GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Desulfovibrio vulgaris Miyazaki F

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 8501090 DvMF_1826 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__Miya:8501090
          Length = 333

 Score =  225 bits (573), Expect = 1e-63
 Identities = 129/332 (38%), Positives = 187/332 (56%), Gaps = 18/332 (5%)

Query: 10  MKPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRP 69
           M+PLL   +L   F      L AV+ +S  + +GE LGLVGESG GKS  G +IL L+  
Sbjct: 1   MQPLLDVSNLTVKFALRDTALTAVNDVSFTLAKGERLGLVGESGAGKSVTGFSILNLVSK 60

Query: 70  DG----GKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124
            G    G + FEGKD+T  + + ++  R  ++ +IFQDP+ +LNP +TVG  + + ++ H
Sbjct: 61  PGFIAGGSVLFEGKDLTRADAETLRDIRGNRISMIFQDPMMTLNPVLTVGTQMIETILAH 120

Query: 125 KIGTKKERRKRVEELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDE 182
           K  T+KE      + L  V I      +  +PHEFSGG +QRI IA AL  +P  I+ DE
Sbjct: 121 KKVTRKEAEAIALDKLRKVYIPSPERRLAQYPHEFSGGMRQRIVIAIALLTSPSLIIADE 180

Query: 183 PVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVD 242
           P +ALDV+IQA+I+DLL E+ Q   +  + I H+L VV  ++ K+AVMY G IVE GD  
Sbjct: 181 PTTALDVTIQAEIMDLLLELCQSEDMGLILITHDLGVVSQVTQKIAVMYAGGIVEMGDTA 240

Query: 243 KIFLNPIHPYTRALLKSVPK-----------IPWDGQKQRFYSLKGELPSPIDLPKGCRF 291
            +   P+HPYTR LL ++P+           +     ++R   + G +PS  D+P+GC F
Sbjct: 241 MVVGEPLHPYTRGLLGALPQCADKADCGLEDVAAPRVRRRLNQIPGSMPSLSDVPRGCPF 300

Query: 292 QTRCTEKKAICFEKEPELTEVEKNHFVSCHLV 323
             RC   + +C    P L         +CH+V
Sbjct: 301 NNRCELCETVCTTTRPLLEVKSDGRMAACHMV 332


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: 280
Number of extensions: 10
Number of successful extensions: 5
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: 333
Length adjustment: 28
Effective length of query: 300
Effective length of database: 305
Effective search space:    91500
Effective search space used:    91500
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