GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Lacinutrix himadriensis E4-9a

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_055444834.1 AMD28_RS14385 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_001418105.1:WP_055444834.1
          Length = 506

 Score =  351 bits (901), Expect = e-101
 Identities = 196/483 (40%), Positives = 296/483 (61%), Gaps = 8/483 (1%)

Query: 14  LALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHI 73
           L +  I K+F  V  L+ V L   +GE+HAL+GENGAGKSTL+KILSG +  D G    +
Sbjct: 10  LEMTGISKSFGVVSVLKNVNLKVKSGEIHALLGENGAGKSTLIKILSGVHQKDTGTVV-L 68

Query: 74  DGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAP 133
           DGQ +        + LG+ V+YQELSL  +LSVAENIYL +    +  +    +++    
Sbjct: 69  DGQEITPKNTHEGQVLGINVVYQELSLVNDLSVAENIYLHKLGANKTWMNWKGLIKDAQE 128

Query: 134 TLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALI 193
            L  L    + +A V  LSI Q+Q+VEIA+A+  + +IL++DEPTT     +  +LF ++
Sbjct: 129 LLDSLDFKINASAKVKDLSIVQKQVVEIAKAISEDTKILILDEPTTVFDPKDVKKLFNIL 188

Query: 194 RQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLSG 253
            +L+ +G +I+YISH + EI ++AD VTVLRDG   G+L  A   +  ++ +M+GR+L  
Sbjct: 189 FKLKEKGTSIIYISHHLDEIFKIADSVTVLRDGVDTGSLAIADTDKDGVIHLMIGRELKD 248

Query: 254 FYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFGA 313
            Y K   +  E  +       A    V   SF ++ GEVLG+AGL G+GRTE A+L+FGA
Sbjct: 249 LYPKRDVKIGEVPIFEVKNLTAKDTMVHDVSFHVKPGEVLGIAGLGGSGRTETAKLIFGA 308

Query: 314 DARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLI 373
           D +  G + +           +    P  A    I +++EDRK +G+FL  S+  NI++ 
Sbjct: 309 DKKKSGTLILEGK-------EIVTNSPVDAARYQIGFVSEDRKEEGVFLPLSIRRNISVT 361

Query: 374 VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQP 433
                +  LG +N  +  ++    I+ L I+  ++++NV  LSGGNQQKV L++ L I+ 
Sbjct: 362 SFDSISSKLGFINVESEYKKVLGLIEKLNIKTPNSEINVKNLSGGNQQKVALAKWLSIES 421

Query: 434 RVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTLA 493
           +V+ +DEPTRGVD+GAK EIY+LIN +A+ GV +++ISS++PE++G+ DR+LVM EGT  
Sbjct: 422 KVIFIDEPTRGVDVGAKIEIYKLINEVAKKGVGVVVISSDMPEIMGISDRILVMHEGTFY 481

Query: 494 GEV 496
           GE+
Sbjct: 482 GEL 484



 Score = 70.5 bits (171), Expect = 1e-16
 Identities = 51/223 (22%), Positives = 104/223 (46%), Gaps = 14/223 (6%)

Query: 39  GEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQE- 97
           GEV  + G  G+G++   K++ GA      G   ++G+ +  + P  A    +  + ++ 
Sbjct: 285 GEVLGIAGLGGSGRTETAKLIFGA-DKKKSGTLILEGKEIVTNSPVDAARYQIGFVSEDR 343

Query: 98  --------LSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLARLGADF-SPAANV 148
                   LS+  N+SV     +   L   G +      +     + +L     +   NV
Sbjct: 344 KEEGVFLPLSIRRNISVTSFDSISSKL---GFINVESEYKKVLGLIEKLNIKTPNSEINV 400

Query: 149 ASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMAILYISH 208
            +LS   +Q V +A+ +  E++++ +DEPT  +       ++ LI ++  +G+ ++ IS 
Sbjct: 401 KNLSGGNQQKVALAKWLSIESKVIFIDEPTRGVDVGAKIEIYKLINEVAKKGVGVVVISS 460

Query: 209 RMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251
            M EI  ++DR+ V+ +G F G L +   S+  +++  +G  L
Sbjct: 461 DMPEIMGISDRILVMHEGTFYGELPKEKFSEENILRYSIGEPL 503


Lambda     K      H
   0.320    0.136    0.382 

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: 550
Number of extensions: 24
Number of successful extensions: 6
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: 540
Length of database: 506
Length adjustment: 35
Effective length of query: 505
Effective length of database: 471
Effective search space:   237855
Effective search space used:   237855
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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