GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Escherichia coli BW25113

Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate 14987 b0862 arginine transporter subunit (NCBI)

Query= reanno::pseudo5_N2C3_1:AO356_09905
         (231 letters)



>FitnessBrowser__Keio:14987
          Length = 238

 Score =  182 bits (462), Expect = 5e-51
 Identities = 97/226 (42%), Positives = 148/226 (65%), Gaps = 13/226 (5%)

Query: 12  LAAGALMTVKLALSALCLGLVLGLLGALAKTSPYKPLQWLGGTYSTLVRGIPELLWVLLI 71
           LA+ A MTV LA+ AL +GL L +  A+ +++ ++P+ W G    T++RG+PE+L VL I
Sbjct: 7   LASAAGMTVGLAVCALIVGLALAMFFAVWESAKWRPVAWAGSALVTILRGLPEILVVLFI 66

Query: 72  YFGTVNLMRALGE-------------YLGMPDLALNAFAAGVIALGLCFGAYATEVFRGA 118
           YFG+  L+  L +              + + +  ++ F  GVIAL L + AYA++  RGA
Sbjct: 67  YFGSSQLLLTLSDGFTINLGFVQIPVQMDIENFDVSPFLCGVIALSLLYAAYASQTLRGA 126

Query: 119 ILAIPKGHREAGVALGLSKWRIFTRLIMPQMWRIALPGLGNLFMILMKDTALVSVIGLEE 178
           + A+P G  E+G ALGLSK  IF RL+MPQMWR ALPGLGN +++L+KDTALVS+I + +
Sbjct: 127 LKAVPVGQWESGQALGLSKSAIFFRLVMPQMWRHALPGLGNQWLVLLKDTALVSLISVND 186

Query: 179 IMRHAQIGVTVSKQPFTFYMVAALMYLGLTVLAMLGMHLLERRAAR 224
           +M   +   T +++PFT+Y+VAA +YL +T+L+   +  ++ RA R
Sbjct: 187 LMLQTKSIATRTQEPFTWYIVAAAIYLVITLLSQYILKRIDLRATR 232


Lambda     K      H
   0.329    0.143    0.435 

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: 181
Number of extensions: 6
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: 231
Length of database: 238
Length adjustment: 23
Effective length of query: 208
Effective length of database: 215
Effective search space:    44720
Effective search space used:    44720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 46 (22.3 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