GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Dinoroseobacter shibae DFL-12

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 3608624 Dshi_2017 ABC transporter related (RefSeq)

Query= TCDB::G3LHY9
         (356 letters)



>FitnessBrowser__Dino:3608624
          Length = 333

 Score =  203 bits (516), Expect = 6e-57
 Identities = 120/357 (33%), Positives = 199/357 (55%), Gaps = 32/357 (8%)

Query: 1   MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60
           MA +TLD+++ ++G      K   +  V  +  +G    ++GPSGCGK+TLL +++GL  
Sbjct: 1   MATLTLDNVKKSFG------KTDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLET 54

Query: 61  PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120
            S G +  DG+ V  L    R+IA VFQ   +Y  M+V+DN+A+ L+   V +A++  RV
Sbjct: 55  VSSGEVRIDGRVVNTLEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIADRV 114

Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180
               +++ L  +  RK + L+  Q+Q++++GR +VR      LFDEPL+ +D  ++  +R
Sbjct: 115 AVAAKLLQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPA-VFLFDEPLSNLDAKLRVQMR 173

Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240
            ++K L ++ G T +YVTHDQ EA+T A++++VM  G   QIG P E++  P   FV  F
Sbjct: 174 LEIKALQRELGVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGF 233

Query: 241 IGSPGMNFMPARIEGSTVKVGDETLTLEYAPKTSGTAKTELGIRPEFIRLGREG-MPITI 299
           IGSP  NF+PA +                    +G A  ++GIRPE +R+  +G +   +
Sbjct: 234 IGSPPTNFLPADM------------------VRAGPAGQQVGIRPEHLRVAPQGRLEAHV 275

Query: 300 SKVEDIGRQKIVRARFADQPIAIVVPEDADIP-----ADARVTFDPSAISIYADSWR 351
           +  E +G + ++  R A Q   + V +DA  P     A  ++ +D S   ++AD+ R
Sbjct: 276 AYAEALGAETLLHLR-ASQGTTLTVRQDAAAPMPAEGATVQLDWDDSDTMLFADNGR 331


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: 297
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: 333
Length adjustment: 29
Effective length of query: 327
Effective length of database: 304
Effective search space:    99408
Effective search space used:    99408
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