GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Dechlorosoma suillum PS

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 Dsui_0841 Dsui_0841 ABC-type branched-chain amino acid transport systems, ATPase component

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__PS:Dsui_0841 Dsui_0841 ABC-type branched-chain
           amino acid transport systems, ATPase component
          Length = 251

 Score =  100 bits (248), Expect = 7e-26
 Identities = 69/244 (28%), Positives = 121/244 (49%), Gaps = 13/244 (5%)

Query: 2   KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61
           KP+LEV  +   +  V AL  VS+    GE+  ++G NGAGK+TL+  + G+  P  GE+
Sbjct: 8   KPVLEVSDLCVAYGKVEALHKVSLRIREGEIVTVIGPNGAGKTTLLSALMGLL-PYRGEV 66

Query: 62  IYEGRGVRWN-HPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120
            Y    +  +    E +  G+  V ++  +   +SV +N+ +G       F  Y+   R+
Sbjct: 67  AYVSHNLDAHVEVEERVGQGLTLVPEKRELFAEMSVEDNLLLG------AFHRYRSGLRD 120

Query: 121 AEKFMKEEFGIEIDPEEK----LGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKE 176
             + M+E F +    +E+     G  S   +QM+ + RA+  K K+L+LDEP+  L    
Sbjct: 121 HAQTMEEVFALFPRLKERRTQAAGTLSGGERQMLAMGRALMAKPKLLMLDEPSLGLAPLI 180

Query: 177 TEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEY-IGTDSIENLTKEKIVE 235
            +++F +V  LK+ GV+I+ +        ++ D   VL  GE  +   S E     +++E
Sbjct: 181 IKEIFRIVAELKQTGVSILLVEQNARAALQVADYGYVLETGEVSLEGPSHELADDPRVIE 240

Query: 236 MMVG 239
             +G
Sbjct: 241 TYLG 244



 Score = 99.8 bits (247), Expect = 1e-25
 Identities = 76/239 (31%), Positives = 121/239 (50%), Gaps = 33/239 (13%)

Query: 250 AHEPGEVVLEVKNL-----SGERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPK 304
           AHEP + VLEV +L       E    VS  +R GEI+   G  GAG+T L+  + G  P 
Sbjct: 4   AHEP-KPVLEVSDLCVAYGKVEALHKVSLRIREGEIVTVIGPNGAGKTTLLSALMGLLPY 62

Query: 305 RGGEIYIEGKRVEINHPLDA-------IEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLD 357
           RG   Y+       +H LDA       + QG+ LVPE R+   L   MS+  N+ L +  
Sbjct: 63  RGEVAYV-------SHNLDAHVEVEERVGQGLTLVPEKRE---LFAEMSVEDNLLLGAFH 112

Query: 358 RIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLY---LSGGNQQKVVLAKWLALKPK 414
           R + G        ++ A    + F + P   +R+      LSGG +Q + + + L  KPK
Sbjct: 113 RYRSGL-------RDHAQTMEEVFALFPRLKERRTQAAGTLSGGERQMLAMGRALMAKPK 165

Query: 415 ILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLA 473
           +L+LDEP+ G+      EI+RI+++L + GV ++++       LQ++D   V+  G+++
Sbjct: 166 LLMLDEPSLGLAPLIIKEIFRIVAELKQTGVSILLVEQNARAALQVADYGYVLETGEVS 224


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: 297
Number of extensions: 19
Number of successful extensions: 4
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: 494
Length of database: 251
Length adjustment: 29
Effective length of query: 465
Effective length of database: 222
Effective search space:   103230
Effective search space used:   103230
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: 49 (23.5 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 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