GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Methanococcus aeolicus Nankai-3

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_052287789.1 MAEO_RS01500 ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>NCBI__GCF_000017185.1:WP_052287789.1
          Length = 383

 Score =  250 bits (639), Expect = 4e-71
 Identities = 139/336 (41%), Positives = 212/336 (63%), Gaps = 16/336 (4%)

Query: 4   VRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIG 63
           +++++V K+ G    + + +L+  DGE +V +GPSGCGKTT L++IAGL +   GNI I 
Sbjct: 2   IKIDNVSKKMGNQNILNNVSLQVHDGEIMVLLGPSGCGKTTLLKIIAGLLKQDSGNIIIN 61

Query: 64  DRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKI 123
           + ++ND P K+R++  VFQ+YAL+PH NVY+N+AFGL+LR+ P++EI+ ++ E   IL+I
Sbjct: 62  NNIINDFPSKERNMGFVFQDYALFPHKNVYDNIAFGLKLRKVPENEINIKINEIMEILEI 121

Query: 124 EHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRL 183
           +HL ++K  +LSGGQ+QRVA+ RA+V +P V L+DEPLS LD  LR ++R E+  +   L
Sbjct: 122 DHLKDKKIPQLSGGQKQRVALARALVIDPDVLLLDEPLSALDPILREKLREELKTILNTL 181

Query: 184 GVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVR 243
           GVT IYVTHD  EAM LG  + VM +G IQQ++ P +++  P N FVA F+G    N ++
Sbjct: 182 GVTGIYVTHDLTEAMILGDNVAVMNNGIIQQIEKPDDIFYHPKNEFVAEFVG--VKNILK 239

Query: 244 AGV-EVQGEKVY-------LVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYT 295
             + E  GE V        L AP F I+ N       +    KE+ L + PE + L    
Sbjct: 240 GRIFEYDGEDVIITINNPNLKAP-FNIKVNNY--PIFERKKEKEISLCIHPEEIKL---N 293

Query: 296 TIPEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVA 331
            +   EN ++G++  + P G+  ++ + + G  L A
Sbjct: 294 NVKNGENNIKGKIINIFPNGSVLKVVLDIGGMELYA 329


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: 337
Number of extensions: 20
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: 383
Length adjustment: 30
Effective length of query: 346
Effective length of database: 353
Effective search space:   122138
Effective search space used:   122138
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.

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