Alignments for a candidate for nupA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Sinorhizobium meliloti 1021

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 SMa2127 SMa2127 ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>FitnessBrowser__Smeli:SMa2127
          Length = 516

 Score =  395 bits (1014), Expect = e-114
 Identities = 213/500 (42%), Positives = 315/500 (63%), Gaps = 2/500 (0%)

Query: 3   QHVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSI 62
           ++++ ++ +TK+F    AND ++LD+RKGEIH L GENGAGKSTL   L G     SG I
Sbjct: 2   ENLLSVQNLTKRFGAVTANDSVDLDVRKGEIHCLFGENGAGKSTLSACLYGYYRADSGVI 61

Query: 63  KINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEI 122
           +  G    ++SP+ + +LGIGMVHQHF+LVE FTV ENII+G+  V   +L    A Q++
Sbjct: 62  RFKGQVAELNSPADALRLGIGMVHQHFVLVENFTVLENIIVGSPDV-GMLLSKSTARQKV 120

Query: 123 KALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMT 182
           + L  + G+ +D + +I  +SVG QQ VEILK LY GA++LI DEPTAVLTP +  +L  
Sbjct: 121 EDLCLRCGIELDLDREIWQLSVGEQQWVEILKALYFGAELLILDEPTAVLTPQQSDQLFV 180

Query: 183 IMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSV 242
           I+  + ++G SIILI+HKL E+   +DRVT++R+GK + TVE + TT++ +  +MVG  V
Sbjct: 181 ILDGMRRQGLSIILISHKLREVMQ-SDRVTILRKGKVVATVETATTTAESITALMVGHQV 239

Query: 243 SFTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQ 302
           +  +      P   +L +   V     G   +  ++  +   EI+G+AG+ GNGQ EL +
Sbjct: 240 TKRVSDRSVAPGREVLVVDHAVAIGEWGEEVLCDINFTIAENEILGLAGVAGNGQKELFE 299

Query: 303 AITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTY 362
            + G+R + SG   + G+ +   ++R++ +  VG VP+DR R+GLI E   AENL L   
Sbjct: 300 VLMGVRTLSSGRFHLNGEAIVAPTSREMLDRGVGLVPDDRFREGLISEFGTAENLVLGWQ 359

Query: 363 YKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPD 422
            K        L+  KIN+  +  ++EF +  A+  +P +  SGGN Q+ I+ARE      
Sbjct: 360 RKPEYRRGPFLDRGKINDLAQRKLEEFRIVAASTDLPVERLSGGNAQRVILAREFLNAKC 419

Query: 423 LLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQG 482
           LL+ +QPTRGLDV A E+++++++ +R EG AV L S ELD++L L DRIAVI  G+I G
Sbjct: 420 LLLANQPTRGLDVAASEFVYEKILEKRAEGFAVFLASEELDDLLRLCDRIAVIFKGKIVG 479

Query: 483 IVTPETTNKQELGILMAGGS 502
            V PE T   ELG++MAG +
Sbjct: 480 TVRPEETTLLELGMMMAGNA 499



 Score = 64.7 bits (156), Expect = 8e-15
 Identities = 63/255 (24%), Positives = 115/255 (45%), Gaps = 19/255 (7%)

Query: 255 ETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGH 314
           E +LS+++L       + A   + L+V+ GEI  + G +G G+S L   + G  +  SG 
Sbjct: 2   ENLLSVQNLTKRFG-AVTANDSVDLDVRKGEIHCLFGENGAGKSTLSACLYGYYRADSGV 60

Query: 315 LTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILE-LTMAENLALQTYYKAPLSHNGVL 373
           +  KGQ     S      L +G V    H+  +++E  T+ EN+ + +     L      
Sbjct: 61  IRFKGQVAELNSPADALRLGIGMV----HQHFVLVENFTVLENIIVGSPDVGMLLSKST- 115

Query: 374 NYSKINEHGRHLMQEFDVRGANELIPAKGF---SGGNQQKAIIAREVDRDPDLLIVSQPT 430
                    R  +++  +R   EL   +     S G QQ   I + +    +LLI+ +PT
Sbjct: 116 --------ARQKVEDLCLRCGIELDLDREIWQLSVGEQQWVEILKALYFGAELLILDEPT 167

Query: 431 RGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTN 490
             L     + +   L   R +G +++L+S +L E++  SDR+ ++  G++   V   TT 
Sbjct: 168 AVLTPQQSDQLFVILDGMRRQGLSIILISHKLREVMQ-SDRVTILRKGKVVATVETATTT 226

Query: 491 KQELGILMAGGSIER 505
            + +  LM G  + +
Sbjct: 227 AESITALMVGHQVTK 241


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: 609
Number of extensions: 31
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: 516
Length adjustment: 35
Effective length of query: 475
Effective length of database: 481
Effective search space:   228475
Effective search space used:   228475
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 17 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 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