GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Azospirillum brasilense Sp245

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 AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein

Query= TCDB::Q00752
         (377 letters)



>FitnessBrowser__azobra:AZOBR_RS25595
          Length = 358

 Score =  297 bits (760), Expect = 3e-85
 Identities = 175/362 (48%), Positives = 224/362 (61%), Gaps = 43/362 (11%)

Query: 21  VEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELKIDGEVVNDKAPKDRDIA 80
           +   DL++ + EF+ FVGPSGCGKST LR++AGLE+ + G+L I G+ VND+ P  R IA
Sbjct: 19  IHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGGDLSIGGQRVNDRPPAARGIA 78

Query: 81  MVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQILGLTEFLERKPADLSGGQ 140
           MVFQ+YALYPHM+ YDNMAFGL L    K  I +RV+ AA++L + + L+RKP DLSGGQ
Sbjct: 79  MVFQSYALYPHMTAYDNMAFGLTLSRTDKGTIAERVRAAARLLQIEDLLDRKPRDLSGGQ 138

Query: 141 RQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHRRIGATTIYVTHDQTEAM 200
           RQRVA+GRAIVR+ +VFL DEPLSNLDA LRV MR EIAK+   + AT IYVTHDQ EAM
Sbjct: 139 RQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRLEIAKLKADLRATMIYVTHDQVEAM 198

Query: 201 TLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVAGFIGSPAMNFFDVTIKD 260
           TLADRIV++++          GRVEQ GTP ELY+RP N+FVAGFIGSPAMNF DV + +
Sbjct: 199 TLADRIVVLNA----------GRVEQAGTPLELYHRPRNRFVAGFIGSPAMNFLDV-VSE 247

Query: 261 GHLVSKDGLTIAVTEGQLKMLESKGF------------KNKNLIFGIRPEDISSSLLVQE 308
           G           +T+G +++    G                 L  G+RPE +  +     
Sbjct: 248 G-----------LTDGSVRVWLPGGVPLDIAVDGAAPAAGTPLTLGVRPEHVGLA----- 291

Query: 309 TYPDATVDAEVVVSELLGSETMLYLKL--GQTEFAARVDARDFHEPGEKVSLTFNVAKGH 366
               A + A ++  E LG ET  +  L  GQ     R+D       GE++ L       H
Sbjct: 292 -DGGAGLLATILAVERLGGETHCHAALEDGQ-RLLVRLDGDRPVAAGERLRLNLRGETAH 349

Query: 367 FF 368
            F
Sbjct: 350 LF 351


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: 397
Number of extensions: 13
Number of successful extensions: 2
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: 358
Length adjustment: 30
Effective length of query: 347
Effective length of database: 328
Effective search space:   113816
Effective search space used:   113816
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