GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Lactobacillus silagei IWT126

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_089136028.1 CES79_RS00805 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q9HU32
         (257 letters)



>NCBI__GCF_002217945.1:WP_089136028.1
          Length = 246

 Score =  222 bits (566), Expect = 5e-63
 Identities = 116/249 (46%), Positives = 172/249 (69%), Gaps = 13/249 (5%)

Query: 8   LEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQILVS 67
           +E  N+ K YGD   L  I+LT   G+ + ++G SGSGKST +R +N LE   +GQ++V+
Sbjct: 4   IEFHNVQKYYGDFHALHDINLTIDAGETVVLIGPSGSGKSTLIRTVNGLERIQEGQLIVN 63

Query: 68  GEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGKSK 127
           G++L  +K+            +NR+R  +G VFQ+FNL+ + +IL+N++ APR VL + +
Sbjct: 64  GQDLANRKT-----------DMNRIRKNVGMVFQHFNLYANKTILENIMLAPRLVLKRPE 112

Query: 128 AEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDPE 187
            E  +IA  +L +VG+AD+    PAQLSGGQQQR AIAR+LAM+PK +LFDEPTSALDPE
Sbjct: 113 EENKKIAMDMLDRVGLADQAPKMPAQLSGGQQQRIAIARSLAMRPKALLFDEPTSALDPE 172

Query: 188 MVQEVLNVIRALA-EEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFE-NPQ 245
           M+ +VLNV++ +A +   TML+VTHEM FAR+V++ VVF+  G + E  + ++ F+  P 
Sbjct: 173 MIDDVLNVMKDIARDSSMTMLVVTHEMGFAREVANRVVFMADGHILEDDSKEKFFDGQPS 232

Query: 246 SARCKQFMS 254
           + R +QF+S
Sbjct: 233 NERARQFLS 241


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: 149
Number of extensions: 5
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: 246
Length adjustment: 24
Effective length of query: 233
Effective length of database: 222
Effective search space:    51726
Effective search space used:    51726
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