GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Dechlorosoma suillum PS

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  207 bits (527), Expect = 4e-58
 Identities = 112/294 (38%), Positives = 177/294 (60%), Gaps = 15/294 (5%)

Query: 4   IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63
           I++ ++ KRFG+ VA+DD+SL I   E + L+GPSGCGK+T LR++AG+ET   G +   
Sbjct: 3   IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62

Query: 64  GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLE---EEEGYTSAERDERVVEVAE 120
           G    +   + R +  VFQ YAL+ HM V +N+ FGL     +E    +E  +RV+++  
Sbjct: 63  GSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLS 122

Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180
            + +  L DR P +LSGGQ+QR+AL RA+  +P+V L+DEP   LD K+R E+R  L+ L
Sbjct: 123 LVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRL 182

Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240
            D++ +++V+VTH+Q EA+ +ADR+ VM+ G ++QV SP E Y  P + FV +F+G   +
Sbjct: 183 HDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN--V 240

Query: 241 NLVRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDA 294
           N+   +R    +          E   + V    + V  +RP DI++   A  ++
Sbjct: 241 NVFH-SRVHGAWA---------EVARDDVPAGQEAVAFIRPHDIDIDTVATPES 284


Lambda     K      H
   0.317    0.135    0.386 

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: 311
Number of extensions: 12
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: 383
Length of database: 360
Length adjustment: 30
Effective length of query: 353
Effective length of database: 330
Effective search space:   116490
Effective search space used:   116490
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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