GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rbsA in Sinorhizobium meliloti 1021

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein

Query= TCDB::Q9X051
         (523 letters)



>lcl|FitnessBrowser__Smeli:SM_b20713 SM_b20713 sugar uptake ABC
           transporter ATP-binding protein
          Length = 513

 Score =  441 bits (1134), Expect = e-128
 Identities = 226/500 (45%), Positives = 337/500 (67%), Gaps = 9/500 (1%)

Query: 10  EVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQI 69
           E LL A  + K FPGV+A+++V  ++ +G V AL+GENGAGKSTLMKILAG+Y   +G++
Sbjct: 21  EYLLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEV 80

Query: 70  FLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQ 129
            L G  +R ++P +A ENGIA+I QEL+L+P ++ AENI++ REP N FG +++ +M   
Sbjct: 81  KLRGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHGEMRRM 140

Query: 130 ASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLF 189
            +KLF +L +++DP+ +V  LS + +QMV IAKA+S ++ ++IMDEPTSA+ +RE   LF
Sbjct: 141 TAKLFERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLF 200

Query: 190 NIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRS 249
            IIR L+++G  ++YI+H++ E+FEIAD   V RDG+ +G     E   D ++R+MVGR 
Sbjct: 201 EIIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGRE 260

Query: 250 IDQFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTEL 309
           I Q F KE   I D +  V+ + L  + R      DVSF VR GE+LG+ GLVG+GR+ +
Sbjct: 261 ITQMFPKEEVPIGDVVLSVKNLTLNGVFR------DVSFDVRAGEILGVAGLVGSGRSNV 314

Query: 310 LEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITL 369
            E +FG  P  + G + I GKE+ I S   A+++ +  + EDRK  G +L + +L N+ +
Sbjct: 315 AETLFGVTPA-SSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQI 373

Query: 370 PSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLA 429
             +  K + R  G +  +           KL +KTP+  + VENLSGGNQQKV++ +WL 
Sbjct: 374 AVLQDKFVKR--GFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGRWLL 431

Query: 430 IKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVMSEG 489
             P++L+LDEPTRGIDV AK+EI++L++E+A +G+ V+M+SSE+PE+L MSDRI+VM EG
Sbjct: 432 TNPRILILDEPTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHEG 491

Query: 490 RKTAEFLREEVTEEDLLKAA 509
           R T    R E T+  +++ A
Sbjct: 492 RVTGILDRAEATQIKVMELA 511



 Score =  106 bits (264), Expect = 2e-27
 Identities = 63/232 (27%), Positives = 127/232 (54%), Gaps = 9/232 (3%)

Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVK 342
           +DDV F +++G V  + G  GAG++ L++ + G +    +G+V + G  I++ SP DA++
Sbjct: 39  LDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYP-DQGEVKLRGAGIRLKSPLDALE 97

Query: 343 NGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNI 402
           NGI ++ ++     L+  M+V  NI     + +    +FG +D    + +     E+L I
Sbjct: 98  NGIAMIHQE---LNLMPFMTVAENIW----IRREPKNRFGFVDHGEMRRMTAKLFERLKI 150

Query: 403 KTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVS 462
               P   V +LS  N+Q V +AK ++ +  VL++DEPT  +     + ++++I ++   
Sbjct: 151 DL-DPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFEIIRDLRSQ 209

Query: 463 GMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSV 514
           G+G+V ++ ++ E+  ++D   V  +G+     L  EVT +D+++  + R +
Sbjct: 210 GIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGREI 261


Lambda     K      H
   0.317    0.137    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: 640
Number of extensions: 37
Number of successful extensions: 9
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: 523
Length of database: 513
Length adjustment: 35
Effective length of query: 488
Effective length of database: 478
Effective search space:   233264
Effective search space used:   233264
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 (21.6 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, the preprint on GapMind for carbon sources, 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