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_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q01937
         (363 letters)



>NCBI__GCF_002115805.1:WP_085638943.1
          Length = 350

 Score =  379 bits (972), Expect = e-110
 Identities = 207/358 (57%), Positives = 251/358 (70%), Gaps = 16/358 (4%)

Query: 1   MAEVRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGEL 60
           M+ V L  + K YG  +VI GV+L+V  GEF VFVGPSGCGKSTLLRM+AGLE+ + G +
Sbjct: 1   MSGVTLESVIKRYGQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEGTI 60

Query: 61  TIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKI 120
            IGG  +  +DPS RG++MVFQTYALYPHMTV ENMGF L+  G A  +I+ +V  A++I
Sbjct: 61  RIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEASRI 120

Query: 121 LELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLH 180
           L+LD  + RKPKALSGGQRQRVAIGRAIVR P+VFLFDEPLSNLDAELRV MRVEIARLH
Sbjct: 121 LKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLH 180

Query: 181 KELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMN 240
           KE+ AT++YVTHDQVEAMTLADKIVV+R G +EQVGAP+ LY DPDN FVAGFIGSP MN
Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPSMN 240

Query: 241 FLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHF-LPAGSGDTQ 299
           F    + G+ +GG+V            +V+     Q G  V +G+RPEH  L  GS    
Sbjct: 241 F----IRGRVQGGEV-----VSDGLVHSVSKTASAQEGQEVLIGLRPEHLELRPGS---- 287

Query: 300 LTAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLFDA 357
            +  VD+ E LG  SY +     GE+II+E E   H    GD + + +     FLFDA
Sbjct: 288 -SHRVDLTESLGGVSYAHLIGPDGEKIIVE-ERGDHRSSDGDMVDLVVDPDHMFLFDA 343


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: 390
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: 363
Length of database: 350
Length adjustment: 29
Effective length of query: 334
Effective length of database: 321
Effective search space:   107214
Effective search space used:   107214
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