GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Luteipulveratus mongoliensis MN07-A0370

Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate WP_052594234.1 VV02_RS19465 sugar ABC transporter permease

Query= reanno::Phaeo:GFF1304
         (288 letters)



>NCBI__GCF_001190945.1:WP_052594234.1
          Length = 310

 Score =  122 bits (305), Expect = 1e-32
 Identities = 90/293 (30%), Positives = 153/293 (52%), Gaps = 21/293 (7%)

Query: 5   HSRSAAR-IMMAPAVILLLGWMLVPLTMTLYFSFKKYLPLRG---GDLGWVGFDNYARFL 60
           H R+AAR I + PAV++L  ++  P+  ++Y +F     LRG    +  +VG DN+    
Sbjct: 22  HRRTAARGIPLLPAVLVLGAFLAGPVLYSIYLAFTNRA-LRGEGASETSFVGLDNFRTAF 80

Query: 61  SSSAFWPSVQATLV--IVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTV 118
            +S FW +V  TLV  +V G++   V LG+ LALLL +     G++   ++   +++P V
Sbjct: 81  DTSEFWNAVGLTLVFTVVSGIIGQNV-LGMALALLLRRSATWVGVLTGTIVVGAWIVPEV 139

Query: 119 SA-LVWKNMFMD--PVNGL--FAHLWKAFGAEPVSWLSEASLQSIILIVSWQWLPFATLI 173
            A  +W     D   +NG+  F HL          WL  + + ++     W+   FA L 
Sbjct: 140 VAGYLWYTFLSDGGSLNGILGFLHLPNQ------DWLIASPIIAVSFANIWRGTAFAMLT 193

Query: 174 LLTAIQSLDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVT 233
              A+  +  E  E+A++DGA PV RF  ITLP L R+I   +++ T+  LS+F  I+V 
Sbjct: 194 YSAALSQVSPELDESAQIDGAGPVRRFWSITLPLLRRSIMTCLMLTTLQTLSVFGLIYVM 253

Query: 234 TQGSFG--TKTLTYLIYQRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGK 284
           T G  G  ++TL   +Y++      +G G+A  +  +++  + A+  +R++ K
Sbjct: 254 TGGGPGIQSQTLPLYMYEQAFSYGQLGYGTAVALMLLLVGGLAALAYLRVLPK 306


Lambda     K      H
   0.328    0.140    0.430 

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: 256
Number of extensions: 18
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: 288
Length of database: 310
Length adjustment: 27
Effective length of query: 261
Effective length of database: 283
Effective search space:    73863
Effective search space used:    73863
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 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