GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SMc02325 SMc02325 ABC transporter
           ATP-binding protein
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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