GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Dechlorosoma suillum PS

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

Query= reanno::Smeli:SM_b21216
         (360 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  219 bits (559), Expect = 7e-62
 Identities = 122/310 (39%), Positives = 183/310 (59%), Gaps = 18/310 (5%)

Query: 3   ALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILI 62
           ++EIRNI KR+G    L  + +++ +GE + LLG SGCGK+TLL IIAG+     G ++ 
Sbjct: 2   SIEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMF 61

Query: 63  GERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMR----RVPQAEHDKAVRDTA 118
                  +H ++R +  VFQ YAL+ +++V  N+ FGL ++    R  ++E  K V D  
Sbjct: 62  EGSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLL 121

Query: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178
            L+Q++ L DR P+QLSGGQRQR+A+ RAL   P+V L DEP   LD K+R E+R  L+R
Sbjct: 122 SLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRR 181

Query: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPP 238
           LH  +  + V+VTHDQ EA+ +A R+ VM  GRIEQ+ +PDEVY  PA+ +V  F+G+  
Sbjct: 182 LHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN-- 239

Query: 239 MNILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTA 298
           +N+  + +  +G   E   + +P          AG+     IRP  + +   +  + L A
Sbjct: 240 VNVFHSRV--HGAWAEVARDDVP----------AGQEAVAFIRPHDIDIDTVATPESLEA 287

Query: 299 SVEVVELTGP 308
            V  V+  GP
Sbjct: 288 KVSYVQTIGP 297


Lambda     K      H
   0.320    0.136    0.385 

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: 309
Number of extensions: 15
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: 360
Length of database: 360
Length adjustment: 29
Effective length of query: 331
Effective length of database: 331
Effective search space:   109561
Effective search space used:   109561
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