GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Sinorhizobium meliloti 1021

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 SMc03065 SMc03065 alpha-glucoside ABC transporter ATP-binding protein

Query= TCDB::Q00752
         (377 letters)



>FitnessBrowser__Smeli:SMc03065
          Length = 362

 Score =  319 bits (818), Expect = 7e-92
 Identities = 193/380 (50%), Positives = 239/380 (62%), Gaps = 27/380 (7%)

Query: 1   MVELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKG 60
           M  L L  I K Y   +   +   DLDIK  EF+VFVGPSGCGKST LRM+AGLE+IT G
Sbjct: 1   MTGLLLKDIRKSY--GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGG 58

Query: 61  ELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120
           ++ IDGE VND  P  R IAMVFQ+YALYPHM+VYDNMAFG+++   SKE ID+RV+ AA
Sbjct: 59  DMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAA 118

Query: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180
            +L LT +L+R P  LSGGQRQRVA+GRAI R+ KVFL DEPLSNLDA LRV+ R EIAK
Sbjct: 119 DMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAK 178

Query: 181 IHRRIGATT-IYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPAN 239
           +  R+  TT IYVTHDQ EAMTLADRIV++S+          G +EQVG P ELY RPAN
Sbjct: 179 LSERMSDTTMIYVTHDQVEAMTLADRIVVLSA----------GHIEQVGAPLELYERPAN 228

Query: 240 KFVAGFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLE---SKGFKNKNLIFGIR 296
            FVA FIGSPAMN    TI      +     +++  G+   L+   +     K   FG+R
Sbjct: 229 LFVARFIGSPAMNVIPATI----TATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVR 284

Query: 297 PEDISSSLLVQETYPDATVDAEVVVSELLGSETMLYLK--LGQTEFAARVDARDFHEPGE 354
           PED    L V E   D   +  V + E LG  T+LY++  +      A++        G+
Sbjct: 285 PED----LRVTEA-DDFLFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGD 339

Query: 355 KVSLTFNVAKGHFFDAETEA 374
           KV  T + AK H FD   ++
Sbjct: 340 KVRFTADKAKLHLFDTNGQS 359


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: 344
Number of extensions: 14
Number of successful extensions: 5
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: 362
Length adjustment: 30
Effective length of query: 347
Effective length of database: 332
Effective search space:   115204
Effective search space used:   115204
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: 49 (23.5 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