GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Marivita geojedonensis DPG-138

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_002115805.1:WP_085637757.1
          Length = 365

 Score =  284 bits (727), Expect = 2e-81
 Identities = 156/313 (49%), Positives = 210/313 (67%), Gaps = 16/313 (5%)

Query: 21  VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80
           +K  N+ I  G+FLVLVGPSGCGKST L  +AGLE +T G+I IG KD+THV+P+DRDIA
Sbjct: 20  LKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSINIGGKDMTHVSPKDRDIA 79

Query: 81  MVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQ 140
           MVFQ+YALYP MTV +N+ F +K+ G  Q   ++++ + A  L +   L R+P  LSGGQ
Sbjct: 80  MVFQSYALYPTMTVAKNITFGMKVRGVDQATQDRKLAQVAQQLQIEPLLNRRPGQLSGGQ 139

Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200
           RQRVAMGRA+VR+P++FL DEPLSNLDAKLRV+ RT+I +L   LG + VYVTHDQ EA+
Sbjct: 140 RQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHHNLGASMVYVTHDQIEAM 199

Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARI 260
           T+  +I V+K G +QQ+G+P E+Y+RPAN+FVA F+GSPAMNL     K   A  G  RI
Sbjct: 200 TLATKIVVMKGGVIQQIGSPAEIYNRPANLFVADFMGSPAMNL--IPAKAHRADEG-TRI 256

Query: 261 KLS---------PETLAAMTPEDNGRITIGFRPEAL-EIIPEGESTDLSIPIKLDFVEEL 310
           +++          +T     PED   + +G RPE + +    G     +    +D VE  
Sbjct: 257 EITRKSGEPIVLTDTKNRDLPED---VILGVRPEDIADPDLRGAEAAQAAECLIDMVEPA 313

Query: 311 GSDSFLYGKLVGE 323
           G+D+F   +L G+
Sbjct: 314 GADTFAVMQLGGK 326


Lambda     K      H
   0.316    0.135    0.380 

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: 387
Number of extensions: 10
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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