GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Actinomyces timonensis 7400942

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_017178050.1 A1QA_RS0106175 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::Smeli:SMc03065
         (362 letters)



>NCBI__GCF_000295095.1:WP_017178050.1
          Length = 375

 Score =  305 bits (780), Expect = 2e-87
 Identities = 173/345 (50%), Positives = 218/345 (63%), Gaps = 16/345 (4%)

Query: 22  IDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGERVNDVPPSKRGIAMVF 81
           ++L+I +GEF+V VGPSGCGKST LRM+AGLE++  G + I    V DV P  R IAMVF
Sbjct: 24  LNLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNSGRILIGDRDVTDVQPKDRDIAMVF 83

Query: 82  QSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTPYLDRLPKALSGGQRQR 141
           Q+YALYPHM+V+DNM F ++IA   KEEID+RVR AA +L LT YLDR PKALSGGQRQR
Sbjct: 84  QNYALYPHMSVHDNMGFALKIAGTPKEEIDKRVREAAKILGLTEYLDRKPKALSGGQRQR 143

Query: 142 VAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSDTTMIYVTHDQVEAMTL 201
           VA+GRAI R PKVFL DEPLSNLDA LRV TR +IA L   +  TT +YVTHDQ EA+T+
Sbjct: 144 VAMGRAIVRKPKVFLMDEPLSNLDAKLRVQTRTQIASLQRSLGVTT-VYVTHDQTEALTM 202

Query: 202 ADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPATITATGQQTAVSLAGG 261
            DRI VL  G ++QVG P E+Y++PAN FVA FIGSPAMN+     T +G   ++  A  
Sbjct: 203 GDRIAVLKDGLLQQVGTPREMYDKPANEFVAGFIGSPAMNL--GHFTVSGDVASIGSAKI 260

Query: 262 KSVTLDVPTNASENGKTASFGVRPEDLRVTEA-DDFLFEGTVSIVEALGEVTLLYIEGL- 319
           +     +     E+G   + G RPE L V  A D+      VS VE LG    +Y E + 
Sbjct: 261 QLSRATLDAIKPEDGGKVAIGFRPESLEVVSASDEHSIPVRVSFVEELGSDAYIYGELVG 320

Query: 320 -----------VENEPIIAKMPGIARVGRGDKVRFTADKAKLHLF 353
                       ++  II ++P     G G+ V       + H+F
Sbjct: 321 AEGSEDKLGSGEDSSQIIVRVPPRTAPGAGETVYVRIKPGQEHIF 365


Lambda     K      H
   0.320    0.137    0.387 

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: 358
Number of extensions: 16
Number of successful extensions: 3
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: 362
Length of database: 375
Length adjustment: 30
Effective length of query: 332
Effective length of database: 345
Effective search space:   114540
Effective search space used:   114540
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 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