GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Tistlia consotensis USBA 355

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>NCBI__GCF_900177295.1:WP_085124759.1
          Length = 518

 Score =  161 bits (407), Expect = 3e-44
 Identities = 89/245 (36%), Positives = 142/245 (57%), Gaps = 9/245 (3%)

Query: 5   PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64
           P+L  RG+ +R+  V ALD+ DF L PGE+  + G+NGAGKS+MI  I+GA+ P EGE R
Sbjct: 22  PLLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFR 81

Query: 65  LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124
             G+P++  S   AR  GI  V+Q  +L P +++ +N+FLG E  + G+       LDR 
Sbjct: 82  FRGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGL-------LDRR 134

Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184
           A+  +A A L  LG          V  L+  ++Q V +A+A      V+I+DEPTA+L  
Sbjct: 135 ALHDRADAILKRLGFPL--RPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTE 192

Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244
           +E+ ++ +LI  V+ +G+ ++ I+H +  +  + DRI + R GR +  ++ +     + V
Sbjct: 193 RETAQLFKLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELV 252

Query: 245 AFMTG 249
             MTG
Sbjct: 253 RLMTG 257



 Score = 74.3 bits (181), Expect = 5e-18
 Identities = 59/207 (28%), Positives = 95/207 (45%), Gaps = 7/207 (3%)

Query: 25  ADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIE 84
           A   +  GEI+ + G  G+GKS + +A  G     EG +RL+G+ +  + P    + G  
Sbjct: 291 ASLSVCAGEIVGLAGLVGSGKSEVARACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFF 350

Query: 85  TV---YQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMT 141
            V    ++  L     + +N+ L      P   G     LDR     + R    +L L  
Sbjct: 351 YVPPDRRDEGLMMMRPVRENVSLPSLTLAPFGNGAL---LDRRGETDRVRRLAEQLNLQP 407

Query: 142 IQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRG 201
              I +AVE  SGG +Q V +A++     +V   DEPT  + V     + E I D+   G
Sbjct: 408 -PRIERAVEAFSGGNQQKVLLAKSRTRPVQVFAFDEPTVGVDVGTRVAIYEFIRDLCEAG 466

Query: 202 LPIVLISHNMPHVFEVADRIHIHRLGR 228
             I+LIS ++P V  +++R ++   GR
Sbjct: 467 AGILLISSDLPEVLNLSNRAYVFYRGR 493


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: 291
Number of extensions: 16
Number of successful extensions: 4
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: 518
Length adjustment: 30
Effective length of query: 230
Effective length of database: 488
Effective search space:   112240
Effective search space used:   112240
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