GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Escherichia coli BW25113

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 16031 b1917 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)

Query= TCDB::Q9HU32
         (257 letters)



>FitnessBrowser__Keio:16031
          Length = 250

 Score =  254 bits (648), Expect = 2e-72
 Identities = 132/247 (53%), Positives = 173/247 (70%), Gaps = 5/247 (2%)

Query: 7   ALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQILV 66
           A+E++NL K++    VL GI L  + G+V++I+G SGSGK+T LR INLLE P  G I V
Sbjct: 3   AIEVKNLVKKFHGQTVLHGIDLEVKPGEVVAIIGPSGSGKTTLLRSINLLEQPEAGTITV 62

Query: 67  SGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGKS 126
               +   +S     ++     I +LR  +GFVFQNFNL+PH ++L+N+IE P  V G+ 
Sbjct: 63  GDITIDTARS-----LSQQKSLIRQLRQHVGFVFQNFNLFPHRTVLENIIEGPVIVKGEP 117

Query: 127 KAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDP 186
           K EA   A  LLAKVG+A K  SYP +LSGGQQQR AIAR LAM+P+VILFDEPTSALDP
Sbjct: 118 KEEATARARELLAKVGLAGKETSYPRRLSGGQQQRVAIARALAMRPEVILFDEPTSALDP 177

Query: 187 EMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENPQS 246
           E+V EVLN IR LA+E RTM++VTHEMSFAR V+   +F+ QG + EQG  + +F +P+ 
Sbjct: 178 ELVGEVLNTIRQLAQEKRTMVIVTHEMSFARDVADRAIFMDQGRIVEQGAAKALFADPEQ 237

Query: 247 ARCKQFM 253
            R +QF+
Sbjct: 238 PRTRQFL 244


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: 188
Number of extensions: 5
Number of successful extensions: 2
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: 250
Length adjustment: 24
Effective length of query: 233
Effective length of database: 226
Effective search space:    52658
Effective search space used:    52658
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