GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Paucidesulfovibrio gracilis DSM 16080

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  225 bits (573), Expect = 4e-63
 Identities = 155/484 (32%), Positives = 254/484 (52%), Gaps = 24/484 (4%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           PL++++ + K F  V A   + L  Y G V AL+GENGAGKSTLM +L+G Y  D  G  
Sbjct: 23  PLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPD-AGTI 81

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
            +DG+ V+    + A + G+ ++YQ   L  +++VAEN+ LG+  +    +   +M    
Sbjct: 82  ALDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQ--EGSFFLNPKEMRNRV 139

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
                R G D  PAA V+ LS+ ++Q VEI + ++ ++R+L+ DEPT  L+  ET  LF 
Sbjct: 140 QELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFE 199

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHL-SQAALVKMMVGRD 250
            + ++  +G +I++ISH++ E+  +AD + +LR G   G    + + S+A L   MVG++
Sbjct: 200 ALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKE 259

Query: 251 L---SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELA 307
           +          HG AV     L VR++  G  ++  +FDL  GEV+ + G+ G G+  L 
Sbjct: 260 VLLEVDREAMPHGDAV-----LQVRNLT-GIGLEDITFDLHQGEVVAVVGVAGNGQKALV 313

Query: 308 RLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVH 367
             + G        + I                 + +    +AY+ EDR   GL   ++++
Sbjct: 314 EAICGLRKPPVDTMFIMGKRWRDFYA-------KPSWKNSLAYIPEDR--LGLATCRNLN 364

Query: 368 ENINLIVAARDALGLGR-LNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLS 426
              NL++  R     G  L++  A R TTE I    IR          LSGGN QK +L+
Sbjct: 365 LVDNLLLTTRQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLA 424

Query: 427 RLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLV 486
           R L   PR+++ ++PT+G+DI A  +++  + A A+    IL+++ +L E + L DRV V
Sbjct: 425 RELYRCPRLIVAEQPTQGLDIAATEQVWNHLLA-AREMAGILLVTGDLNEALQLADRVAV 483

Query: 487 MREG 490
           +  G
Sbjct: 484 IYRG 487



 Score = 68.6 bits (166), Expect = 6e-16
 Identities = 62/214 (28%), Positives = 98/214 (45%), Gaps = 20/214 (9%)

Query: 284 SFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPA--GGPR 341
           S ++  G V  L G  GAG++ L  ++ G         R    AG+  L   P      R
Sbjct: 44  SLNIYPGRVKALLGENGAGKSTLMSMLAG---------RYQPDAGTIALDGKPVRFSSAR 94

Query: 342 QAIDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTL 401
            AI+AGI  +      Q   L +S+    N+++      G   LN    R R  E     
Sbjct: 95  DAIEAGIGMV-----YQHFMLVESMTVAENVLLGQE---GSFFLNPKEMRNRVQELSVRY 146

Query: 402 GIRVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALA 461
           G+ +  A   V  LS G +Q+V + +LL    RVLI DEPT  +       ++  +  +A
Sbjct: 147 GLDIDPA-ARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIA 205

Query: 462 QSGVAILMISSELPEVVGLCDRVLVMREGTLAGE 495
           + G +I+ IS +L EV+ + D + ++R+G + GE
Sbjct: 206 EQGKSIVFISHKLEEVLAVADEIAILRQGRIEGE 239


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: 540
Number of extensions: 20
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: 514
Length adjustment: 35
Effective length of query: 505
Effective length of database: 479
Effective search space:   241895
Effective search space used:   241895
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 Apr 09 2024. 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