GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Desulfacinum infernum DSM 9756

Align LacK, component of Lactose porter (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q01937
         (363 letters)



>NCBI__GCF_900129305.1:WP_073038605.1
          Length = 368

 Score =  313 bits (801), Expect = 6e-90
 Identities = 183/363 (50%), Positives = 226/363 (62%), Gaps = 12/363 (3%)

Query: 1   MAEVRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGEL 60
           MAE++L  + K +    V++   L V+  EFVV VGPSGCGKST LRMIAGLE+++SGE+
Sbjct: 1   MAEIKLDQVNKRFKKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEI 60

Query: 61  TIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKI 120
           +IGG V+N V P  R IAMVFQ+YALYPHM V +NM F L   G+ +DEI+RRV  AA+I
Sbjct: 61  SIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEI 120

Query: 121 LELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLH 180
           L +  L+ R+P  LSGGQRQRVA+GRAIVR P  FLFDEPLSNLDA+LRV MR E+A+LH
Sbjct: 121 LGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLH 180

Query: 181 KELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMN 240
           + L +TIVYVTHDQ+EAMTLAD+IVVM+ G + QVG PL +Y+ P N FVAGFIGSP MN
Sbjct: 181 ERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMN 240

Query: 241 FLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHF-------LPA 293
           FL   ++ +A G         R       A A        V  G+RPE         LP 
Sbjct: 241 FLDVRLVEEA-GDLWVDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVKERPGDALP- 298

Query: 294 GSGDTQLTAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSF 353
             G   L A VDV E +G  S V      G      +       R  D I + ++     
Sbjct: 299 -EGVEPLRAEVDVREPIG--SEVIITATVGSHAFTARISPNVAVRVHDPIDLAVNMNKMH 355

Query: 354 LFD 356
           LFD
Sbjct: 356 LFD 358


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: 375
Number of extensions: 12
Number of successful extensions: 1
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: 368
Length adjustment: 30
Effective length of query: 333
Effective length of database: 338
Effective search space:   112554
Effective search space used:   112554
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 Apr 09 2024. 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