GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Paucidesulfovibrio gracilis DSM 16080

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  223 bits (569), Expect = 1e-62
 Identities = 147/483 (30%), Positives = 253/483 (52%), Gaps = 16/483 (3%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           ++ ++ +TK F  V A ++++L +  G + AL+GENGAGKSTLM +L+G Y      G I
Sbjct: 24  LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDA--GTI 81

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124
             +G    F +  D+ + GI +++Q   LV  +++AEN+ LG E   +  ++ ++  NR 
Sbjct: 82  ALDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE--GSFFLNPKEMRNRV 139

Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184
           +EL  + GL   P   ++D+ +G++Q VEI K L +  ++LI DEPTA L   ++  L  
Sbjct: 140 QELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFE 199

Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244
            L +   QG + + I+HKL EV  VAD+I +LR G  ++      E  S+  +   MVG+
Sbjct: 200 ALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQG-RIEGEFSESEVTSKADLACRMVGK 258

Query: 245 DLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRT 304
           ++        +P G+ +L+V+N             L DI   + +GEVV + G+ G G+ 
Sbjct: 259 EVLLEVDREAMPHGDAVLQVRNLTGIG--------LEDITFDLHQGEVVAVVGVAGNGQK 310

Query: 305 EFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHN 364
               ++ G       T  + I GK       + +    LAY+ EDR  L    N N++ N
Sbjct: 311 ALVEAICGLRKPPVDT--MFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDN 368

Query: 365 TTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLF 424
             L    G ++   +D  K  +  ++   +  IR   I      LSGGN QK VL++ L+
Sbjct: 369 LLLTTRQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELY 428

Query: 425 SNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEG 484
             P +++ ++PT+G+D+ A  +++  +   A +  G+L+++ ++ E L   DR+ V+  G
Sbjct: 429 RCPRLIVAEQPTQGLDIAATEQVWNHL-LAAREMAGILLVTGDLNEALQLADRVAVIYRG 487

Query: 485 RIV 487
           R +
Sbjct: 488 RFM 490



 Score = 84.0 bits (206), Expect = 1e-20
 Identities = 59/220 (26%), Positives = 107/220 (48%), Gaps = 14/220 (6%)

Query: 282 DINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDA 341
           DI++ +  G V  + G  GAG++     + G+       G + +DGKPV  S+ R AI+A
Sbjct: 42  DISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPD--AGTIALDGKPVRFSSARDAIEA 99

Query: 342 GLAYVTEDRKHLGLVLNDNILHNTTLANLAG--VSKASIIDDIKEMKVASDFRTRLRIRS 399
           G+  V +   H  LV +  +  N  L       ++   + + ++E+ V          R 
Sbjct: 100 GIGMVYQ---HFMLVESMTVAENVLLGQEGSFFLNPKEMRNRVQELSVRYGLDIDPAARV 156

Query: 400 SGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGK 459
           S       +LS G +Q+V + K L+ +  VLI DEPT  +     + ++  + ++A  GK
Sbjct: 157 S-------DLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGK 209

Query: 460 GVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQES 499
            ++ IS ++ E+L   D I ++ +GRI  E  + E + ++
Sbjct: 210 SIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKA 249


Lambda     K      H
   0.316    0.135    0.374 

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: 581
Number of extensions: 31
Number of successful extensions: 11
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: 512
Length of database: 514
Length adjustment: 35
Effective length of query: 477
Effective length of database: 479
Effective search space:   228483
Effective search space used:   228483
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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