Alignments for a candidate for mglA in Nocardioides dokdonensis FR1436

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Nocardioides dokdonensis FR1436

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_068105359.1 I601_RS01185 ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_001653335.1:WP_068105359.1
          Length = 504

 Score =  297 bits (760), Expect = 7e-85
 Identities = 170/485 (35%), Positives = 282/485 (58%), Gaps = 15/485 (3%)

Query: 5   LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64
           L ++ + KRF  + A   +S+    GE+H ++GENGAGKSTLM ++ G+Y+ D GEI+ +
Sbjct: 3   LALREVTKRFGSLVANDRISLTVEGGEIHCLLGENGAGKSTLMNVLYGLYRADGGEIVLD 62

Query: 65  GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKF 124
           G    +  P +AI AGI  V Q   ++   +VAEN+ +G+E+         +  R   + 
Sbjct: 63  GEVQHFTGPGDAIAAGIGMVHQHFMLVPVFTVAENVMLGNEQTGFAGSLDLEAARARVRE 122

Query: 125 MKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVV 184
           + + FG  +DP+  +G   + +QQ VEI + + + AKVL+ DEPT+ LT +ET++L E++
Sbjct: 123 ISDRFGFHVDPDAVVGDLPVGVQQRVEIIKVLSRDAKVLVFDEPTAVLTPQETDELMEIM 182

Query: 185 KSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEK 244
           + L+  G AI+FI+H+L E+ E+ D+++V+R G  +G ++    +  ++  MMVGR +E 
Sbjct: 183 RELRRSGAAIVFITHKLREVREVADRITVIRRGTVVG-EADPAASNAELAAMMVGRPVEL 241

Query: 245 FYIKEAHEPGEVVLEVKNLSG------ERFENVSFSLRRGEILGFAGLVGAGRTELMETI 298
              K+  E G   L V  LS          +++SF +R GEIL  AG+ G G+TEL E +
Sbjct: 242 TVDKQDPELGGTALVVDGLSVFDSAGLVHVDDISFEVRAGEILAVAGVQGNGQTELTEAL 301

Query: 299 FGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDR 358
            G +    G I ++G+ +      D ++ G+G VPEDR+  GL+   +I  N+    LDR
Sbjct: 302 LGLQDHVEGSILLDGQELVGRKVRDVLDAGVGFVPEDRQVDGLVGSFTIAENL---MLDR 358

Query: 359 IKKGPFI-----SFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKP 413
               PF+          +  A+  ++ +D+R          LSGGNQQKVV+A+ L+ + 
Sbjct: 359 SFDAPFVRHGSLQLSALQAFAEEKLEQYDVRAPGITTPAGNLSGGNQQKVVVARELSREL 418

Query: 414 KILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLA 473
           ++L+  +PTRG+DVG+   I++ +      GV V+++S+EL EV+ ++DRI V+  G++ 
Sbjct: 419 RLLVAAQPTRGVDVGSIEFIHQQIVATRDAGVPVLVVSTELDEVVALADRIMVLFRGRIV 478

Query: 474 GIIDA 478
           GI+ A
Sbjct: 479 GIVPA 483



 Score = 90.5 bits (223), Expect = 1e-22
 Identities = 65/219 (29%), Positives = 107/219 (48%), Gaps = 11/219 (5%)

Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQG 328
           + +S ++  GEI    G  GAG++ LM  ++G     GGEI ++G+      P DAI  G
Sbjct: 19  DRISLTVEGGEIHCLLGENGAGKSTLMNVLYGLYRADGGEIVLDGEVQHFTGPGDAIAAG 78

Query: 329 IGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAY- 387
           IG+V    +   L+ + ++  NV L +      G       + E A   ++    R  + 
Sbjct: 79  IGMV---HQHFMLVPVFTVAENVMLGNEQTGFAGSL-----DLEAARARVREISDRFGFH 130

Query: 388 --PDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGV 445
             PD  V  L  G QQ+V + K L+   K+L+ DEPT  +      E+  IM +L + G 
Sbjct: 131 VDPDAVVGDLPVGVQQRVEIIKVLSRDAKVLVFDEPTAVLTPQETDELMEIMRELRRSGA 190

Query: 446 GVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQE 484
            ++ I+ +L EV +++DRI V+  G + G  D   ++ E
Sbjct: 191 AIVFITHKLREVREVADRITVIRRGTVVGEADPAASNAE 229


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: 612
Number of extensions: 36
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: 504
Length adjustment: 34
Effective length of query: 460
Effective length of database: 470
Effective search space:   216200
Effective search space used:   216200
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:

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
the source code
instructions for running GapMind on your computer

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