GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Caldicellulosiruptor hydrothermalis 108

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_083790252.1 CALHY_RS03450 sugar ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_000166355.1:WP_083790252.1
          Length = 494

 Score =  389 bits (999), Expect = e-112
 Identities = 217/500 (43%), Positives = 327/500 (65%), Gaps = 18/500 (3%)

Query: 8   MRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIHYE 67
           M  I K+FPGV+AL+N   ++  GEIHALVGENGAGKSTLMK+L+GVY      G I Y+
Sbjct: 1   MEGIEKSFPGVQALKNARFELMPGEIHALVGENGAGKSTLMKILTGVYQKDA--GRIVYK 58

Query: 68  GAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGV---ISWQQTFNRT 124
           G          ++++GI I+HQEL L+P L++A+NIF+G E         +  ++   +T
Sbjct: 59  GREVEIPNPKIAQEMGISIVHQELNLMPHLTVAQNIFIGREPRRKSFSLFLDEEEMNKKT 118

Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184
           +ELL  + LK  P+T + ++ V KQQ+VEIAKALS + ++LI+DEPTA+L+E + E L N
Sbjct: 119 KELLDMLHLKVDPKTKVANLTVAKQQMVEIAKALSFNSEVLIMDEPTAALSEGEVEELFN 178

Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244
           +L + +  GM  I I+H+L E++++AD++TV+RDG  + T     +EI+ D II  MVGR
Sbjct: 179 ILRKLKANGMGIIYISHRLEELKQIADRVTVMRDGQYIGTAKI--DEITIDEIISMMVGR 236

Query: 245 DLEDRYPPRDVPIG-ETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303
           ++ +    ++V    E +LEV N    ++       + D++  +RKGE++G AGL+GAGR
Sbjct: 237 EIYETLREKEVKENSEIVLEVSNLKRGNE-------IKDVSFKLRKGEILGFAGLVGAGR 289

Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363
           TE A +VFG       +G++ + GK V + +   AI  G+AY++EDRK  GL+L  ++  
Sbjct: 290 TEVARAVFGADPVE--SGEIYVRGKKVHIKSPSDAIKHGIAYLSEDRKRYGLMLGLDVES 347

Query: 364 NTTLANLAG-VSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKW 422
           N  L ++   ++    +   +  ++ +++  +LRI++  + Q+  NLSGGNQQKV+++KW
Sbjct: 348 NMVLPSMKEFLNPLGFVKKKRAERICNEYVKKLRIKTPSLNQKVRNLSGGNQQKVIIAKW 407

Query: 423 LFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMN 482
           L  N D+LI DEPTRGIDVGAK EIY ++N+L  +GK ++MISSE+PE+L    RI VM 
Sbjct: 408 LMKNCDILIFDEPTRGIDVGAKNEIYKLLNELVNEGKSIIMISSELPEILRMSHRIIVMC 467

Query: 483 EGRIVAELPKGEASQESIMR 502
           EGRI AEL   EA++E IM+
Sbjct: 468 EGRITAELSGKEATEELIMK 487


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: 694
Number of extensions: 35
Number of successful extensions: 10
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: 512
Length of database: 494
Length adjustment: 34
Effective length of query: 478
Effective length of database: 460
Effective search space:   219880
Effective search space used:   219880
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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