GapMind for catabolism of small carbon sources

 

Alignments for a candidate for argT in Paraburkholderia bryophila 376MFSha3.1

Align lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized)
to candidate H281DRAFT_01522 H281DRAFT_01522 amino acid ABC transporter substrate-binding protein, PAAT family

Query= CharProtDB::CH_003045
         (260 letters)



>FitnessBrowser__Burk376:H281DRAFT_01522
          Length = 260

 Score =  286 bits (733), Expect = 2e-82
 Identities = 136/259 (52%), Positives = 184/259 (71%)

Query: 1   MKKTVLALSLLIGLGATAASYAALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMC 60
           +KK + AL++ +    +  ++A    T+R G D +Y PF SK + G+ +GFDIDLGNE+C
Sbjct: 1   VKKLLAALTVALLATVSIGAHAKDWSTIRFGVDASYPPFESKGSDGKLVGFDIDLGNEIC 60

Query: 61  KRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAK 120
            R++ KC WV +DFD +IP+LKAKK D ++SS+S+T +R +++AFS KL+   +RL+A K
Sbjct: 61  ARLKAKCVWVENDFDGMIPALKAKKFDGVLSSMSMTPQRAEQVAFSSKLFNTPTRLVAKK 120

Query: 121 GSPIQPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAA 180
           GS I PT ESLKGK VGV QG+ QE YA   W  KG  VV Y NQD +Y+DL +GRLDAA
Sbjct: 121 GSGILPTAESLKGKTVGVEQGTIQETYAKTYWEPKGAKVVPYQNQDQVYADLLSGRLDAA 180

Query: 181 LQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELR 240
           LQD V A  GFLK P G  + F G ++ D K  G+G G+G+RK+DT+LKA  DKA+ ++ 
Sbjct: 181 LQDAVQAEIGFLKTPRGAGFDFVGKNLDDPKILGNGAGIGMRKEDTDLKAKVDKAIADII 240

Query: 241 QDGTYDKMAKKYFDFNVYG 259
           +DGTY K+ KKYFDF+VYG
Sbjct: 241 KDGTYKKLEKKYFDFDVYG 259


Lambda     K      H
   0.315    0.132    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: 275
Number of extensions: 10
Number of successful extensions: 1
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: 260
Length of database: 260
Length adjustment: 24
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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