GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Sinorhizobium fredii NGR234

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_164924745.1 NGR_RS30975 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_000018545.1:WP_164924745.1
          Length = 355

 Score =  317 bits (812), Expect = 3e-91
 Identities = 186/382 (48%), Positives = 244/382 (63%), Gaps = 36/382 (9%)

Query: 1   MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60
           M  VT ++ +  Y       + + +  I DGEF+VLVGPSGCGKST LRMLAGLE ++ G
Sbjct: 1   MTDVTIRNVTKRYGALT--VIPQLSFRIEDGEFVVLVGPSGCGKSTLLRMLAGLEEISGG 58

Query: 61  AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120
            + +G   +     ++RD+A+VFQNYALYPHMTV ENMGFALK+  + + EI++RVD+AA
Sbjct: 59  DLLMGADVINDRPAKERDMAIVFQNYALYPHMTVAENMGFALKLRKRPRAEIDERVDKAA 118

Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180
           A LGL + L+R P+ALSGGQRQRVAMGRAIVR+PQVFL DEPLSNLDAKLRVQ R +I A
Sbjct: 119 AILGLGKLLDRYPRALSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKA 178

Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240
           L ++L +TTVYVTHDQ EA+TM D+I V+ +G ++Q+G P ELYDRPAN+FVAGFIGSP+
Sbjct: 179 LHQRLKITTVYVTHDQIEAMTMADKIVVMNEGRVEQMGTPLELYDRPANIFVAGFIGSPS 238

Query: 241 MNLGTFSVKDGDATSGHARIKLSPETLAAMTPEDNG-------RITIGFRPEALEIIPEG 293
           MN    +V    AT+G   +  +PE +A   P D G        +T G RPE L++   G
Sbjct: 239 MNFLPATVA---ATNG--PLLKTPEGVA--LPIDGGPTLTGRSEVTYGIRPEHLQL---G 288

Query: 294 ESTDLSIPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGS 353
           E+    IP ++  VE  GS++ LY  + G               ++V          PG 
Sbjct: 289 ET---GIPAEVVVVEPTGSETQLYVTVGGR--------------EVVAVLRDRVDVRPGE 331

Query: 354 VFHARIVEGGQHNFSASTGKRL 375
                  +G  H F  +TG R+
Sbjct: 332 KIWLTPRKGCAHLFDPNTGARI 353


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: 443
Number of extensions: 18
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: 355
Length adjustment: 30
Effective length of query: 346
Effective length of database: 325
Effective search space:   112450
Effective search space used:   112450
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 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