GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05255 in Collimonas arenae Ter10

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_061535474.1 CAter10_RS19695 ABC transporter permease

Query= uniprot:D8J112
         (347 letters)



>NCBI__GCF_001584165.1:WP_061535474.1
          Length = 329

 Score =  200 bits (509), Expect = 4e-56
 Identities = 116/332 (34%), Positives = 183/332 (55%), Gaps = 10/332 (3%)

Query: 13  TTMANTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAV 72
           TT+++++S      R  +   +  L    +LL M + FSF S NF+ +    ++      
Sbjct: 2   TTLSSSSSRSSSLTRSMS-GLKNYLGLIGALLAMCVLFSFLSENFLTLATFTTLSNDIPT 60

Query: 73  NGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWI 132
             V+A+  T+V+I  GIDLSVG++M   A +  + +  WG PL      A+   +L G +
Sbjct: 61  LVVMAVGMTFVLIIGGIDLSVGSVMALAASVLSMAMVRWGWPLFGAGVLAVLVASLCGMV 120

Query: 133 SGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSL 192
           +G++    ++P FI +LG++ + +GL+  ++ +R  Y         I+   L+G      
Sbjct: 121 TGVISVGWRIPSFIVSLGVLEMARGLAYQVTNSRTEYIGSA--VDGISSPILLG------ 172

Query: 193 PIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAI 252
            +  A L   L+ I   ++L KTV GR+   +G+NEEA+RL+G+     KV V+   G +
Sbjct: 173 -MSPAFLSAILIVIIGHLVLTKTVLGRHWIGIGTNEEAVRLAGINPRPSKVLVFALMGLL 231

Query: 253 CGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVN 312
            G+  L   SRL +A P  G G EL  IAAVVIGGTSL GG G+++ T IG  I+SVL  
Sbjct: 232 AGVGALFQVSRLEAADPNGGVGMELQVIAAVVIGGTSLMGGRGSVISTFIGVLIISVLEA 291

Query: 313 GLRIMSVAQEWQTVVTGVIIILAVYLDILRRR 344
           GL  + V++  + +VTG++I+ AV LD  RRR
Sbjct: 292 GLAQVGVSEPMKRIVTGLVIVAAVVLDTYRRR 323


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: 236
Number of extensions: 18
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: 329
Length adjustment: 28
Effective length of query: 319
Effective length of database: 301
Effective search space:    96019
Effective search space used:    96019
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