GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Marivita geojedonensis DPG-138

Align LacK, component of Lactose porter (characterized)
to candidate WP_085638891.1 MGEO_RS13900 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q01937
         (363 letters)



>NCBI__GCF_002115805.1:WP_085638891.1
          Length = 362

 Score =  332 bits (852), Expect = 7e-96
 Identities = 184/357 (51%), Positives = 237/357 (66%), Gaps = 6/357 (1%)

Query: 1   MAEVRLTDIRKSY-GSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGE 59
           MA ++LT++ K+Y G++ V+  +NL++  GE +VFVGPSGCGKSTLLRMIAGLE I+ G 
Sbjct: 1   MANLKLTNVEKTYAGAVNVLNNINLDIEKGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 60

Query: 60  LTIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAK 119
           L I G V+ND+ P+ RGIAMVFQ+YALYPHMTVRENM FAL+ A   + EI+  V  AAK
Sbjct: 61  LEIDGQVVNDMPPAMRGIAMVFQSYALYPHMTVRENMSFALKIAKKPQSEIDAAVERAAK 120

Query: 120 ILELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARL 179
           +L+LD  +DR PKALSGGQRQRVAIGR+IVR P V+LFDEPLSNLDA LRV  R+EIA+L
Sbjct: 121 MLQLDPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQL 180

Query: 180 HKEL-NATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPR 238
            +++  +T++YVTHDQVEAMTLA +IVV+    + QVGAPL LY+ P++ FVA FIGSP 
Sbjct: 181 KEQMPESTMIYVTHDQVEAMTLASRIVVLANKGIAQVGAPLELYERPNSEFVAQFIGSPS 240

Query: 239 MNFLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDT 298
           MN LP  ++G    GQ T          ++    T    G  V VGVRPE F+   SGD 
Sbjct: 241 MNLLPGEIVGT---GQQTTVKMDGGGVAVSDYPTTDADMGLKVNVGVRPEDFV-GTSGDH 296

Query: 299 QLTAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLF 355
                V++ E LG  + +Y         +I +    H    G  + +G S     +F
Sbjct: 297 IFEGRVEITEALGEVTLLYFEKQGDGHAVIGKLPGIHAELRGKTVKLGASPDKVHIF 353


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: 387
Number of extensions: 17
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: 363
Length of database: 362
Length adjustment: 29
Effective length of query: 334
Effective length of database: 333
Effective search space:   111222
Effective search space used:   111222
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