Alignments for a candidate for nupA in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Rhodobacter viridis JA737

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_110806166.1 C8J30_RS12430 ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_003217355.1:WP_110806166.1
          Length = 530

 Score =  441 bits (1135), Expect = e-128
 Identities = 247/507 (48%), Positives = 329/507 (64%), Gaps = 18/507 (3%)

Query: 6   IEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKIN 65
           IE+R I+K F    AN  I++ +R G IH ++GENGAGKSTLM++L G     +G I I+
Sbjct: 22  IELRGISKSFGAVQANKDISIRVRPGTIHGIVGENGAGKSTLMSILYGFYRADAGEILID 81

Query: 66  GSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGIL---DLKKAGQEI 122
           G    I     + + GIGMV QHF LV  F+V EN+ILG E   +G L    L KA + +
Sbjct: 82  GRPTVIPDSQSAIRAGIGMVFQHFKLVPNFSVLENVILGAE---DGALLRPSLAKARKTL 138

Query: 123 KALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMT 182
             L+  Y L VDP+A + ++SVG QQRVEILK LYR ADILI DEPT VLTP E   L  
Sbjct: 139 ADLARDYELDVDPDALVEELSVGHQQRVEILKALYRHADILILDEPTGVLTPDEADHLFR 198

Query: 183 IMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSV 242
           I++ L  +GK+I+LITHKL EI  + D V+V+RRG+ + TV  + T+ + LAE+MVGR V
Sbjct: 199 ILRGLKAQGKTILLITHKLREIMEITDEVSVMRRGEMVATVTTADTSPEQLAELMVGRKV 258

Query: 243 SFTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQ 302
              + K P  P   +L + DL V +  G+  +KG++L ++AGEI+GIAG+ GNGQSEL+Q
Sbjct: 259 LLHVPKGPANPGREVLRVSDLHVTDALGVERLKGINLTIRAGEILGIAGVAGNGQSELLQ 318

Query: 303 AITGLRK-IKSGHLTIKGQDVTKL------STRKITELSVGHVPEDRHRDGLILELTMAE 355
            + G  K   SG + ++G  +          TR+  ++ + HVPEDRH  GLIL+    E
Sbjct: 319 VLGGFAKGTVSGMIAVEGAQIPAAGKGATGQTRR--QIGISHVPEDRHHLGLILDFAAWE 376

Query: 356 NLALQTYYKAPLSHNGVL--NYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAII 413
           N+A   Y+ AP      L  +   I       M  FDVR  +  +PAK FSGGNQQK ++
Sbjct: 377 NIAF-GYHSAPEYQANALFMDNDAILRDTEGKMDRFDVRPPDPSLPAKSFSGGNQQKIVL 435

Query: 414 AREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIA 473
           ARE++R+P LL+V QPTRG+D+GAIE+IH+R++  RD G AVLLVS ELDEIL+LSDRIA
Sbjct: 436 AREIERNPVLLLVGQPTRGVDIGAIEFIHRRIVELRDAGAAVLLVSVELDEILSLSDRIA 495

Query: 474 VIHDGQIQGIVTPETTNKQELGILMAG 500
           V+ DGQI G   P  TN++ELG+LMAG
Sbjct: 496 VMFDGQIMGERLPAETNERELGLLMAG 522



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 57/233 (24%), Positives = 117/233 (50%), Gaps = 8/233 (3%)

Query: 271 IPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRKI 330
           + A K +S+ V+ G I GI G +G G+S L+  + G  +  +G + I G+      ++  
Sbjct: 34  VQANKDISIRVRPGTIHGIVGENGAGKSTLMSILYGFYRADAGEILIDGRPTVIPDSQSA 93

Query: 331 TELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEFD 390
               +G V +      L+   ++ EN+ L     A L  +     +K  +    L ++++
Sbjct: 94  IRAGIGMVFQHFK---LVPNFSVLENVILGAEDGALLRPS----LAKARKTLADLARDYE 146

Query: 391 VRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERD 450
           +    + +  +  S G+QQ+  I + + R  D+LI+ +PT  L     +++ + L   + 
Sbjct: 147 LDVDPDAL-VEELSVGHQQRVEILKALYRHADILILDEPTGVLTPDEADHLFRILRGLKA 205

Query: 451 EGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGGSI 503
           +GK +LL++ +L EI+ ++D ++V+  G++   VT   T+ ++L  LM G  +
Sbjct: 206 QGKTILLITHKLREIMEITDEVSVMRRGEMVATVTTADTSPEQLAELMVGRKV 258


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: 654
Number of extensions: 29
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 510
Length of database: 530
Length adjustment: 35
Effective length of query: 475
Effective length of database: 495
Effective search space:   235125
Effective search space used:   235125
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)
SQLite3 databases

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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