GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupB in Lactobacillus delbrueckii ZN7a-9

Align RnsC, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate WP_002878337.1 B506_RS03300 ABC transporter permease

Query= TCDB::Q8DU38
         (358 letters)



>NCBI__GCF_000387565.1:WP_002878337.1
          Length = 379

 Score =  342 bits (878), Expect = 7e-99
 Identities = 171/352 (48%), Positives = 243/352 (69%), Gaps = 4/352 (1%)

Query: 1   MSKKTQKLVVPLISVILGIILGAIIMMIFGYDPIWAYEGLFQKAFGSLKDIGEIFRAMSP 60
           +S KT++L+VP++SVI G ++GAIIM+++ YDP  AY  +F+ A GS   IGE  R  +P
Sbjct: 4   VSPKTKRLLVPIVSVIAGFLVGAIIMLVWSYDPFQAYSSMFESALGSANGIGETIRNATP 63

Query: 61  LILIALGFAVASRAGFFNIGLSGQAYAGWIAAGWFALANPSLPRPLMILMTVLIGAASGG 120
           LI IA+GF ++S AGFFNIGL GQA AGW+ A W  LA   LP  +++   ++ G+ +G 
Sbjct: 64  LIFIAIGFQISSAAGFFNIGLPGQAQAGWLTAIWIGLAFKGLPVYILLPFEIIAGSLAGA 123

Query: 121 VVGAIPGFLRAYLGTSEVIVTIMMNYIVLYIGNAIIQDGFAKNIMRNSDSSIYVGHNASY 180
           +V  I G+LRAY GT+EVI TIM+NYIVLY+   + QD   K++  ++D++  +G + S 
Sbjct: 124 LVAGIAGWLRAYFGTNEVISTIMLNYIVLYLCQYLHQDVMNKSLRVDTDTTKTIGASGSL 183

Query: 181 QTEWLRALTNNSRMNIGFFLAIIAIVVVWYLLNKTTLGFEIRSVGLNPHASEYAGMSAKR 240
           +  WL  +   SR++ G FLAIIA+V+ W+L+ KTT+GFEI++VGLNP AS YAGMS K+
Sbjct: 184 RIPWLSEMFGGSRISGGIFLAIIALVIFWFLMKKTTVGFEIKAVGLNPFASRYAGMSDKK 243

Query: 241 TIVLSMIISGALAGLGGVVEGLGTFGNVYVQTSSLAIGFDGMAVSLLASNSPIGIFLSAF 300
            I++SM++SGA  GLGGVV+GLGT+ N + QT++L IG+DGM+V+LL   S IGI L++ 
Sbjct: 244 NIIISMLLSGAFCGLGGVVQGLGTYQNYFTQTTTLDIGWDGMSVALLGGMSAIGILLASL 303

Query: 301 LFGALSVGAPGMSISDATHVGTPPELIKVVTALIIFFVGAHYIIEHYIKPRK 352
           LF  L +G  GM     T  G P E++ +V A IIFFV   + +    K +K
Sbjct: 304 LFSILKIGGLGMQ----TAAGIPFEIVSIVIAAIIFFVAISWAVGLLFKEKK 351


Lambda     K      H
   0.325    0.141    0.416 

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: 400
Number of extensions: 19
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: 358
Length of database: 379
Length adjustment: 30
Effective length of query: 328
Effective length of database: 349
Effective search space:   114472
Effective search space used:   114472
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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