GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Shewanella loihica PV-4

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 5207560 Shew_0094 ABC transporter-related protein (RefSeq)

Query= TCDB::Q00752
         (377 letters)



>FitnessBrowser__PV4:5207560
          Length = 369

 Score =  138 bits (347), Expect = 3e-37
 Identities = 86/242 (35%), Positives = 131/242 (54%), Gaps = 20/242 (8%)

Query: 23  DFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELKIDGEVVNDK------APKD 76
           D +   K  E +  VGPSG GKST +RM+AGL     GE++    V           P+ 
Sbjct: 21  DAEFVCKAGEVLAVVGPSGGGKSTLMRMIAGLTKPESGEIRYGDSVWFSSESGRYLTPQQ 80

Query: 77  RDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQILGLTEFLERKPADL 136
           R +  V Q++ L+P+M+   N+   L   H  K     R K+  + + L    +R PA+L
Sbjct: 81  RHLGYVPQHFGLFPNMTALANVVAALD--HIPKAERVARAKDWLERVNLHGLPDRLPANL 138

Query: 137 SGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHRRIGATTIYVTHDQ 196
           SGGQRQRVA+ RA+ R+ +V L+DEP S +D + R  +  E+A++  ++    I VTHD 
Sbjct: 139 SGGQRQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKEQLAIPVIMVTHDL 198

Query: 197 TEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVAGFIGSPAMNFFDV 256
            EA+ LADR++++S           G + Q G+P+E+ +RP N+ VA  +G    N FD 
Sbjct: 199 NEALLLADRMILISQ----------GTLLQQGSPREVLSRPRNEAVAKQMG--LRNLFDA 246

Query: 257 TI 258
            +
Sbjct: 247 HV 248


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: 268
Number of extensions: 7
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: 369
Length adjustment: 30
Effective length of query: 347
Effective length of database: 339
Effective search space:   117633
Effective search space used:   117633
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: 50 (23.9 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