GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0548 in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate H281DRAFT_03746 H281DRAFT_03746 carbohydrate ABC transporter membrane protein 1, CUT1 family

Query= reanno::Dino:3607126
         (288 letters)



>FitnessBrowser__Burk376:H281DRAFT_03746
          Length = 296

 Score =  132 bits (333), Expect = 7e-36
 Identities = 82/275 (29%), Positives = 144/275 (52%), Gaps = 8/275 (2%)

Query: 14  IGPAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQAMGRTF 73
           I P+++    +   P+   +W SLH  +     R +F GL+N++T+  D  F  A  RT 
Sbjct: 16  IAPSLVLALFIISYPIFNIVWQSLHEVSRFGAIR-DFTGLQNFYTIFGDPAFLAAARRTI 74

Query: 74  FLLGTALPLQIALGLGIALVLHQPGLTLVKTLARLSLVLPMATTYAVVGLLGQVMFNQKF 133
                 +   + + + +ALVL+Q      + +AR  ++LP + +  +  ++ +  FN  +
Sbjct: 75  VWTVFVVGGTVLISVPVALVLNQDFYG--RGVARTIVMLPWSVSLTMTAVVWRWAFNDDY 132

Query: 134 GVVN---QLLG--GADINWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEVEEA 188
           G+VN   Q LG  G  I+W+  PE AF + I   +    PF   +LL GL+ VPG++ EA
Sbjct: 133 GMVNVTLQRLGLIGGPIHWLATPEFAFPVEIAVGILVSIPFTVTILLGGLSSVPGDIYEA 192

Query: 189 ARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFISLM 248
           AR++  S W   R + LP L P +   ++L        F +++ +T+GGP +ST  +   
Sbjct: 193 ARIDGASAWQQFRKLTLPLLRPFINMTILLNVIYVFNSFPIIWVMTQGGPDNSTHILVTY 252

Query: 249 IQRVGFRGFDQGLASAQAIILLIITIVLAQIYIRV 283
           +  +GFR    G A+A ++I+L++  V +  Y+R+
Sbjct: 253 LYELGFRLGRPGEAAAVSLIMLVMLFVFSMAYLRL 287


Lambda     K      H
   0.329    0.144    0.440 

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: 306
Number of extensions: 19
Number of successful extensions: 3
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: 288
Length of database: 296
Length adjustment: 26
Effective length of query: 262
Effective length of database: 270
Effective search space:    70740
Effective search space used:    70740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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