GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Caldicellulosiruptor hydrothermalis 108

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_013402887.1 CALHY_RS04860 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>NCBI__GCF_000166355.1:WP_013402887.1
          Length = 503

 Score =  102 bits (254), Expect = 1e-26
 Identities = 69/223 (30%), Positives = 110/223 (49%), Gaps = 4/223 (1%)

Query: 11  LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70
           +LQV  +   +GNI+A   V + V KGE+ +++G NGAGKSTLM  I G     +G + F
Sbjct: 4   ILQVKDISKRFGNIQANDNVCLDVKKGEVHAILGENGAGKSTLMNIIYGLYTPDSGEIYF 63

Query: 71  EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLF 130
           EG+ +     HE     I    +   + P  TV EN+ +G      +   ++ EK     
Sbjct: 64  EGQKLEVKGPHEAIEKGIGMVHQHFMLIPVFTVAENIVLGFEPKGFRFNVQEAEKKILEI 123

Query: 131 PR---LKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIR 187
            +   L+     + G LS G QQ + I +A     +LL+LDEP+  L P   + +F+ I 
Sbjct: 124 SKKYNLEIDPKAKVGDLSVGMQQRVEILKAFYRDARLLILDEPTAMLTPQETRELFKIIN 183

Query: 188 KLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKE 230
            L +A+G+++  +       + +S R  VM  GK   + + KE
Sbjct: 184 NL-KAQGISILFISHKLDEVMEISDRVTVMRRGKTIKTLNTKE 225



 Score = 72.8 bits (177), Expect = 1e-17
 Identities = 59/232 (25%), Positives = 104/232 (44%), Gaps = 15/232 (6%)

Query: 4   EVMTGQPLLQVNGVETYYGN-IRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQ 62
           E   G+ +L+V  +     N +  +  V   V +GEI  + G +G G++ L+  I G   
Sbjct: 248 EPRLGETVLKVENLSVKLKNGVEKVKDVSFEVRRGEIFGIAGVDGNGQNELVEAIVGLIS 307

Query: 63  ARTGSVVFEGRDITRMPTHEIARLRIAQSPEGRR---IFPRMTVLENLQM---------G 110
           + TG ++F G++I  +PT +     IA  P  R+   +    TV EN+ +          
Sbjct: 308 S-TGKIIFNGQEIQNLPTRKRYEKGIAYIPADRQQDGLVLNFTVAENIVLKRYYKNPYSN 366

Query: 111 AGLDNLKHFAEDVEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEP 170
            G  N K    + +++   F      +      LSGG QQ + + R   + P LL+  +P
Sbjct: 367 RGFLNYKVITLEADRLIHEFDVRPPDYKLFAKNLSGGNQQKVILAREFSSSPDLLIAVQP 426

Query: 171 SLGLAPLIVKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKV 222
           + G+    ++ I   + +L ++ G  + LV       L LS R  VM +G++
Sbjct: 427 TRGMDVGAIEYIHRKLIELRDS-GKAILLVSLELDEILNLSDRIAVMYSGRI 477


Lambda     K      H
   0.320    0.137    0.387 

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: 280
Number of extensions: 13
Number of successful extensions: 5
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: 247
Length of database: 503
Length adjustment: 29
Effective length of query: 218
Effective length of database: 474
Effective search space:   103332
Effective search space used:   103332
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 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