GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Dinoroseobacter shibae DFL-12

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 3610414 Dshi_3795 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__Dino:3610414
          Length = 331

 Score =  258 bits (659), Expect = 1e-73
 Identities = 134/316 (42%), Positives = 205/316 (64%), Gaps = 10/316 (3%)

Query: 13  LLQTVDLKKYFPQG-----KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL 67
           +L   +L K+FP G     +R+++AVD ++ E+  GETLG+VGESGCGKST  R +++LL
Sbjct: 10  VLSAHNLVKHFPLGGWGKNRRVVRAVDDVTFEVAPGETLGVVGESGCGKSTTARLLVQLL 69

Query: 68  RPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIG 127
             D G++ F+G       +  +K +R+ +Q++FQD   SLNP+M++   I     +H + 
Sbjct: 70  GADSGEVRFQGHVAGT--EMPLKEFRRHVQMVFQDSYASLNPRMSMLDAIAFGPTVHGV- 126

Query: 128 TKKERRKRVEELLDMVGIG-REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSA 186
           ++ E ++   +LLD VG+    F   +PHE SGGQ+QR+ IARALA  P+ IV DE VSA
Sbjct: 127 SEAEAQRIARDLLDRVGLDPSRFGPRYPHELSGGQRQRVNIARALAFQPEVIVLDEAVSA 186

Query: 187 LDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFL 246
           LD S++AQ+++LL +++++  ++Y+FI+H+L VV H+S +V VMYLG++ E G   +++ 
Sbjct: 187 LDKSVEAQVLNLLMDLKRERNLTYVFISHDLNVVRHVSDRVMVMYLGEVAEIGPTAEMYA 246

Query: 247 NPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKE 306
           +P HPYTRALL ++P +  D ++     L G+ P+PID P GCRF TRC E    C  + 
Sbjct: 247 DPRHPYTRALLAAMPSLDPD-RRTTEAPLSGDPPNPIDPPSGCRFHTRCAEAFGACSAQR 305

Query: 307 PELTEVEKNHFVSCHL 322
           P    V   H+ SCHL
Sbjct: 306 PSNLRVGAGHYASCHL 321


Lambda     K      H
   0.321    0.142    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: 276
Number of extensions: 14
Number of successful extensions: 4
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: 328
Length of database: 331
Length adjustment: 28
Effective length of query: 300
Effective length of database: 303
Effective search space:    90900
Effective search space used:    90900
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