GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Dinoroseobacter shibae DFL-12

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 3609459 Dshi_2843 ABC transporter related (RefSeq)

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Dino:3609459
          Length = 548

 Score =  322 bits (824), Expect = 3e-92
 Identities = 190/506 (37%), Positives = 292/506 (57%), Gaps = 20/506 (3%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P +E++ I K F  V A K +S+   PG +H I+GENGAGKSTLM I+ G Y+ D GEI 
Sbjct: 24  PAIELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIF 83

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEK---RGIFIDYKKMYR 119
            +G+         AI AGI  VFQ   +++N +V EN+ +G EE    R      +K+ R
Sbjct: 84  IKGQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLGAEEGALLRPSLAKARKLLR 143

Query: 120 EAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEK 179
           E    + EE+ + + P+  +   S+  QQ VEI +A+Y+KA +LILDEPT  LT  E + 
Sbjct: 144 E----LSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADH 199

Query: 180 LFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG 239
           LF +++ LK +G  II I+H+L EI E  D VSV+R GE   T    + + E++ E+MVG
Sbjct: 200 LFRILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAELMVG 259

Query: 240 RKLEKFYIKEAHEPGEVVLEVKNL------SGERFENVSFSLRRGEILGFAGLVGAGRTE 293
           RK+     K   +PG  +L V +L        ER + +S  +R GE+LG AG+ G G++E
Sbjct: 260 RKVLLRVDKTPAQPGAPILTVDDLRVVDDQGVERVKGISLQVRAGEVLGIAGVAGNGQSE 319

Query: 294 LMETIFGFRPKRGGEIYIEGKRVEI----NHPLDAIEQGIGLVPEDRKKLGLILIMSIMH 349
           L+E + G RP   G + + G+++++    ++      QGI  VPEDR+  GLI+      
Sbjct: 320 LLEVLGGMRPAT-GRVTVSGQQIDLTGKHSNGKTRRAQGIAHVPEDRQAEGLIMDYHAWE 378

Query: 350 NVSLPSLD--RIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAK 407
           NV+    D     +G  +  +  +  A+  I  FD+RPA         SGGNQQK+VLA+
Sbjct: 379 NVAFGYHDDPAYNRGLLMDNRAVRADAEGKIARFDVRPADCWLAAKNFSGGNQQKIVLAR 438

Query: 408 WLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVM 467
            +   P++L++ +PTRG+D+GA   I++ +  L   G  ++++S EL E+L +SDR+AVM
Sbjct: 439 EIERNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLSDRVAVM 498

Query: 468 SFGKLAGIIDAKEASQEKVMKLAAGL 493
             G++ G   A E +++++  L AG+
Sbjct: 499 FDGRIMGERPAAETNEKELGLLMAGI 524


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: 707
Number of extensions: 44
Number of successful extensions: 9
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: 548
Length adjustment: 35
Effective length of query: 459
Effective length of database: 513
Effective search space:   235467
Effective search space used:   235467
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