GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Methanobacterium veterum MK4

Align LacK, component of Lactose porter (characterized)
to candidate WP_048081463.1 EJ01_RS05505 molybdenum ABC transporter ATP-binding protein

Query= TCDB::Q01937
         (363 letters)



>NCBI__GCF_000745485.1:WP_048081463.1
          Length = 361

 Score =  169 bits (427), Expect = 1e-46
 Identities = 89/273 (32%), Positives = 151/273 (55%), Gaps = 7/273 (2%)

Query: 19  IKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGELTIGGTVMNDVDPSKRGIA 78
           +  VNL +    ++V +GP+G GKS LL  IAG      G++ + G  + +++P  RGI+
Sbjct: 17  LDNVNLSLDKNSYMVIIGPTGSGKSVLLETIAGFYRAEKGKIFLEGKEITELNPENRGIS 76

Query: 79  MVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKILELDALMDRKPKALSGGQ 138
           +V+Q Y L+PHM + EN+ + L+     ++ I+ +V   AK+L++D L+ R P  LSGG+
Sbjct: 77  IVYQDYVLFPHMNIFENISYGLKKKTKDEEIIKSKVLKMAKLLKIDHLLHRNPDTLSGGE 136

Query: 139 RQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLHKELNATIVYVTHDQVEAM 198
           +QR AI R+++ +P + L DEP S +D     ++   I  +  +   T ++VTH+  +  
Sbjct: 137 KQRTAIARSLIVEPRILLMDEPFSAVDVSTHAYLTKLIKNVIADYETTCIHVTHNFNDVW 196

Query: 199 TLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMNFLPAVVIGQAEGGQVTVA 258
            LADK+ VM+ G + Q   P  ++  P + FVA F+G    N     +I + EG    + 
Sbjct: 197 NLADKVAVMKEGKILQQDIPTEVFSKPSHNFVADFVGI--HNIFEGEII-EKEGSLTKIK 253

Query: 259 LKARPDTQLTVACATPPQGGDAVTVGVRPEHFL 291
           L    D+ L V  +   +    + VG+RPE+ +
Sbjct: 254 L----DSDLIVYSSDSSEDSGKILVGIRPENVI 282


Lambda     K      H
   0.320    0.137    0.390 

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: 243
Number of extensions: 6
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: 363
Length of database: 361
Length adjustment: 29
Effective length of query: 334
Effective length of database: 332
Effective search space:   110888
Effective search space used:   110888
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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