GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Burkholderia phytofirmans PsJN

Align Probable ATP-binding component of ABC transporter, 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 BPHYT_RS24015 BPHYT_RS24015 ATP-binding protein

Query= TCDB::Q9HU32
         (257 letters)



>FitnessBrowser__BFirm:BPHYT_RS24015
          Length = 263

 Score =  335 bits (858), Expect = 7e-97
 Identities = 166/256 (64%), Positives = 207/256 (80%)

Query: 2   AEATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQ 61
           A A  AL ++N+HK +GD  VLKGISL A  GDVISILG+SGSGKSTFLRC+NLLE P  
Sbjct: 3   ATAPVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDD 62

Query: 62  GQILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRR 121
           G + ++GEEL++K+  +G L  +D +Q++R+RS+LG VFQNFNLW HM++L+N+IE P R
Sbjct: 63  GSVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMR 122

Query: 122 VLGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPT 181
           V  +S+AE++E AE LLAKVG+A+KR  YPA LSGGQQQR AIAR LAM PKV+LFDEPT
Sbjct: 123 VQKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPT 182

Query: 182 SALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVF 241
           SALDPE+V EVL V+R+LAEEGRTML+VTHEM FAR VS+ V+FLHQG VE  GTP +VF
Sbjct: 183 SALDPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVF 242

Query: 242 ENPQSARCKQFMSSHR 257
              +S R +QF+SSH+
Sbjct: 243 VECKSDRFRQFVSSHQ 258


Lambda     K      H
   0.317    0.133    0.367 

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: 214
Number of extensions: 5
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: 257
Length of database: 263
Length adjustment: 24
Effective length of query: 233
Effective length of database: 239
Effective search space:    55687
Effective search space used:    55687
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