GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltJ in Phaeobacter inhibens BS107

Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate GFF2619 PGA1_c26600 amino acid ABC transporter, permease protein

Query= TCDB::Q88NY3
         (248 letters)



>FitnessBrowser__Phaeo:GFF2619
          Length = 273

 Score =  103 bits (256), Expect = 5e-27
 Identities = 70/222 (31%), Positives = 122/222 (54%), Gaps = 11/222 (4%)

Query: 22  LDWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNR--LVSGIATAYVELFRNVPLLV 79
           L   + G+  TI + + ++ +A LLG  LG+     +R  ++   A  Y+E+ R +P++V
Sbjct: 46  LSTLMRGVQLTIFVTLISFFLASLLG--LGLALAAGSRWLVIRQGARFYIEVVRGIPIIV 103

Query: 80  QLFIWYFLVPDLLPEGLQEWFKQD--LNPTTSA----LISVVICLGLFTAARVCEQVRTG 133
            L    F++   L E L+ W      L+P  +     L   +I L +  +A + E  R G
Sbjct: 104 LLLYVAFVLAPALVE-LRNWLGDHIGLDPIRTRNFPLLWRAIIALMIAYSAFISEVFRAG 162

Query: 134 IQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLME 193
           +Q++ +GQ  AA+++G S    +  ++ PQA R I+PPL ++F+ + K+SS+ S++G+ +
Sbjct: 163 LQSVDEGQIEAAKSLGLSRWHRFRFIVFPQAIRTILPPLGNDFVALVKDSSLVSVLGVAD 222

Query: 194 LLAQTKQTAEFSANLFEAFTLATLIYFTLNMGLMLLMRMVEK 235
           +    K TA  +   FE + +  LIY TL +GL LL+R  EK
Sbjct: 223 VTQLGKLTAVGNFRYFETYNVVALIYLTLTIGLSLLLRRFEK 264


Lambda     K      H
   0.325    0.139    0.425 

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: 147
Number of extensions: 9
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: 248
Length of database: 273
Length adjustment: 24
Effective length of query: 224
Effective length of database: 249
Effective search space:    55776
Effective search space used:    55776
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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