GapMind for catabolism of small carbon sources

 

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

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate H281DRAFT_05882 H281DRAFT_05882 amino acid ABC transporter substrate-binding protein, PAAT family

Query= TCDB::Q9HU31
         (250 letters)



>FitnessBrowser__Burk376:H281DRAFT_05882
          Length = 262

 Score =  161 bits (408), Expect = 1e-44
 Identities = 94/246 (38%), Positives = 144/246 (58%), Gaps = 7/246 (2%)

Query: 7   ILLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCAKMKTEC 66
           +L+AA A     +   + + LR G E AYPPF     +GQ  GFD+D+G A+CAK+  +C
Sbjct: 10  LLVAATAASLSTVTTQSQETLRFGIEAAYPPFESKSPTGQLQGFDVDVGNAVCAKLGMKC 69

Query: 67  EVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKSVDFKTD 126
             V + +DG+IPAL A+KFD I ++M+IT++RKQ+++FT P Y   +  VA ++     D
Sbjct: 70  VWVENAFDGLIPALQARKFDVINSAMNITEKRKQSIEFTKPIYVVPIVMVARRASGLLPD 129

Query: 127 KDSLKGKVIGAQRATIAGTWLEDNMADV-VTIKLYDTQENAYLDLSSGRLDGVLAD-KFV 184
             SL+GK +G  +A+    +L+ + A   VT+  Y  Q+  Y DL +GRLD  + + + V
Sbjct: 130 VKSLQGKRVGVLQASSQEDFLKRHWAPAGVTVVPYADQDQVYADLVAGRLDAAVQEAQTV 189

Query: 185 QYDWLKSDAGKEFEFKGEPVFD----NDKIGIAVRKGDP-LREKLNAALKEIVADGTYKK 239
           Q  +L   AG E+   G+P+ D     +  G  +RKGD  L  K++AAL  +  DGT   
Sbjct: 190 QDGFLVKPAGHEYAIVGKPLSDPATLGEGTGWGLRKGDKVLVAKVDAALDALKKDGTLSS 249

Query: 240 INDKYF 245
           ++ KYF
Sbjct: 250 LSQKYF 255


Lambda     K      H
   0.317    0.135    0.392 

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: 160
Number of extensions: 8
Number of successful extensions: 3
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: 250
Length of database: 262
Length adjustment: 24
Effective length of query: 226
Effective length of database: 238
Effective search space:    53788
Effective search space used:    53788
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 (21.7 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