GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Oscillibacter ruminantium GH1

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 WP_040659554.1 ON16_RS03945 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_000307265.1:WP_040659554.1
          Length = 511

 Score =  329 bits (843), Expect = 2e-94
 Identities = 190/497 (38%), Positives = 294/497 (59%), Gaps = 14/497 (2%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +L V++I K F     LKG+S++  PGE+ A+VG NGAGKSTLMKII G+Y  D G+I  
Sbjct: 13  LLSVQNIRKSFGLNAVLKGISLDVAPGEILALVGGNGAGKSTLMKIIMGIYTQDGGDIYI 72

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEK 123
           +G  V  N P++A+  GI  V QE  +  N++V ENI +G  + +       +++RE   
Sbjct: 73  KGEHVVLNKPAQALAKGIYMVPQEPLLFPNMTVEENITIGFSQNKA------ELHRELVA 126

Query: 124 FMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEV 183
            M +E G  ++   +    SIA QQ+VEI R + + A++LILDEPTS+LT  E E LF+ 
Sbjct: 127 TM-DEIGWHLNLTRRASSLSIAEQQLVEILRGLLRHAQILILDEPTSALTFDEVESLFKC 185

Query: 184 VKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLE 243
           V+ L+ KG+ II+I+HRL E+FE+   V+++RDG      ++   T+E +V  ++   ++
Sbjct: 186 VRDLQSKGIGIIYITHRLTEVFELATHVAIMRDGIIAVKGAVSGFTREDLVRGLLPPDMD 245

Query: 244 KFYIKEAHEPGEV------VLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELMET 297
                    P  V      VLE++N  G  F  ++  +  GEILG AG+VGAGRTEL  T
Sbjct: 246 ACKDGGCPVPTAVDYTKAPVLELQNFGGYGFSGINLKIYPGEILGMAGVVGAGRTELATT 305

Query: 298 IFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLD 357
           IFG     GG++ + G+ +        I+ G+  VPEDR   GL  I  +  N S   L 
Sbjct: 306 IFGMDKVLGGKVLLNGRDITGLKTRAVIQAGLNYVPEDRHLNGLFKISDVACNTSSALLG 365

Query: 358 RIKKGPFI-SFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKIL 416
               G F+ + K+E+ L    +  F  +    ++ V  LSGGNQQKVV+A+ L+  P+++
Sbjct: 366 DGSLGKFLLNRKKEQTLTQRYVDDFRTKITGQEQAVGSLSGGNQQKVVIARSLSTSPRVI 425

Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII 476
           ILDEPTRGID  A+ ++YRI+ QL  +GV +++ISS++ E+++++DR   +  G++ G  
Sbjct: 426 ILDEPTRGIDAAARGDVYRIIHQLRDQGVSILLISSDMEEIVELADRAVTVFQGRVNGEF 485

Query: 477 DAKEASQEKVMKLAAGL 493
              + +Q+++M  A G+
Sbjct: 486 KGADINQDRLMAAAFGV 502



 Score = 93.6 bits (231), Expect = 1e-23
 Identities = 62/249 (24%), Positives = 124/249 (49%), Gaps = 13/249 (5%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+LE+++      G +   G++++ YPGE+  + G  GAG++ L   I G+ +   G+++
Sbjct: 264 PVLELQNF-----GGYGFSGINLKIYPGEILGMAGVVGAGRTELATTIFGMDKVLGGKVL 318

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQE------LSVMDNLSVAENIFMGDEEKRGIFIDYKK 116
             GR +        I AG+  V ++        + D      +  +GD       ++ KK
Sbjct: 319 LNGRDITGLKTRAVIQAGLNYVPEDRHLNGLFKISDVACNTSSALLGDGSLGKFLLNRKK 378

Query: 117 MYREAEKFMKEEFGIEIDPEEK-LGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQK 175
                ++++ ++F  +I  +E+ +G  S   QQ V IAR++    +V+ILDEPT  +   
Sbjct: 379 EQTLTQRYV-DDFRTKITGQEQAVGSLSGGNQQKVVIARSLSTSPRVIILDEPTRGIDAA 437

Query: 176 ETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVE 235
               ++ ++  L+++GV+I+ IS  +EEI E+ D+   +  G   G     ++ +++++ 
Sbjct: 438 ARGDVYRIIHQLRDQGVSILLISSDMEEIVELADRAVTVFQGRVNGEFKGADINQDRLMA 497

Query: 236 MMVGRKLEK 244
              G   EK
Sbjct: 498 AAFGVSEEK 506


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: 661
Number of extensions: 38
Number of successful extensions: 8
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: 511
Length adjustment: 34
Effective length of query: 460
Effective length of database: 477
Effective search space:   219420
Effective search space used:   219420
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 24 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