GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Collimonas pratensis Ter91

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_061938416.1 CPter91_RS06295 sugar ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>NCBI__GCF_001584185.1:WP_061938416.1
          Length = 379

 Score =  271 bits (692), Expect = 3e-77
 Identities = 154/376 (40%), Positives = 224/376 (59%), Gaps = 11/376 (2%)

Query: 20  IRSNIREY---GMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIV 76
           ++   R+Y    +LIA+  I  FF + T G    P NL+NL+ Q S   ++A GM+LVI+
Sbjct: 6   LKQLFRQYKIMALLIAIALIWAFFSWKTEGGFVTPRNLSNLLRQMSITGVLACGMVLVII 65

Query: 77  AGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSF 136
           AG IDLSVGS++  +G +AA+L V   +   L  L+ L+ G  +G   GY  AY RIPSF
Sbjct: 66  AGEIDLSVGSMLGLLGGVAAVLDVTHHLPLSLNLLLVLLAGLALGLFNGYLTAYMRIPSF 125

Query: 137 IVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITV 196
           IV L GML FRG+ L V GG  I P  ++   +  G+LP   GI         L + +  
Sbjct: 126 IVGLGGMLAFRGILLGVTGGLTIAPVSSEMVYLGQGYLPPQLGIA--------LGIGLFA 177

Query: 197 ALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVL 256
               L+WRRR    +HG+ V       V+ LLI   +L     L+TY G+P  ++++L L
Sbjct: 178 LALVLSWRRRSNRQQHGLPVPSVWRDAVRVLLIGAVLLAFVRTLNTYDGIPVPVLLLLAL 237

Query: 257 IALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRL 316
           + L+S++T +T  GRR+Y++G N +AT+LSG+N + +    F  MGV+  LAG++   RL
Sbjct: 238 LGLFSYLTTQTVFGRRIYSVGSNMEATRLSGVNVQAVKLWVFGIMGVMCALAGLVNTARL 297

Query: 317 NSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQ 376
            + +P AG   ELD IAACFIGG S  GG G + GA+IGA +M  ++NGMS++ +   +Q
Sbjct: 298 AAGSPSAGNMGELDAIAACFIGGTSMRGGYGTVYGALIGALVMASLDNGMSMLDVDTYWQ 357

Query: 377 QMVKGLVLLAAVFFDV 392
            +VKG +L+ AV+ DV
Sbjct: 358 MIVKGGILMLAVWVDV 373


Lambda     K      H
   0.329    0.145    0.422 

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: 551
Number of extensions: 36
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: 398
Length of database: 379
Length adjustment: 30
Effective length of query: 368
Effective length of database: 349
Effective search space:   128432
Effective search space used:   128432
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 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