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_110806491.1 C8J30_RS14105 sugar ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_003217355.1:WP_110806491.1
          Length = 513

 Score =  308 bits (789), Expect = 3e-88
 Identities = 166/484 (34%), Positives = 276/484 (57%), Gaps = 8/484 (1%)

Query: 3   QHVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSI 62
           + ++E+  + K+F   VA D++ L +R G +HAL+GENGAGKSTLM ++AG+  P  G +
Sbjct: 20  EFILEVDGVRKEFPGVVALDNVQLKIRPGSVHALMGENGAGKSTLMKIIAGVYNPDRGEV 79

Query: 63  KINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKN-GILDLKKAGQE 121
           +  G  + I +P  +   GI M+HQ   L+   TV EN+ +  E     G++D  + G  
Sbjct: 80  RFAGEKLVIRTPIDALNCGIAMIHQELNLMNTMTVAENVWIRREPKGAFGLIDHARMGTM 139

Query: 122 IKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELM 181
              L     + +DP A + D++V  +Q +EI K +   +D+LI DEPT+ +T +E++ L 
Sbjct: 140 TAELFASLNIHLDPLAIVGDLTVAQKQMIEIAKAVSYNSDVLIMDEPTSAITETEVEHLF 199

Query: 182 TIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRS 241
            I++ L   G  I+ ITHK++EI  +AD +TV R GK I TV  S  T  D+  MMVGR 
Sbjct: 200 AIIRDLRARGVGIVYITHKMNEIFEIADELTVFRDGKYISTVPASEVTRDDIIRMMVGRE 259

Query: 242 VSFTIEKTPTKPKETILSIKDLVVNENRGIPAI-KGLSLEVKAGEIIGIAGIDGNGQSEL 300
           ++    K      + IL +++L       +P +   +S +++ GEI+G+AG+ G+G+S +
Sbjct: 260 ITEMFPKVDCPIGDVILDVQNL------SLPGVFDNISFKLRKGEILGVAGLVGSGRSNV 313

Query: 301 VQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQ 360
            +A+ G+   ++G + I G+ V   S +   +  +  + EDR   G  L L   EN+ + 
Sbjct: 314 AEALFGVHPAETGDIWIDGEHVVMTSPQVAMDHGLAFLTEDRKETGCFLVLDCLENMQMA 373

Query: 361 TYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRD 420
              +  ++  G +  +++    +    +  V+  N     +  SGGNQQK +IAR +  +
Sbjct: 374 LITRDKVNGAGFVQQAEVTRLVQEYSAKLRVKTPNLAERVENLSGGNQQKLLIARWLLTN 433

Query: 421 PDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQI 480
           P +LI+ +PTRG+DVGA   IH+ + A   +G AVL++S EL E+L +SDRI V+H+G++
Sbjct: 434 PRILILDEPTRGIDVGAKSEIHRLITALAGQGVAVLMISSELPEVLGMSDRIMVMHEGRV 493

Query: 481 QGIV 484
            G +
Sbjct: 494 SGFL 497



 Score = 68.6 bits (166), Expect = 5e-16
 Identities = 50/249 (20%), Positives = 117/249 (46%), Gaps = 8/249 (3%)

Query: 255 ETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGH 314
           E IL + D V  E  G+ A+  + L+++ G +  + G +G G+S L++ I G+     G 
Sbjct: 20  EFILEV-DGVRKEFPGVVALDNVQLKIRPGSVHALMGENGAGKSTLMKIIAGVYNPDRGE 78

Query: 315 LTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLN 374
           +   G+ +   +        +  + ++ +   L+  +T+AEN+ ++   + P    G+++
Sbjct: 79  VRFAGEKLVIRTPIDALNCGIAMIHQELN---LMNTMTVAENVWIR---REPKGAFGLID 132

Query: 375 YSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLD 434
           ++++      L    ++   + L      +   +Q   IA+ V  + D+LI+ +PT  + 
Sbjct: 133 HARMGTMTAELFASLNIH-LDPLAIVGDLTVAQKQMIEIAKAVSYNSDVLIMDEPTSAIT 191

Query: 435 VGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQEL 494
              +E++   +   R  G  ++ ++ +++EI  ++D + V  DG+    V      + ++
Sbjct: 192 ETEVEHLFAIIRDLRARGVGIVYITHKMNEIFEIADELTVFRDGKYISTVPASEVTRDDI 251

Query: 495 GILMAGGSI 503
             +M G  I
Sbjct: 252 IRMMVGREI 260


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: 546
Number of extensions: 25
Number of successful extensions: 6
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: 513
Length adjustment: 35
Effective length of query: 475
Effective length of database: 478
Effective search space:   227050
Effective search space used:   227050
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