GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dino:3610414 Dshi_3795 oligopeptide/dipeptide
           ABC transporter, ATPase subunit (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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