GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Paucidesulfovibrio gracilis DSM 16080

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 WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>NCBI__GCF_900167125.1:WP_200806763.1
          Length = 406

 Score =  260 bits (665), Expect = 4e-74
 Identities = 151/352 (42%), Positives = 220/352 (62%), Gaps = 12/352 (3%)

Query: 4   VRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIG 63
           VRL+ + KRFGK VAV++ +L  E GE V  +GPSGCGKTT LRMIAGLE  ++G+IYI 
Sbjct: 45  VRLQGLMKRFGKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYIK 104

Query: 64  DRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKI 123
            R +ND P   R++ M+FQNYAL+PH  ++EN+AFGL+ R   ++E+  +V +A  ++++
Sbjct: 105 GRRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMVRL 164

Query: 124 EHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRL 183
             +  R   +LSGGQ+QR+A+ RAIV EP V LMDEPLS LD KLR EMR EI  +Q++L
Sbjct: 165 PGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQL 224

Query: 184 GVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVR 243
            +TT++VTHDQ EA+++ ++IVVMKDG  QQ  TP ++YD+P N FVA F+G  +    R
Sbjct: 225 NLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGHANFFDAR 284

Query: 244 AGVEVQGEKVYL-VAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEE-- 300
               +  ++V + +A G    A+ V     +   G++V L +R + + +       EE  
Sbjct: 285 VLEVLDNDQVRVRIAEGLEFTADHV----GRWRQGQDVHLVMRAQKINVTSPDLADEELE 340

Query: 301 ---ENVLRGEVEVVEPLGAETEIHVAV-NGTLL-VAKVDGHAPVKPGDKVEL 347
               N   G++     +G ET   V + NG  L +  +    P + GD+V L
Sbjct: 341 STDLNYYPGKIYDRSYMGGETSYFVELANGVRLHIISMVRRRPHRIGDEVVL 392


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: 418
Number of extensions: 15
Number of successful extensions: 1
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: 406
Length adjustment: 31
Effective length of query: 345
Effective length of database: 375
Effective search space:   129375
Effective search space used:   129375
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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