GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Desulfacinum infernum DSM 9756

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_900129305.1:WP_073038605.1
          Length = 368

 Score =  305 bits (782), Expect = 1e-87
 Identities = 168/306 (54%), Positives = 210/306 (68%), Gaps = 12/306 (3%)

Query: 17  KEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRD 76
           K   V+ F L +AD EF+VLVGPSGCGKSTTLRM+AGLE VT G I IG + V HV P+D
Sbjct: 15  KNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEISIGGRVVNHVPPKD 74

Query: 77  RDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKAL 136
           RDIAMVFQ+YALYPHM V +NM F L   G  +DEI++RV +AA  LG+++ L+R+P  L
Sbjct: 75  RDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEILGISDLLQRRPAQL 134

Query: 137 SGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQ 196
           SGGQRQRVAMGRAIVR+PQ FL DEPLSNLDAKLRVQ R ++A L  +L  T VYVTHDQ
Sbjct: 135 SGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLHERLQSTIVYVTHDQ 194

Query: 197 TEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKD--GDA- 253
            EA+T+ DRI V+KDG + QVG P E+Y+RPAN FVAGFIGSP+MN     + +  GD  
Sbjct: 195 IEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMNFLDVRLVEEAGDLW 254

Query: 254 TSGHA-RIKLSPETLAAMTPEDNGRITIGFRPEAL-----EIIPEGESTDLSIPIKLDFV 307
             G + R+K+      A     N  +  G RPE +     + +PEG      +  ++D  
Sbjct: 255 VDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVKERPGDALPEGVE---PLRAEVDVR 311

Query: 308 EELGSD 313
           E +GS+
Sbjct: 312 EPIGSE 317


Lambda     K      H
   0.316    0.135    0.380 

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: 414
Number of extensions: 8
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: 376
Length of database: 368
Length adjustment: 30
Effective length of query: 346
Effective length of database: 338
Effective search space:   116948
Effective search space used:   116948
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 (21.6 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