GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03645 in Dinoroseobacter shibae DFL-12

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)

Query= uniprot:D8IZC8
         (344 letters)



>FitnessBrowser__Dino:3609043
          Length = 327

 Score =  193 bits (491), Expect = 5e-54
 Identities = 108/279 (38%), Positives = 167/279 (59%), Gaps = 6/279 (2%)

Query: 60  FASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWA 119
           F +  N  ++    +  ++LA G   VILT  IDLSV + LA++ ++   V++ AAPG  
Sbjct: 31  FIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVAANLALTGMVVSMVNV-AAPGLP 89

Query: 120 IPMF----IFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDI- 174
           I +     I  G ++GM NG +V  L I   VVTLGTMT FRG  +L++DG  V ++++ 
Sbjct: 90  IVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLGTMTIFRGIIFLISDGKWVNSHEMS 149

Query: 175 PSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGL 234
           P+F+     + L +P L W+A+  V+L  +++ +T LG   YA GGN  AA   GI VG 
Sbjct: 150 PAFKAFPRAELLGLPVLSWIAILAVILFTIVMTRTTLGRAFYAAGGNPHAATYAGIDVGK 209

Query: 235 VLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGT 294
              + ++ISG  +GL G +  SR   +  +   G+ELD +AA V+GG S+MGGVG++ G 
Sbjct: 210 TQFWAFTISGALAGLTGYLWVSRFAVSYVDIAGGFELDVVAACVIGGVSIMGGVGTVGGA 269

Query: 295 VVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILD 333
           ++GAL +G++ N L ++ +S FWQ    G  I++AV L+
Sbjct: 270 LLGALFLGIIKNALPVVDISPFWQLAISGGAIIIAVALN 308


Lambda     K      H
   0.324    0.138    0.417 

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: 296
Number of extensions: 18
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: 344
Length of database: 327
Length adjustment: 28
Effective length of query: 316
Effective length of database: 299
Effective search space:    94484
Effective search space used:    94484
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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