GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12640 in Methanoculleus horonobensis T10

Align D-lactate transporter, ATP-binding component (characterized)
to candidate WP_067075333.1 MCUHO_RS06265 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF1248
         (251 letters)



>NCBI__GCF_001602375.1:WP_067075333.1
          Length = 255

 Score = 85.1 bits (209), Expect = 1e-21
 Identities = 65/220 (29%), Positives = 107/220 (48%), Gaps = 13/220 (5%)

Query: 3   ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62
           ++EV++V  R  G   L DVNL+V ++  +AIIGPNG GK+TLL  ++G L P  G+V  
Sbjct: 5   VIEVEDVRVRLRGHTVLEDVNLTVHQDDFYAIIGPNGGGKTTLLRVILGLLQPSRGTVRI 64

Query: 63  DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQ 122
            G    G       ++G    F+T +    ++V E ++    + R G   +  I    G 
Sbjct: 65  LG----GTGAAARKELGYVPQFRTFDFEYPITVREMIL----SGRLG--HITRIPRRYGA 114

Query: 123 RDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARA 182
            D   + E  L  M +AD        +S G+++R  I   L  +P++LLLDEPT  +   
Sbjct: 115 ED-HARTEEALRMMGIADLADRQIRDLSGGEQQRAIIARALVGDPKVLLLDEPTVYVDAP 173

Query: 183 DTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVL 222
                  +L +++    + I ++ HD+ V+     R+  L
Sbjct: 174 TAAQFYSILDRLRER--MAIVLVTHDIGVIPEHVTRVACL 211


Lambda     K      H
   0.318    0.135    0.379 

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: 170
Number of extensions: 7
Number of successful extensions: 2
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: 251
Length of database: 255
Length adjustment: 24
Effective length of query: 227
Effective length of database: 231
Effective search space:    52437
Effective search space used:    52437
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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