GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Desulfovibrio vulgaris Hildenborough

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 209027 DVU0098 polyamine ABC transporter, ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>MicrobesOnline__882:209027
          Length = 368

 Score =  249 bits (636), Expect = 9e-71
 Identities = 139/326 (42%), Positives = 203/326 (62%), Gaps = 12/326 (3%)

Query: 4   VRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIG 63
           + L  V K F    A+ + +LE  +GEF+  +GPSGCGKTT LR+I+G E+   G I + 
Sbjct: 8   IELRGVTKNFEDTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVITLK 67

Query: 64  DRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKI 123
            + ++D PP+ R +  VFQNYAL+PHM+V EN+ FGLR++R PKDEI RRV +A R++ +
Sbjct: 68  GQRMDDAPPEARQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALRMVHL 127

Query: 124 EHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRL 183
           E   +R+PR+LSGGQ+QRVA+ RA+V  P V L+DEP S LD KLR +M+ EI  LQR+L
Sbjct: 128 EAHADRRPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHLQRQL 187

Query: 184 GVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVR 243
           G+T ++VTHDQ EA  +  R+VVM DG+I+Q+ +P  +Y+ PAN +VA F+G   +N + 
Sbjct: 188 GITFVFVTHDQEEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVG--EINILN 245

Query: 244 AGVEV-QGEKVY---LVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPE 299
           A +    G+ +Y   +    F IR+            G +V + +RPE L +   T    
Sbjct: 246 AVIAANHGDGLYDAVIEGVTFPIRSQRTFA------PGDKVNVLLRPEDLRVYTLTEDRP 299

Query: 300 EENVLRGEVEVVEPLGAETEIHVAVN 325
               L G +E     GA  ++ V ++
Sbjct: 300 AGPHLTGRIEESVYKGATVDLIVTLS 325



 Score = 24.6 bits (52), Expect = 0.004
 Identities = 11/26 (42%), Positives = 14/26 (53%)

Query: 341 PGDKVELLADTQRLHAFDLETDRTIG 366
           PGDKV +L   + L  + L  DR  G
Sbjct: 276 PGDKVNVLLRPEDLRVYTLTEDRPAG 301


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: 387
Number of extensions: 17
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 376
Length of database: 368
Length adjustment: 30
Effective length of query: 346
Effective length of database: 338
Effective search space:   116948
Effective search space used:   116948
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