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_013402438.1 CALHY_RS02475 sugar ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_000166355.1:WP_013402438.1
          Length = 499

 Score =  393 bits (1009), Expect = e-114
 Identities = 208/502 (41%), Positives = 334/502 (66%), Gaps = 20/502 (3%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           +L +  ITK FPG  AL +V+  V + EIHA+VGENGAGKSTLM ++SG       +GEI
Sbjct: 9   LLRLHGITKIFPGTVALSDVSFSVNKAEIHAIVGENGAGKSTLMNIISGSLLPD--KGEI 66

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGN-EVASNGVISWQQTFNR 123
           + EG   N R+  D++++GI I+HQELAL P L++AENI++G     S  ++ +++    
Sbjct: 67  YLEGKKVNIRSPRDAQNLGISIVHQELALCPHLTVAENIYIGRLPEKSAKIVDFKKLNQM 126

Query: 124 TRELLK---KVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180
           ++E+L    +V +K  P   + ++ V +QQ+VEIAKA++ + KLLILDEPT++L+E+D+ 
Sbjct: 127 SQEVLSLFDEVNIK--PTDKVANLNVAQQQIVEIAKAITFNCKLLILDEPTSALSEADAA 184

Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240
            L  ++ + + +G++ + I+H+L E+ ++AD+ITVLRDG  + TL+    E + D ++  
Sbjct: 185 VLFKIIKDLKAKGISILYISHRLREIFELADRITVLRDGRYITTLNT--AETNPDQVVSL 242

Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300
           MVGR++++ YPP+   IG  +  V+N ++   Q+        ++  + +GE++G AGL+G
Sbjct: 243 MVGREIKEMYPPKSSKIGREVFRVENISSDKVQN--------VSFALHEGEILGFAGLVG 294

Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360
           +GRTE A ++ G    H   G++ ++GK +++++   AI   + YVTEDRK  GL L   
Sbjct: 295 SGRTELAQTICGILPKH--CGEIYLEGKKIEINSFEDAIRHKIGYVTEDRKQYGLFLKLP 352

Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420
           + HN +  +L    K  +ID  KE+ +A +F  +L +++S   Q  ++LSGGNQQKV+++
Sbjct: 353 VAHNVSAIHLKYDYKRLLIDRQKELSLAQEFVKKLNVKTSSYVQLVMSLSGGNQQKVMIA 412

Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480
           KWL   P +LILDEPTRGIDVGAK EI++++ +LA +G G+++ISSE+PE++G CDR+ V
Sbjct: 413 KWLAIKPRILILDEPTRGIDVGAKAEIHSLLRELAKNGIGIILISSELPEIIGMCDRVLV 472

Query: 481 MNEGRIVAELPKGEASQESIMR 502
           M EGRI  EL     ++E+IM+
Sbjct: 473 MREGRITGELSGSSITEENIMQ 494


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: 649
Number of extensions: 38
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: 499
Length adjustment: 34
Effective length of query: 478
Effective length of database: 465
Effective search space:   222270
Effective search space used:   222270
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.

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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