GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Dechlorosoma suillum PS

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

Query= reanno::Smeli:SM_b21106
         (365 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  207 bits (528), Expect = 3e-58
 Identities = 101/237 (42%), Positives = 153/237 (64%), Gaps = 4/237 (1%)

Query: 4   VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63
           + ++ + KR+G    +  + L +   E +AL+GPSGCGK+T LR+IAG+E    G +   
Sbjct: 3   IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62

Query: 64  GRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGR---PAE-EIKTRVAEAAA 119
           G +   L  R R +  VFQ YAL+ HM V EN+ F L++  R   P E EI+ RV +  +
Sbjct: 63  GSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLS 122

Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179
           ++ L  L +R P+QLSGGQRQR+A+ RA+  +P V L DEP   LD K+R ++R  +++L
Sbjct: 123 LVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRL 182

Query: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGS 236
           H  M  + ++VTHDQ EA+ ++DR+V+M  G IEQVG+P++V+  PA+ FV  F+G+
Sbjct: 183 HDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN 239



 Score = 25.0 bits (53), Expect = 0.003
 Identities = 17/64 (26%), Positives = 25/64 (39%)

Query: 158 DEPLSNLDAKLRTQVRTEIKKLHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGT 217
           DE  SN  +    Q    +   H+R+      V  D V A   +   +   D  I+ V T
Sbjct: 222 DEVYSNPASPFVYQFLGNVNVFHSRVHGAWAEVARDDVPAGQEAVAFIRPHDIDIDTVAT 281

Query: 218 PEDV 221
           PE +
Sbjct: 282 PESL 285


Lambda     K      H
   0.320    0.137    0.397 

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: 331
Number of extensions: 10
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 365
Length of database: 360
Length adjustment: 29
Effective length of query: 336
Effective length of database: 331
Effective search space:   111216
Effective search space used:   111216
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 Apr 09 2024. 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