GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Nocardioides daejeonensis MJ31

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 WP_110206230.1 DNK54_RS07055 ABC transporter ATP-binding protein

Query= TCDB::Q9HU32
         (257 letters)



>NCBI__GCF_003194585.1:WP_110206230.1
          Length = 231

 Score =  152 bits (384), Expect = 6e-42
 Identities = 91/237 (38%), Positives = 135/237 (56%), Gaps = 17/237 (7%)

Query: 4   ATPALEIRNLHKRY----GDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENP 59
           +TP LE++ + K Y    G +E ++GI      G+ ++++G SGSGKST +  +  L+ P
Sbjct: 2   STPVLELQGVRKTYSTGAGAVEAVRGIDAVVVAGEYVAVVGPSGSGKSTLMHILGCLDVP 61

Query: 60  HQGQILVSGEELRLKKSKNGDLVAADSQQINRLRS-ELGFVFQNFNLWPHMSILDNVIEA 118
             G+ LV G+          D+ A D  Q+  +R+ E+GFVFQ F+L P ++ L NV E 
Sbjct: 62  TSGRQLVRGQ----------DVAAMDEAQLAAVRNREIGFVFQQFHLLPGLTALRNV-EL 110

Query: 119 PRRVLGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFD 178
           P    G +  E    A   L +VG+ D+    P +LSGGQQQR AIAR L   P ++L D
Sbjct: 111 PLIYAGVTALERRRRATVALTRVGLGDRADHRPGELSGGQQQRVAIARALVTDPALVLAD 170

Query: 179 EPTSALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQG 235
           EPT  LD     +VL + R L ++GRT++L+THE   A + +  V+ L  GL+E+ G
Sbjct: 171 EPTGNLDSRATADVLALFRELHDQGRTIVLITHEQEVAAE-ADRVLTLRDGLLEDAG 226


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: 111
Number of extensions: 7
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: 257
Length of database: 231
Length adjustment: 24
Effective length of query: 233
Effective length of database: 207
Effective search space:    48231
Effective search space used:    48231
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: 46 (22.3 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