GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Sinorhizobium fredii NGR234

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_015887278.1 NGR_RS05625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>NCBI__GCF_000018545.1:WP_015887278.1
          Length = 360

 Score =  206 bits (524), Expect = 8e-58
 Identities = 133/358 (37%), Positives = 201/358 (56%), Gaps = 15/358 (4%)

Query: 3   LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62
           L + +I K+ G    L  + +AL+SG   VLLG++  GK++L+ I+AGL  P+ G + + 
Sbjct: 4   LEIRNIRKRYGDVETLKSIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIG 63

Query: 63  GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNIDAR--VREIASRLHI 120
            + + G   +DR++AMV+Q +  YP+M VA NI   L++R     +    VR+ A  L I
Sbjct: 64  ERSILGAHPKDRDIAMVFQSYALYPNMSVARNIGFGLEMRKVPAAEREKAVRDTARLLQI 123

Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180
           +  LDR P++LSGGQ+QRVA+ RAL +   + L DEPL NLD KLR E+R EL +L    
Sbjct: 124 ENLLDRKPSQLSGGQRQRVAIGRALVREPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183

Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMA 240
           ++TVVY T +  EA+ L    AV+ +G++ Q G  AE++  P +L VA     PPMN++ 
Sbjct: 184 KTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLGTPAEIYDRPATLYVAGFVGSPPMNILD 243

Query: 241 ASATAQGVRLQGGAELTLPL----PQGAATAAGLTVGVRASALRVHARPGDVSVAG---- 292
           A  T  G+R+  G+E TLPL    P G  T   + VG+R  ALR+    GD +  G    
Sbjct: 244 AEGTGSGLRIL-GSENTLPLGGAFPNG-TTGRRVKVGIRPEALRL---AGDDATGGRLTA 298

Query: 293 VVELAEISGSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLA 350
           +VE+ E++G +  + A      + A L      E G+      D A  ++F  +  L+
Sbjct: 299 IVEVMELTGPELVITARIGEQRITACLPPRTSLEPGSTQAFSFDEAALHLFDPESGLS 356


Lambda     K      H
   0.318    0.133    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: 303
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: 363
Length of database: 360
Length adjustment: 29
Effective length of query: 334
Effective length of database: 331
Effective search space:   110554
Effective search space used:   110554
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 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