GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Desulfacinum hydrothermale DSM 13146

Align glucose transporter, ATPase component (characterized)
to candidate WP_170920503.1 B9A12_RS09210 energy-coupling factor transporter ATPase

Query= reanno::Phaeo:GFF3641
         (260 letters)



>NCBI__GCF_900176285.1:WP_170920503.1
          Length = 571

 Score = 89.0 bits (219), Expect = 2e-22
 Identities = 73/221 (33%), Positives = 117/221 (52%), Gaps = 16/221 (7%)

Query: 16  VEMKDISISFG-GIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRV 74
           +EM   S ++G G  A+++VS  +  GE + L+G NGAGKSTL   L+G  +   G+  +
Sbjct: 312 LEMLGFSYAYGDGTVALENVSFQVGRGERLALVGPNGAGKSTLAACLAGI-RWGTGQYLL 370

Query: 75  NGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECR 134
           +G KVE    R+   H +  ++Q     D+ D       G E+   FGL +    E+  R
Sbjct: 371 DGRKVEGAFRRNLWRH-VGLVFQ-----DSADQMVCSRCGDEVA--FGLRNLGWPESRIR 422

Query: 135 KIMNRLN--PNFQKFSEPVSA-LSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQM 191
           K +  +      + F + V   LSGG+R+ +A+A  +    ++LI+DEPTA L P   Q 
Sbjct: 423 KKVQAMLHWAGLEGFEDRVPQHLSGGERKRLALAAVLAMEPEVLILDEPTAGLDPQTEQK 482

Query: 192 VAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLV 232
           + +L+ +++A    + LI HDV  V  L DR  +M  G++V
Sbjct: 483 LLQLLDEVEAT---LVLISHDVCFVSMLTDRTLLMHRGRIV 520



 Score = 79.3 bits (194), Expect = 2e-19
 Identities = 60/208 (28%), Positives = 97/208 (46%), Gaps = 18/208 (8%)

Query: 27  GIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVNGDKVEITNPRD 86
           G +A+ H+ + ++ GE + +LGHNG+GK+TL +VLSG      G +   GD +      D
Sbjct: 31  GRQALRHIDLSIHEGERIAVLGHNGSGKTTLARVLSGLAPPTQGRVLFQGDPLSRERLED 90

Query: 87  ARSHNIETIYQTLALADNLDAASNLFLGREL-VTPFGL----VDDSAMEAECRKIMNRLN 141
            R   +  ++Q        D    LF    L    FGL    V     E   RK +  + 
Sbjct: 91  LR-QRVGFLFQ--------DPDDQLFCPTVLDDVLFGLLNFQVPPKEAEERARKALAAMG 141

Query: 142 PNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAELIQQLKA 201
              +    P   LS GQR+  A+A  +     +LI+DEPTA + P    +++++++    
Sbjct: 142 LEAEAHRAP-HHLSYGQRKRAALAAILALEPDVLILDEPTANMDPTSEALLSKVLKDYPG 200

Query: 202 QGIGIFLIDHDVNAVMELCDRASVMKNG 229
               +  I HD+  +  LC RA V++ G
Sbjct: 201 T---LICISHDILFLYGLCTRAVVLQAG 225


Lambda     K      H
   0.317    0.135    0.373 

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: 288
Number of extensions: 19
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 260
Length of database: 571
Length adjustment: 30
Effective length of query: 230
Effective length of database: 541
Effective search space:   124430
Effective search space used:   124430
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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