +  ++R +  VFQ+YAL+ HMNV+EN+AFGLR++    R  + EI +RV +   
Sbjct: 63  GSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLS 122

Query: 120 ILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKL 179
           +++++ L +R P +LSGGQRQR+A+ RA+  EPKV L+DEP   LD K+R E+R  + +L
Sbjct: 123 LVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRL 182

Query: 180 QRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSM 239
              + +++++VTHDQ EA+ +  R+VVM  G I+QV +P  +Y  PA+ FV  F+G+ ++
Sbjct: 183 HDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGNVNV 242

Query: 240 NFVR---AGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTT 296
              R   A  EV  + V                      AG+E    +RP  + +    T
Sbjct: 243 FHSRVHGAWAEVARDDV---------------------PAGQEAVAFIRPHDIDIDTVAT 281

Query: 297 IPEEENVLRGEVEVVEPLGAETEIHVAVNGTLL 329
            PE    L  +V  V+ +G    + V   G L+
Sbjct: 282 -PES---LEAKVSYVQTIGPLVRVEVIHQGELV 310


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: 360
Number of extensions: 18
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: 376
Length of database: 360
Length adjustment: 30
Effective length of query: 346
Effective length of database: 330
Effective search space:   114180
Effective search space used:   114180
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