GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Gallaecimonas xiamenensis 3-C-1

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_008483162.1 B3C1_RS04305 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= TCDB::Q72L52
         (376 letters)



>NCBI__GCF_000299915.1:WP_008483162.1
          Length = 365

 Score =  229 bits (585), Expect = 7e-65
 Identities = 115/232 (49%), Positives = 161/232 (69%)

Query: 4   VRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIG 63
           V L  V K F     +   +LE  DGEF   +GPSGCGKTT LR+IAGLE    G I I 
Sbjct: 11  VVLSGVEKAFDGKAVLAGLDLEIRDGEFFTILGPSGCGKTTALRLIAGLENADAGRIQIA 70

Query: 64  DRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKI 123
                 +P + R++  VFQ+YAL+PHM V+EN+AFGL++++ PK E  +RV +A +++++
Sbjct: 71  GVDNTQLPAEKRNVNTVFQSYALFPHMTVFENVAFGLQMQKVPKAEQQQRVLDALKMVQL 130

Query: 124 EHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRL 183
           +    RKP +LSGGQ+QRVA+ RA+V +PKV L+DE LS LD KLR  M+ E+ +LQRRL
Sbjct: 131 DSFAKRKPHQLSGGQQQRVAIARAVVNKPKVLLLDESLSALDYKLRKAMQWELKQLQRRL 190

Query: 184 GVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIG 235
           G+T I+VTHDQ EA+++  RI+VM +G  +Q+ TP  +Y+ P++ FVA FIG
Sbjct: 191 GITFIFVTHDQEEALSMSDRILVMNNGRAEQLGTPREIYETPSSLFVARFIG 242


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: 336
Number of extensions: 13
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: 365
Length adjustment: 30
Effective length of query: 346
Effective length of database: 335
Effective search space:   115910
Effective search space used:   115910
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 24 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