GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Phyllobacterium brassicacearum STM 196

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_106713889.1 CU102_RS25570 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>NCBI__GCF_003010955.1:WP_106713889.1
          Length = 506

 Score =  358 bits (918), Expect = e-103
 Identities = 193/476 (40%), Positives = 301/476 (63%), Gaps = 3/476 (0%)

Query: 5   TPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64
           TP L  RGI K+FPGVKAL D++   YAG+V AL+GENGAGKSTL+KIL+G Y    G +
Sbjct: 13  TPLLEMRGISKSFPGVKALNDVNIALYAGKVTALIGENGAGKSTLVKILTGIYQSDEGEI 72

Query: 65  VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPH-KGGIVNRSLLNYE 123
            ++G  ++F++   A++ GV  I+QE  L  E++VAENI+LG  P  + G VN   +N  
Sbjct: 73  HVDGSPVAFANAQDAIDFGVTAIHQETVLFDELSVAENIFLGHAPKTRLGFVNWKAVNAR 132

Query: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183
           A   L  L  +IDP T LK LSI Q  +V IA+AL+ +A+I+  DEPT++LS +E+D+LF
Sbjct: 133 ALALLHSLESNIDPRTRLKDLSIAQRHLVAIARALSVDARIVIMDEPTAALSRKEVDDLF 192

Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243
           ++++ L+  G+ IL++SH+ +E++ ++D   VF+DG+ V +   +  V  D +V+ MVGR
Sbjct: 193 QIVKRLKSHGKAILFISHKFDEVYEIADNFAVFRDGKAVGSGV-LAGVAQDEIVRLMVGR 251

Query: 244 DIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMF 303
            I   +       GE  L ++    P     I+ A++ GEI G++GLVGAGRSE+ + +F
Sbjct: 252 SIEHAFPKVAIPLGEAVLSVENYTHPTEFRDITFALKKGEIFGIYGLVGAGRSEICQSLF 311

Query: 304 GGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKH 363
           G T+ + G + +D + I IR P  AI AG++  PE+R   G +    +  NI++ +  + 
Sbjct: 312 GVTRPSGGTLKLDGKEIVIRSPGDAIKAGIVYVPEERGRHGAVLQLPIYQNISLPSLVRT 371

Query: 364 VLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILL 423
              G  +    E   A  +    +++       +  LSGGNQQK ++G+WL+   K+++L
Sbjct: 372 SRSG-FLRAAEEFALARKYAERFDLRAAALSVPVGTLSGGNQQKVVIGKWLATHPKILIL 430

Query: 424 DEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAG 479
           DEPT+GID+G+K  ++  I  LA +G++++  SS+LPE+LG++DR++VMREG  AG
Sbjct: 431 DEPTKGIDIGSKAAVHAFISELAGEGLSIIMVSSELPEILGMSDRVLVMREGLSAG 486


Lambda     K      H
   0.319    0.136    0.391 

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: 668
Number of extensions: 34
Number of successful extensions: 8
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: 504
Length of database: 506
Length adjustment: 34
Effective length of query: 470
Effective length of database: 472
Effective search space:   221840
Effective search space used:   221840
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 (21.7 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