GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein

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



>MicrobesOnline__882:209027
          Length = 368

 Score =  244 bits (622), Expect = 3e-69
 Identities = 131/289 (45%), Positives = 188/289 (65%), Gaps = 11/289 (3%)

Query: 6   LKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGE 65
           L+ + K++     +  IDL+I+ GEF+  +GPSGCGK+T+LR+I+G E+   G + + G+
Sbjct: 10  LRGVTKNFEDTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVITLKGQ 69

Query: 66  RVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTP 125
           R++D PP  R +  VFQ+YAL+PHM+V +N+ FG+R+ R  K+EI RRV  A  M+ L  
Sbjct: 70  RMDDAPPEARQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALRMVHLEA 129

Query: 126 YLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSD 185
           + DR P+ LSGGQ+QRVAI RA+  NP V L DEP S LD  LR   ++EI  L +R   
Sbjct: 130 HADRRPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHL-QRQLG 188

Query: 186 TTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPA 245
            T ++VTHDQ EA  ++DR+VV++ G IEQ+G+P E+YE PANL+VARF+G   +N++ A
Sbjct: 189 ITFVFVTHDQEEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVGE--INILNA 246

Query: 246 TITAT---GQQTAVSLAGGKSVTLDVPTNAS-ENGKTASFGVRPEDLRV 290
            I A    G   AV     + VT  + +  +   G   +  +RPEDLRV
Sbjct: 247 VIAANHGDGLYDAVI----EGVTFPIRSQRTFAPGDKVNVLLRPEDLRV 291


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: 364
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: 362
Length of database: 368
Length adjustment: 30
Effective length of query: 332
Effective length of database: 338
Effective search space:   112216
Effective search space used:   112216
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