GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Sinorhizobium meliloti 1021

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate SMc02325 SMc02325 ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Smeli:SMc02325
          Length = 503

 Score =  415 bits (1067), Expect = e-120
 Identities = 225/499 (45%), Positives = 323/499 (64%), Gaps = 9/499 (1%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           MKP + ++ I K FPGV AL  VS+  YPG V A+VGENGAGKSTL+KI+ G+YQPD G 
Sbjct: 1   MKPAIALEGISKSFPGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGT 60

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYR 119
           I        +     A  AG+  + QE  + D LSVAENIF+G   +     ID+K++  
Sbjct: 61  IRLGDTETTFPTALAASRAGVTAIHQETVLFDELSVAENIFLGHAPRNRFGLIDWKQLNA 120

Query: 120 EAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEK 179
           +A+  +    G + DP  +L    IA + +V IARA+   A+V+I+DEPT++L+ KE  +
Sbjct: 121 DAQALLGRA-GADFDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHE 179

Query: 180 LFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG 239
           L+++++ LK  G A++FISH+ +EIF I D+ +V RDG  IG   I +++++ +V MMVG
Sbjct: 180 LYDLIERLKADGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVG 239

Query: 240 RKLEKFYIKEAHEPGEVVLEVKNLSGER----FENVSFSLRRGEILGFAGLVGAGRTELM 295
           R +   Y K+    G+ VL V   SG R    FE+++F LRRGEILGF GLVGAGR+E M
Sbjct: 240 RAVGSVYPKKEVTIGQPVLTV---SGYRHPTEFEDINFELRRGEILGFYGLVGAGRSEFM 296

Query: 296 ETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPS 355
           +++ G      G + ++G+ + I  P +AI  GI  VPE+R + G I+ M I  NV+LPS
Sbjct: 297 QSLIGITRPSAGAVKLDGEVLVIRSPAEAIRAGIVYVPEERGRQGAIIGMPIFQNVTLPS 356

Query: 356 LDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKI 415
           L    +  F+    E  LA       D+R A  D+ V  LSGGNQQKVV+AKWLA +PK+
Sbjct: 357 LSHTSRSGFLRLAEEFALAREYTSRLDLRAAALDQDVGTLSGGNQQKVVIAKWLATRPKV 416

Query: 416 LILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGI 475
           +ILDEPT+GID+G+KA ++  MS+LA +G+ VIM+SSE+PE++ MSDR+ VM  G++AG 
Sbjct: 417 IILDEPTKGIDIGSKAAVHAFMSELAAQGLSVIMVSSEIPEIMGMSDRVIVMREGRVAGR 476

Query: 476 IDAKEASQEKVMKLAAGLE 494
            +  E + EK+++ AAG+E
Sbjct: 477 YERSELTAEKLVRAAAGIE 495


Lambda     K      H
   0.318    0.138    0.385 

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: 657
Number of extensions: 27
Number of successful extensions: 7
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: 494
Length of database: 503
Length adjustment: 34
Effective length of query: 460
Effective length of database: 469
Effective search space:   215740
Effective search space used:   215740
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