GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Desulfoscipio geothermicus DSM 3669

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_092484692.1 BM299_RS12340 ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_900115975.1:WP_092484692.1
          Length = 509

 Score =  339 bits (869), Expect = 2e-97
 Identities = 177/497 (35%), Positives = 306/497 (61%), Gaps = 10/497 (2%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           ++E+K+I KRFPGV A   V+     GE+H ++GENG+GKSTLM ++AG+Y+PDEGEII 
Sbjct: 6   LIELKNITKRFPGVIANDKVNFNVKQGEIHVLLGENGSGKSTLMSVLAGLYRPDEGEIIV 65

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEK 123
            G  + +  P +AI+AG+  V Q   ++D+ SVAEN+ +GD     + ++ K +     +
Sbjct: 66  RGTQMVFRSPGDAISAGVGMVHQHFKLIDSFSVAENVILGDHNVAPV-LNMKDIENNLAQ 124

Query: 124 FMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEV 183
            + + +G+ IDP  ++ + S+  +Q VEI + +Y+ ++VLILDEPT+ LT +ET +LF+ 
Sbjct: 125 -LSQRYGLHIDPSARVWQLSVGEKQRVEIVKMLYRGSRVLILDEPTAVLTPQETAELFKN 183

Query: 184 VKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLE 243
           ++ +   G  ++ I+H+++E+ EI D+V+VLR G+ + T   + + +  +  +MVG+ + 
Sbjct: 184 LREMARSGRGVVVITHKMQEVMEIADRVTVLRKGKAVATLEKKQINRRDLAWLMVGQDVV 243

Query: 244 KFYIKEAHEPGEVVLEVK------NLSGERFENVSFSLRRGEILGFAGLVGAGRTELMET 297
           + Y K++      VLE++      +L     +NV+F++  GEI G AG+ G G+ EL E 
Sbjct: 244 RQYKKKSPPGEHKVLELQGVHCMNDLGRPCLQNVTFTVHSGEIFGIAGVAGNGQRELAEV 303

Query: 298 IFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPS-- 355
           + G RP  GG IYI+G  +    P   I+ G+ LVPEDR   GL+  +  + N+ L    
Sbjct: 304 VSGLRPVTGGSIYIKGNEITGGSPRRIIDHGVALVPEDRLGTGLVPNLGAVDNLILKDYR 363

Query: 356 LDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKI 415
             ++++GPF++ ++ +E     +  F+I+ +  D  V  LSGGN Q+++LA+ +  +P +
Sbjct: 364 TGKLQRGPFLNLRQARENTKNLVNRFEIKLSSLDAPVKLLSGGNLQRLLLAREITAEPHL 423

Query: 416 LILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGI 475
           L+   P RG+D+ A   I+ ++ Q  ++G+ +++IS +L E+ ++SDRI V+  G++ GI
Sbjct: 424 LVAVYPVRGLDIKATEAIHNLLLQQREKGMAILLISEDLDEIFKLSDRIGVLCNGQITGI 483

Query: 476 IDAKEASQEKVMKLAAG 492
           I A+    E+V  L  G
Sbjct: 484 IPAEMTDIEEVGLLMMG 500


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: 669
Number of extensions: 37
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: 509
Length adjustment: 34
Effective length of query: 460
Effective length of database: 475
Effective search space:   218500
Effective search space used:   218500
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 Apr 09 2024. 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