GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Sinorhizobium meliloti 1021

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate SMc02325 SMc02325 ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__Smeli:SMc02325
          Length = 503

 Score =  439 bits (1130), Expect = e-128
 Identities = 229/494 (46%), Positives = 328/494 (66%), Gaps = 2/494 (0%)

Query: 1   MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60
           M+  + L+GI K+FPGV+ALS  +L +YPG V ALVGENGAGKST++K+LTGIY  DAGT
Sbjct: 1   MKPAIALEGISKSFPGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGT 60

Query: 61  LLWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120
           +     ETTF    ++  AG+  IHQE  L  +L++AENIFLG    NRFG IDWK + A
Sbjct: 61  IRLGDTETTFPTALAASRAGVTAIHQETVLFDELSVAENIFLGHAPRNRFGLIDWKQLNA 120

Query: 121 EADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180
           +A  LL +    F     + DL I  + +V IA+ LS +++V+IMDEPT AL+  E   L
Sbjct: 121 DAQALLGRAGADFDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHEL 180

Query: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240
           + +I  LK+ G+ +++ISH+  EIF I D  TVFRDG  I E  +A +++D L+ MMVGR
Sbjct: 181 YDLIERLKADGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVGR 240

Query: 241 KLEDQYPHLDKAPGDIRLKVDNLCGP-GVNDVSFTLRKGEILGVSGLMGAGRTELMKVLY 299
            +   YP  +   G   L V     P    D++F LR+GEILG  GL+GAGR+E M+ L 
Sbjct: 241 AVGSVYPKKEVTIGQPVLTVSGYRHPTEFEDINFELRRGEILGFYGLVGAGRSEFMQSLI 300

Query: 300 GALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYF 359
           G    ++G V LDG  +V RSP + +  GIVY+ E+R R G ++GM + +N++L +L + 
Sbjct: 301 GITRPSAGAVKLDGEVLVIRSPAEAIRAGIVYVPEERGRQGAIIGMPIFQNVTLPSLSHT 360

Query: 360 SRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLIL 419
           SR+ G L+ A+E     ++    +++  +++Q +G LSGGNQQKV IA+ L TRPKV+IL
Sbjct: 361 SRS-GFLRLAEEFALAREYTSRLDLRAAALDQDVGTLSGGNQQKVVIAKWLATRPKVIIL 419

Query: 420 DEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTR 479
           DEPT+G+D+G+K  ++  +++  A GLS+I+VSSE+PE++GMSDR+IVM EG ++G + R
Sbjct: 420 DEPTKGIDIGSKAAVHAFMSELAAQGLSVIMVSSEIPEIMGMSDRVIVMREGRVAGRYER 479

Query: 480 EQATQEVLMAAAVG 493
            + T E L+ AA G
Sbjct: 480 SELTAEKLVRAAAG 493



 Score = 80.1 bits (196), Expect = 2e-19
 Identities = 69/234 (29%), Positives = 109/234 (46%), Gaps = 13/234 (5%)

Query: 266 PGV---NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322
           PGV   +DVS  L  G +  + G  GAG++ L+K+L G     +G + L   E    +  
Sbjct: 15  PGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGTIRLGDTETTFPTAL 74

Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLF 382
                G+  I ++     L   +SV EN+ L    +  R    L   D +Q  +D   L 
Sbjct: 75  AASRAGVTAIHQETV---LFDELSVAENIFLG---HAPRNRFGL--IDWKQLNADAQALL 126

Query: 383 NVKTPSMEQAIGLLSGGNQQK--VAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQ 440
                  +  I L   G  +K  VAIAR L    +V+I+DEPT  +      E+Y LI +
Sbjct: 127 GRAGADFDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHELYDLIER 186

Query: 441 FKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
            KADG +++ +S +  E+  ++DR  V  +G + GE      +Q+ L+   VG+
Sbjct: 187 LKADGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVGR 240


Lambda     K      H
   0.318    0.137    0.380 

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: 674
Number of extensions: 28
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: 501
Length of database: 503
Length adjustment: 34
Effective length of query: 467
Effective length of database: 469
Effective search space:   219023
Effective search space used:   219023
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: 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 (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