Alignments for a candidate for nupA in Lactobacillus shenzhenensis LY-73

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Lactobacillus shenzhenensis LY-73

Align RnsB, 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_022528026.1 L248_RS00360 sugar ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_000469325.1:WP_022528026.1
          Length = 515

 Score =  263 bits (671), Expect = 1e-74
 Identities = 157/495 (31%), Positives = 275/495 (55%), Gaps = 14/495 (2%)

Query: 5   VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64
           ++ +R ++K F      DHI++D++KG +  L+GENGAGKST+M  L G+     G   +
Sbjct: 22  MLSIRGLSKSFGRNRVLDHIDMDVKKGSVMGLMGENGAGKSTMMKCLFGIKTRDEGKFYL 81

Query: 65  NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKN-GILDLKKAGQEIK 123
           +G  V+   P  + + GI MVHQ        +V +N+ LG   V   G++D ++  +E  
Sbjct: 82  DGKEVSFQGPKDALENGIAMVHQELNQALDRSVVDNLFLGRYPVNALGVVDERQMRREAT 141

Query: 124 ALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTI 183
            L  + G+ V+    +  +SV  +Q VEI K +   + +++ DEPT+ L   E+ +L  +
Sbjct: 142 ELFRRLGMTVNLTQPMRKMSVSQRQMVEIAKAISYHSKVIVLDEPTSSLMAQEVDKLFDM 201

Query: 184 MKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSVS 243
           ++ L K+G SII I+HK+DE+  + D V+V+R G  + T + + T   +L + MVGR + 
Sbjct: 202 VRMLKKQGISIIFISHKMDEVFQICDEVSVLRDGHLVMTKKTADTNMNELVKAMVGRPLD 261

Query: 244 FTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQA 303
                      +TIL +  L     +  P ++ ++  V  GEI G+ G+ G G++EL++ 
Sbjct: 262 NRFPPVDNVVGKTILQVSHL---STKFSPYLQDITFSVGQGEIFGLYGLVGAGRTELLET 318

Query: 304 ITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTY- 362
           I G+R   +G +   G+     S ++  +     + E+R  +GL L+ ++  N  +    
Sbjct: 319 IFGVRTRAAGRVYFNGKLANFNSAKEAMDHGFAMITEERKANGLFLKGSLTFNTTITNLD 378

Query: 363 -YKAPLSHNGVLNYSKINEHGRHLMQEFDVR--GANELIPAKGFSGGNQQKAIIAREVDR 419
            YK  ++    L+  K+ +     +Q  + +  G +ELI +   SGGNQQK II + ++R
Sbjct: 379 AYKRGVA----LSEQKMTKATLKEIQVMNTKTMGPDELIAS--LSGGNQQKVIIGKWLER 432

Query: 420 DPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQ 479
            P L ++ +PTRG+DVGA   I++ +I    +GK +++VS E+ EIL +++RI V+ +G+
Sbjct: 433 LPQLFMMDEPTRGIDVGAKYEIYELIIQMAKQGKTIIVVSSEMPEILGITNRIGVMSNGR 492

Query: 480 IQGIVTPETTNKQEL 494
           + GIV  + TN++EL
Sbjct: 493 LAGIVNTKQTNQEEL 507



 Score = 84.0 bits (206), Expect = 1e-20
 Identities = 57/238 (23%), Positives = 114/238 (47%), Gaps = 8/238 (3%)

Query: 5   VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64
           ++++  ++ KF  ++ +  I   + +GEI  L G  GAG++ L+  + G+    +G +  
Sbjct: 275 ILQVSHLSTKFSPYLQD--ITFSVGQGEIFGLYGLVGAGRTELLETIFGVRTRAAGRVYF 332

Query: 65  NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAF---TVTENIILGN-EVVKNGIL--DLKKA 118
           NG     +S  ++   G  M+ +       F   ++T N  + N +  K G+   + K  
Sbjct: 333 NGKLANFNSAKEAMDHGFAMITEERKANGLFLKGSLTFNTTITNLDAYKRGVALSEQKMT 392

Query: 119 GQEIKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQ 178
              +K +       + P+  IA +S G QQ+V I K L R   + + DEPT  +      
Sbjct: 393 KATLKEIQVMNTKTMGPDELIASLSGGNQQKVIIGKWLERLPQLFMMDEPTRGIDVGAKY 452

Query: 179 ELMTIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEM 236
           E+  ++  + K+GK+II+++ ++ EI  + +R+ V+  G+    V    T  ++L  +
Sbjct: 453 EIYELIIQMAKQGKTIIVVSSEMPEILGITNRIGVMSNGRLAGIVNTKQTNQEELLRL 510



 Score = 79.0 bits (193), Expect = 4e-19
 Identities = 52/255 (20%), Positives = 122/255 (47%), Gaps = 8/255 (3%)

Query: 250 PTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRK 309
           P    + +LSI+ L  +  R    +  + ++VK G ++G+ G +G G+S +++ + G++ 
Sbjct: 15  PPVDSDVMLSIRGLSKSFGRN-RVLDHIDMDVKKGSVMGLMGENGAGKSTMMKCLFGIKT 73

Query: 310 IKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSH 369
              G   + G++V+    +   E  +  V ++ ++    L+ ++ +NL L  Y   P++ 
Sbjct: 74  RDEGKFYLDGKEVSFQGPKDALENGIAMVHQELNQ---ALDRSVVDNLFLGRY---PVNA 127

Query: 370 NGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQP 429
            GV++  ++      L +   +   N   P +  S   +Q   IA+ +     ++++ +P
Sbjct: 128 LGVVDERQMRREATELFRRLGMT-VNLTQPMRKMSVSQRQMVEIAKAISYHSKVIVLDEP 186

Query: 430 TRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETT 489
           T  L    ++ +   +   + +G +++ +S ++DE+  + D ++V+ DG +        T
Sbjct: 187 TSSLMAQEVDKLFDMVRMLKKQGISIIFISHKMDEVFQICDEVSVLRDGHLVMTKKTADT 246

Query: 490 NKQELGILMAGGSIE 504
           N  EL   M G  ++
Sbjct: 247 NMNELVKAMVGRPLD 261


Lambda     K      H
   0.315    0.135    0.363 

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: 548
Number of extensions: 21
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 510
Length of database: 515
Length adjustment: 35
Effective length of query: 475
Effective length of database: 480
Effective search space:   228000
Effective search space used:   228000
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: 42 (22.0 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources