GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05255 in Collimonas pratensis Ter91

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_061946568.1 CPter91_RS23415 ABC transporter permease

Query= uniprot:D8J112
         (347 letters)



>NCBI__GCF_001584185.1:WP_061946568.1
          Length = 333

 Score =  194 bits (492), Expect = 4e-54
 Identities = 114/335 (34%), Positives = 179/335 (53%), Gaps = 12/335 (3%)

Query: 13  TTMANTASAQGLRARLFNPAA---RQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQS 69
           TT + ++S    R   FN +    +  L    +LL M   FS  S NF+      ++   
Sbjct: 2   TTSSRSSSRLSSRWSSFNGSISGLKNYLGLIGALLAMCALFSVLSENFLTAATFTTLSND 61

Query: 70  TAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALS 129
                V+A+  T+V+I  GIDLSVG++M   A +  + +  WG PL      A+   +L 
Sbjct: 62  IPTLVVMAVGMTFVLIIGGIDLSVGSVMALAASVLSMAMVRWGWPLFTAGILAMLVASLC 121

Query: 130 GWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLI 189
           G ++G++    ++P FI +LG++ + +GL+  ++ +R  Y         I+   L G   
Sbjct: 122 GMVTGLISVGWRIPSFIVSLGVLEMARGLAYQVTNSRTEYIGSA--VDGISSPILFG--- 176

Query: 190 PSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFS 249
               +  A +   ++ I   ++L KTV GR+   +G+NEEA+RL+G+     KV V+   
Sbjct: 177 ----MSPAFISAIVIVIVGHLVLTKTVLGRHWIGIGTNEEAVRLAGINPRPPKVLVFALM 232

Query: 250 GAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSV 309
           G + G+  L   SRL +A P  G G EL  IAAVVIGGTSL GG G+++ T IG  I+SV
Sbjct: 233 GLLAGVGALFQVSRLEAADPNGGVGMELQVIAAVVIGGTSLMGGRGSVISTFIGVLIISV 292

Query: 310 LVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRR 344
           L  GL  + V++  + ++TG++I+ AV LD  RRR
Sbjct: 293 LEAGLAQVGVSEPMKRIITGLVIVAAVVLDTYRRR 327


Lambda     K      H
   0.326    0.139    0.398 

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: 247
Number of extensions: 14
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: 347
Length of database: 333
Length adjustment: 28
Effective length of query: 319
Effective length of database: 305
Effective search space:    97295
Effective search space used:    97295
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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