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

GapMind for catabolism of small carbon sources

Aligments 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources