GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpT in Desulfovibrio vulgaris Hildenborough

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein

Query= TCDB::G3LHY9
         (356 letters)



>lcl|MicrobesOnline__882:208681 DVU3161 ABC transporter, ATP-binding
           protein
          Length = 349

 Score =  205 bits (521), Expect = 2e-57
 Identities = 124/342 (36%), Positives = 189/342 (55%), Gaps = 22/342 (6%)

Query: 1   MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60
           M+ I LD +   +G     D      +V  E   G    LLGPSGCGK+T L +I+GL  
Sbjct: 1   MSTIVLDKVSRHWGDVRAVD------DVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLES 54

Query: 61  PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120
            + GRIL  G+DVTNL    R +A VFQ   ++  +TV DN+ F L  R V  A+  +R+
Sbjct: 55  VTSGRILIGGRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRL 114

Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180
              +E++ L     RK   L+  Q+Q+++LGR LV  +    L DEPL+ +D  ++  +R
Sbjct: 115 DRAVEILGLGKLLERKPGELSGGQQQRVALGRALVA-EAAVCLMDEPLSNLDAKLRQEMR 173

Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240
            +++ L +  G TMVYVTHDQTEA++ A+++++M  G+IVQ  TP E++ RP+  F G F
Sbjct: 174 REIRALQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSF 233

Query: 241 IGSPGMNFMPARIEGSTVKVGDETLTLEYAPKTSGT------AKTELGIRPEFIRLGREG 294
           IG+P MN +  R++G+     D+ + +  A   SG       A   LGIRPE IR+  +G
Sbjct: 234 IGTPPMNLV--RLQGN-----DDGIRV--AGSRSGRVTCHAGADCMLGIRPEHIRIVDDG 284

Query: 295 MPITISKVEDIGRQKIVRARFADQPIAIVVPEDADIPADARV 336
               +  VE +G   ++  R   + +++VV    D    A +
Sbjct: 285 WRAVVESVEYLGSNSVLSCRVGSEELSVVVHGVTDTVVGAEI 326


Lambda     K      H
   0.321    0.137    0.405 

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: 257
Number of extensions: 11
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: 356
Length of database: 349
Length adjustment: 29
Effective length of query: 327
Effective length of database: 320
Effective search space:   104640
Effective search space used:   104640
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.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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