GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01113 in Sinorhizobium meliloti 1021

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate SM_b21344 SM_b21344 sugar uptake ABC transporter ATP-binding protein

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__Smeli:SM_b21344
          Length = 497

 Score =  328 bits (841), Expect = 3e-94
 Identities = 193/499 (38%), Positives = 286/499 (57%), Gaps = 13/499 (2%)

Query: 16  LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75
           L + G+ K F G+ ALR  SL     ++  L+G+NG GKSTLIKI++GA   DEG +V  
Sbjct: 3   LSMQGICKSFNGIPALRAASLEVGEAEVMALVGQNGAGKSTLIKILTGAYRRDEGAVVFA 62

Query: 76  GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135
           G   +     E+ A GI T+YQ+++L P  SVAEN+ L+      E R     DRR +  
Sbjct: 63  GEGVSFSMPAESQARGIATIYQEINLAPQRSVAENIYLS-----REPRRFGLIDRRAMRD 117

Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195
            AA  L A  L  + +     +     ATRQ+VAIARA+  +A+ VIMDEPT+SL ++EV
Sbjct: 118 GAAAVLRAFNLEIDVDQP---VAGFSAATRQMVAIARAVTQKARLVIMDEPTSSLDEREV 174

Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255
             L   +  L+  GV+V+F+ H+L+E Y I   V ++RDG+ +A   +A+  K  +   M
Sbjct: 175 GILFDTIRTLKRGGVSVVFIGHRLEELYRICDRVTIMRDGKTVATAAMADMPKLALVRHM 234

Query: 256 TGRHLSN----ERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRN 311
            G+ L+      +  +    + + L VR      +  DVS  +  GEI G+ GLL SGR 
Sbjct: 235 LGKELAAFEAIAKDADEGAQRPVRLSVRNAGAGVRVRDVSLTVREGEISGLAGLLGSGRT 294

Query: 312 ELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVI 371
           E A  + G    Q G++  +G+  A R P+DA    IG V EDR  +G+  D  IR+N+ 
Sbjct: 295 ETANLIFGADRLQRGEIRYNGEARAYRQPADAIADGIGLVAEDRKVDGIIPDMSIRENMT 354

Query: 372 TAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAI 431
            A++  L  R G +DR R   + E+ +  L I     D+P++ LSGGNQQ+VL+GRWL  
Sbjct: 355 LALLPKLA-RAGIVDRARQDEIVERYITALAIKCTSPDQPIKELSGGNQQKVLLGRWLCT 413

Query: 432 DPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGH 491
           DP++LI+  PT G+D+G+K  I R+++RL+  G+G+++IS +L ELL   DR+ ++  G 
Sbjct: 414 DPKLLIVDEPTRGIDIGAKSEILRLLRRLADEGLGVLMISSELEELLAAADRVTVLSDGT 473

Query: 492 VSAEYRADELSEADLYHAL 510
             A     ELSEA L+ A+
Sbjct: 474 SVAVLPRKELSEAALFAAM 492


Lambda     K      H
   0.319    0.135    0.376 

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: 582
Number of extensions: 27
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 515
Length of database: 497
Length adjustment: 34
Effective length of query: 481
Effective length of database: 463
Effective search space:   222703
Effective search space used:   222703
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

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

Links

Downloads

Related tools

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:

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:

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:

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:

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