GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Rhodobacter johrii JA192

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  376 bits (966), Expect = e-109
 Identities = 226/504 (44%), Positives = 306/504 (60%), Gaps = 16/504 (3%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           P+LA+R + + F  V+ L  V+     GEVHAL+GENGAGKST MKIL+G Y A   GE 
Sbjct: 4   PVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAG-YLAPSAGEV 62

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
            +DG+ V     + A   GV +I+QE +LA  L+V ENI+LGR L+R   +    M    
Sbjct: 63  LLDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAMQAES 122

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
              L RL     P A V++LS+  RQ+VEIA+A+  +AR+L+MDEPT  L+  ETD L  
Sbjct: 123 RRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLE 182

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251
            + +LR  G AILY SH++ E+  +ADRVTVLRDG  V T     LS+  + + MVGR+L
Sbjct: 183 QVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGREL 242

Query: 252 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 311
           SG +      A   E +L V  +     V+  SF LR GEVLG AGLVG+GRTEL   + 
Sbjct: 243 SGLFPPKSSPA--PEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGIV 300

Query: 312 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 371
           G    T GEVR+           LP      A  AG+ YLTEDRK +GL L + + EN+ 
Sbjct: 301 GLRPAT-GEVRMEGS-------PLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLT 352

Query: 372 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431
           L+  A D  G   +++ A  R  T+AI    IRV    ++ G+LSGGNQQK++L++ +  
Sbjct: 353 LL--ALDRFGRVLIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLA 410

Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491
           +PRV+I+DEPTRG+D+G K +IY  I  LA  G +++++SSELPEV+GL +RV+VM  G 
Sbjct: 411 EPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGR 470

Query: 492 LAGEVRPAGSAAETQERIIALATG 515
           +AGEV      A T+E I+ LA G
Sbjct: 471 IAGEVE---GEAITEENIVRLAMG 491


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: 656
Number of extensions: 33
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: 540
Length of database: 499
Length adjustment: 35
Effective length of query: 505
Effective length of database: 464
Effective search space:   234320
Effective search space used:   234320
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.

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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