GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aatQ in Sinorhizobium meliloti 1021

Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate SMa2197 SMa2197 ABC transporter permease

Query= reanno::pseudo1_N1B4:Pf1N1B4_772
         (248 letters)



>lcl|FitnessBrowser__Smeli:SMa2197 SMa2197 ABC transporter permease
          Length = 304

 Score =  108 bits (271), Expect = 1e-28
 Identities = 70/242 (28%), Positives = 113/242 (46%), Gaps = 11/242 (4%)

Query: 2   NYNWDWGVFFKSTGVGSEIYFDWYLSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIV 61
           N N+ W V      V   ++    L GL  T+ + V   +I ++LG+I  +M    N ++
Sbjct: 49  NPNFGWDV------VADYLFDSRILWGLSLTVWLTVVTMVIGVVLGTIFAIMAMADNVVI 102

Query: 62  SGIATCYVELFRNVPLLVQLFIWY---FLVPDLLPAD--IQEWYKQDLNPTTSAFLSVVV 116
           S +A  Y+  FR  P+LVQL  WY    L P L         W     N   S   + V+
Sbjct: 103 STVANAYIWFFRGTPVLVQLIFWYNLGALFPQLSVGVPFTSLWVSVPTNTLISPVTAAVL 162

Query: 117 CLGLFTTARVCEQVRTGIQALPRGQEAAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEF 176
            LGL   A + E +R+G+ ++  GQ  AA+++G    +  W +LLPQA  +IIPP  ++ 
Sbjct: 163 GLGLNEGAYMSEIIRSGLMSVDPGQRQAAKSLGMTNGKTLWRILLPQAMPVIIPPTGNQT 222

Query: 177 LNVFKNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRSVEKK 236
           + + K SS+ S+I L +LL   +     +        +A + Y      L  +   +E+ 
Sbjct: 223 IGMLKTSSLVSVISLADLLYSAQTIYSRNFQTIPLLIVACIWYLAATTILSAVQVRIERH 282

Query: 237 VA 238
            A
Sbjct: 283 FA 284


Lambda     K      H
   0.326    0.140    0.433 

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: 191
Number of extensions: 8
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: 248
Length of database: 304
Length adjustment: 25
Effective length of query: 223
Effective length of database: 279
Effective search space:    62217
Effective search space used:    62217
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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