GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Paucidesulfovibrio gracilis DSM 16080

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  149 bits (375), Expect = 2e-40
 Identities = 84/226 (37%), Positives = 135/226 (59%), Gaps = 15/226 (6%)

Query: 5   PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64
           P+++ +GL KR+G+V A D    ++YPG + A++G+NGAGKS+++  ++G   PD G I 
Sbjct: 23  PLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIA 82

Query: 65  LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124
           L+GKP++F S  +A +AGI  VYQ+  L  ++++A+N+ LG+E       G +F +    
Sbjct: 83  LDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE-------GSFFLN---- 131

Query: 125 AMEKQARAKLSELGLMTIQNINQA--VETLSGGQRQGVAVARAAAFGSKVVIMDEPTAAL 182
              K+ R ++ EL +    +I+ A  V  LS G++Q V + +     S+V+I DEPTA L
Sbjct: 132 --PKEMRNRVQELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVL 189

Query: 183 GVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGR 228
             +E+  + E +  +  +G  IV ISH +  V  VAD I I R GR
Sbjct: 190 TPRETFHLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGR 235



 Score = 60.8 bits (146), Expect = 5e-14
 Identities = 55/234 (23%), Positives = 102/234 (43%), Gaps = 10/234 (4%)

Query: 22  LDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGK---PIQFRSPMEA 78
           L+   FDL+ GE++AV+G  G G+ ++++AI G   P    + + GK       +   + 
Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKN 345

Query: 79  RQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELG 138
             A I      LA    L++ DN+ L    R+    G W   LD+    +     + +  
Sbjct: 346 SLAYIPEDRLGLATCRNLNLVDNLLL--TTRQGFARGPW---LDKKKAARDTTELIKKFD 400

Query: 139 LMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVR 198
           +     I      LSGG  Q   +AR      ++++ ++PT  L +  + +V   +L  R
Sbjct: 401 IRP-GRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHLLAAR 459

Query: 199 RRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTGAKE 252
                I+L++ ++    ++ADR+ +   GR + V +  D    + +  M    E
Sbjct: 460 EMA-GILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMMAGVE 512


Lambda     K      H
   0.321    0.136    0.383 

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: 284
Number of extensions: 12
Number of successful extensions: 3
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: 260
Length of database: 514
Length adjustment: 29
Effective length of query: 231
Effective length of database: 485
Effective search space:   112035
Effective search space used:   112035
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: 49 (23.5 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