GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Acidovorax sp. GW101-3H11

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)

Query= reanno::Smeli:SM_b21216
         (360 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2066
          Length = 355

 Score =  348 bits (892), Expect = e-100
 Identities = 191/361 (52%), Positives = 241/361 (66%), Gaps = 15/361 (4%)

Query: 2   SALEIRNIRKRYGE----VETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSG 57
           S+L+I  I KR+G+    VE L+ +DI +  GEFL+L+G SGCGKSTLLNIIAGL EP+ 
Sbjct: 3   SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62

Query: 58  GDILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDT 117
           G+I IG ++V+G+ P+DRDIAMVFQSYALYP LSVA NIGF LEMR++P+ E  K + + 
Sbjct: 63  GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122

Query: 118 ARLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELK 177
           A +LQI +LLDR+PSQLSGGQRQRVA+GRAL R PQ+FLFDEPLSNLDAKLR+EMR E+K
Sbjct: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182

Query: 178 RLHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSP 237
           RLHQ    T VYVTHDQ+EAMTL +RIAVM+ G ++QL  PDE+Y+RPA  YVA F+GSP
Sbjct: 183 RLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSP 242

Query: 238 PMNILDAEMTANGLKIEGCE-EVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRL 296
            MN+L   +T     I+G    + P P++ N        V +G+RPE L +    E    
Sbjct: 243 TMNLLRGAVTGGQFGIQGAALNLAPPPSSAN-------EVLLGVRPEHLVM---QETAPW 292

Query: 297 TASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESGRS 356
              V VVE TGP+        +  +T     +T V  G            H FD +S   
Sbjct: 293 RGRVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEER 352

Query: 357 L 357
           L
Sbjct: 353 L 353


Lambda     K      H
   0.320    0.136    0.385 

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: 393
Number of extensions: 12
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: 360
Length of database: 355
Length adjustment: 29
Effective length of query: 331
Effective length of database: 326
Effective search space:   107906
Effective search space used:   107906
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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