GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Dechlorosoma suillum PS

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= reanno::Dino:3607124
         (338 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  213 bits (543), Expect = 5e-60
 Identities = 121/279 (43%), Positives = 173/279 (62%), Gaps = 18/279 (6%)

Query: 4   IKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIG 63
           I+I  I K +G   AL D++L I  GE V  +GPSGCGK+TLLR +AG+E    G++   
Sbjct: 3   IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62

Query: 64  GRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNG-----FEPDLRKERIAEAA 118
           G + T +   +R +  VFQ YAL+ HM V EN+ FG++V        E ++RK R+ +  
Sbjct: 63  GSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRK-RVMDLL 121

Query: 119 RVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEG 178
            ++QL+   DR P QLSGGQRQR+A+ RA+   P V L DEP   LD K+R ++R  L  
Sbjct: 122 SLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRR 181

Query: 179 LHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPA 238
           LH ++  + ++VTHDQ EA+ +AD++VV+N+GRIEQVGSP ++Y  P S FV +F+G+  
Sbjct: 182 LHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN-- 239

Query: 239 MNVFSS-------DVGLQDISLDASA-AFVGCRPEHIEI 269
           +NVF S       +V   D+     A AF+  RP  I+I
Sbjct: 240 VNVFHSRVHGAWAEVARDDVPAGQEAVAFI--RPHDIDI 276


Lambda     K      H
   0.320    0.139    0.396 

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: 313
Number of extensions: 11
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: 338
Length of database: 360
Length adjustment: 29
Effective length of query: 309
Effective length of database: 331
Effective search space:   102279
Effective search space used:   102279
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