GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 in Sinorhizobium meliloti 1021

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__Smeli:SM_b20713
          Length = 513

 Score =  483 bits (1244), Expect = e-141
 Identities = 258/511 (50%), Positives = 351/511 (68%), Gaps = 9/511 (1%)

Query: 9   TTGVAASSSSSVP----VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTL 64
           TT  A  +S +VP    ++    V K FPGV+ALD+ +F+L  G VHALMGENGAGKSTL
Sbjct: 6   TTMAAVRASGAVPKSEYLLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTL 65

Query: 65  MKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREP 124
           MKIL+G+Y  D G++ L G  + +  P  A   GI +IHQELNLM  ++ A+NI+I REP
Sbjct: 66  MKILAGIYYPDQGEVKLRGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREP 125

Query: 125 RKAMGLFIDEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIM 184
           +   G F+D  E+ R  A +F R+++D+DP   V  L+VA +QMVEIAKA+S++S VLIM
Sbjct: 126 KNRFG-FVDHGEMRRMTAKLFERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIM 184

Query: 185 DEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPM 244
           DEPT+AL   E+A LF IIRDL++QG+GIVYI+HKM+EL +IAD  SV RDGKYI T   
Sbjct: 185 DEPTSALTEREVAHLFEIIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLS 244

Query: 245 QETSMDTIISMMVGRALDGEQRIP-PDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILG 303
            E + D II MMVGR +   Q  P  +    DVVL V+ L      RDVSF +R GEILG
Sbjct: 245 NEVTRDDIIRMMVGREI--TQMFPKEEVPIGDVVLSVKNLTLNGVFRDVSFDVRAGEILG 302

Query: 304 FAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLA 363
            AGL+G+GR+ VA  +FG  P  +G I I G + VI S   A+ H + +L+EDRK  G  
Sbjct: 303 VAGLVGSGRSNVAETLFGVTPASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCL 362

Query: 364 VGMDVQANIALSSM-GRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQ 422
           + +D+  N+ ++ +  +F + GF+ +R +  A +   R+L +KTP+++++   LSGGNQQ
Sbjct: 363 LILDILENMQIAVLQDKFVKRGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQ 422

Query: 423 KIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMS 482
           K++I +WLL +  IL  DEPTRGIDVGAK+EI++L+  LA  G A++MISSE+PEVL MS
Sbjct: 423 KVLIGRWLLTNPRILILDEPTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMS 482

Query: 483 HRVLVMCEGRITGELARADATQEKIMQLATQ 513
            R++VM EGR+TG L RA+ATQ K+M+LA +
Sbjct: 483 DRIMVMHEGRVTGILDRAEATQIKVMELAAR 513



 Score = 91.3 bits (225), Expect = 8e-23
 Identities = 63/229 (27%), Positives = 115/229 (50%), Gaps = 7/229 (3%)

Query: 288 AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVA 347
           A+ DV F L++G +    G  GAG++ + + + G    + GE+ + G    +KSP DA+ 
Sbjct: 38  ALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKLRGAGIRLKSPLDALE 97

Query: 348 HGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIRE-AAQMYVRQLAIKT 406
           +GI  + ++     L   M V  NI +    +  R GF+D   +R   A+++ R      
Sbjct: 98  NGIAMIHQE---LNLMPFMTVAENIWIRREPK-NRFGFVDHGEMRRMTAKLFERLKIDLD 153

Query: 407 PSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGK 466
           P +E   R LS  N+Q + IAK +  + D+L  DEPT  +     + +++++  L  QG 
Sbjct: 154 PEIE--VRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFEIIRDLRSQGI 211

Query: 467 AIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRE 515
            IV I+ ++ E+  ++    V  +G+  G     + T++ I+++   RE
Sbjct: 212 GIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGRE 260


Lambda     K      H
   0.320    0.135    0.372 

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: 641
Number of extensions: 25
Number of successful extensions: 8
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: 520
Length of database: 513
Length adjustment: 35
Effective length of query: 485
Effective length of database: 478
Effective search space:   231830
Effective search space used:   231830
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 (21.8 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 (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