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 Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate SMc04127 SMc04127 ABC transporter ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Smeli:SMc04127
          Length = 511

 Score =  471 bits (1212), Expect = e-137
 Identities = 249/502 (49%), Positives = 346/502 (68%), Gaps = 4/502 (0%)

Query: 3   NETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGE 62
           N   I++  + K FG   AN  +NL ++KG IH ++GENGAGKSTLM+IL G  +   GE
Sbjct: 2   NNIAIELRGIDKSFGLVHANRNINLRVRKGTIHGIIGENGAGKSTLMSILYGFYQADNGE 61

Query: 63  VHVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKK 122
           + V GK  +I  P+ A ++GIGMVHQHFMLV+ FTV EN++LG E ++ +N  +  A+++
Sbjct: 62  ILVDGKPVSIRDPNAAISVGIGMVHQHFMLVENFTVLENVMLGAEDSQILNKGIAKARQE 121

Query: 123 ILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELM 182
           +  L + Y L V PDALI ++ VG QQRVEILK LYR ADILI DEPT VLTPAE   L 
Sbjct: 122 LKRLEKEYALEVNPDALIEELPVGLQQRVEILKALYRRADILILDEPTGVLTPAEADHLF 181

Query: 183 QIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRS 242
           +I+  L  +GK+IILITHKL EI A+ D ++V+RRG+ + T    + + +ELAELMVGR 
Sbjct: 182 RILGQLKAQGKTIILITHKLREIMAITDEVSVMRRGEMVATRTTRETSVEELAELMVGRR 241

Query: 243 VSFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELV 302
           V    EK  + P DV L ++ L +K+SRG   V  +S DVRAGEIVG+AG+ GNGQ+EL+
Sbjct: 242 VLLRVEKGESNPGDVKLAVQGLTVKDSRGVTMVDNVSFDVRAGEIVGIAGVAGNGQSELL 301

Query: 303 KAITGLTKVDSGSIKLHNK--DIT-NQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIA 359
           +AI G+ K  SG++ L+ +  D+T N    ++  + + HVPEDRH  GLVL+    EN  
Sbjct: 302 EAIAGIRKAASGTVLLNGRPVDVTGNADAAELRGRGLAHVPEDRHHVGLVLKFEECENAI 361

Query: 360 LQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREID 419
           L  ++ P  +   FL+ + I   A E + ++D+R     +  ++ SGGNQQK ++ARE++
Sbjct: 362 LGYHHDPRFANGMFLNIDAIRKDAEEKIAKYDIRPPNARLRTANFSGGNQQKVVLAREME 421

Query: 420 RNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDG 479
           R+PD+LI+ QPTRG+DVGAIE+IHKR+I+ RD+GKAVL++S ELDEI ++SDRI V+  G
Sbjct: 422 RDPDVLIIGQPTRGVDVGAIEFIHKRIIEMRDQGKAVLLVSVELDEIRSLSDRILVMFAG 481

Query: 480 QIQGIVSPETTTKQELGILMVG 501
           ++ G  SPE  T+ ELG+LM G
Sbjct: 482 RVVGERSPE-ATEGELGLLMAG 502



 Score = 84.7 bits (208), Expect = 7e-21
 Identities = 59/230 (25%), Positives = 117/230 (50%), Gaps = 10/230 (4%)

Query: 276 KGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQS 335
           + ++L VR G I G+ G +G G++ L+  + G  + D+G I +  K ++ + P       
Sbjct: 22  RNINLRVRKGTIHGIIGENGAGKSTLMSILYGFYQADNGEILVDGKPVSIRDPNAAISVG 81

Query: 336 VGHVPEDRHRDGLVLE-MTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRG 394
           +G V    H+  +++E  TV EN+ L       ++K       K     + L +E+ +  
Sbjct: 82  IGMV----HQHFMLVENFTVLENVMLGAEDSQILNK----GIAKARQELKRLEKEYALEV 133

Query: 395 AGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGK 454
             + +    L  G QQ+  I + + R  D+LI+ +PT  L     +++ + L Q + +GK
Sbjct: 134 NPDAL-IEELPVGLQQRVEILKALYRRADILILDEPTGVLTPAEADHLFRILGQLKAQGK 192

Query: 455 AVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNI 504
            +++I+ +L EI+ ++D ++V+  G++    +   T+ +EL  LMVG  +
Sbjct: 193 TIILITHKLREIMAITDEVSVMRRGEMVATRTTRETSVEELAELMVGRRV 242


Lambda     K      H
   0.315    0.135    0.365 

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: 715
Number of extensions: 34
Number of successful extensions: 5
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: 506
Length of database: 511
Length adjustment: 34
Effective length of query: 472
Effective length of database: 477
Effective search space:   225144
Effective search space used:   225144
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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