GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SM_b21344 SM_b21344 sugar uptake ABC
           transporter ATP-binding protein
          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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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