GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Rhizorhabdus wittichii RW1

Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= TCDB::Q00752
         (377 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  137 bits (344), Expect = 4e-37
 Identities = 78/209 (37%), Positives = 117/209 (55%), Gaps = 5/209 (2%)

Query: 4   LNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELK 63
           ++ +H+ K Y  +  + ++D  L I+   F+  VG SG GK+T L+ +  L +I  G + 
Sbjct: 2   ISFDHVGKHY--AGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIA 59

Query: 64  IDGEVVNDK--APKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQ 121
           I+G  V  +  A   R I  VFQ   L+PHMSV +N+A   +L+   +E    RV E   
Sbjct: 60  IEGRDVAAQPVAELRRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLD 119

Query: 122 ILGL-TEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180
           ++ L  +F ER+PA LSGGQ QRV   RA+     + LMDEP   LD   R  + A    
Sbjct: 120 LVALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRA 179

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIM 209
           +H  +G T++ VTHD  EA+ LADR++++
Sbjct: 180 LHEAMGLTSLIVTHDMAEALLLADRVIVI 208


Lambda     K      H
   0.318    0.135    0.375 

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: 179
Number of extensions: 9
Number of successful extensions: 3
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: 377
Length of database: 252
Length adjustment: 27
Effective length of query: 350
Effective length of database: 225
Effective search space:    78750
Effective search space used:    78750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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