GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Dechlorosoma suillum PS

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  187 bits (476), Expect = 3e-52
 Identities = 111/311 (35%), Positives = 169/311 (54%), Gaps = 21/311 (6%)

Query: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63
           +++  + K +G+   L +++L I  GEL+  +GPSGCGK+TLLR+IAG+E    G +  +
Sbjct: 3   IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62

Query: 64  GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKS----QAEIDAAVEAAAE 119
           G+    +   +R +  VFQ YAL+ HM V EN++F L++  +     ++EI   V     
Sbjct: 63  GSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLS 122

Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179
            +QL    DR P  LSGGQRQR+A+ R++  +PKV L DEP   LD  +R   R  + +L
Sbjct: 123 LVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRL 182

Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPK 239
            + M  S+ V+VTHDQ EA+ +A R+VV+  G I QVGSP E+Y  P + FV QF+G+  
Sbjct: 183 HDEMHISS-VFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN-- 239

Query: 240 MNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVF 299
           +N+   ++ G  A+                 DD   G      +RP D+           
Sbjct: 240 VNVFHSRVHGAWAEVA--------------RDDVPAGQEAVAFIRPHDIDIDTVATPESL 285

Query: 300 EGKVAITEALG 310
           E KV+  + +G
Sbjct: 286 EAKVSYVQTIG 296


Lambda     K      H
   0.316    0.135    0.379 

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: 288
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 373
Length of database: 360
Length adjustment: 30
Effective length of query: 343
Effective length of database: 330
Effective search space:   113190
Effective search space used:   113190
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