GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutC in Azospirillum brasilense Sp245

Align Protein containing DUF162 (characterized, see rationale)
to candidate AZOBR_RS25105 AZOBR_RS25105 hypothetical protein

Query= uniprot:E4PLR7
         (223 letters)



>FitnessBrowser__azobra:AZOBR_RS25105
          Length = 223

 Score =  180 bits (457), Expect = 2e-50
 Identities = 98/220 (44%), Positives = 134/220 (60%), Gaps = 3/220 (1%)

Query: 3   ARANILGKLRNSLAGTTPRPDEFDERLVTAPWRYAPEDRIERLRSLMEAVHTEVHPCRSD 62
           +R  ILGKLR         P E D  ++    R+   +R+ER++ +MEAVHTE       
Sbjct: 4   SRNAILGKLRAGRDAHPLTPPESDFAVLRNK-RWDGAERLERIKRMMEAVHTEFLETTEA 62

Query: 63  NWPELVAELLNKRNLTNLLCAPSKEHGRALQAYFEATEQK--VELLAYDQPVEAWKEELF 120
           +WP  V   L  +   NLL  P+ E G  L + + A+      EL+ Y   VE +KE LF
Sbjct: 63  DWPADVQAFLTAQGTRNLLFGPATEAGGRLSSEWAASGMAGGPELIPYADRVETFKERLF 122

Query: 121 WSVEASLTGTLGGIAATGTLVLWPDCHEPRLMSLVPPVHIALLKASEIHDNLYDMMVAQD 180
             ++A +T TLG IA TG+L++WP   EPRLMSLVP +H+ALL+A  ++D  +  M    
Sbjct: 123 DGIDAGITTTLGAIADTGSLIVWPTPEEPRLMSLVPHMHLALLRADALYDTFWQAMTENR 182

Query: 181 WAAGLPTNVLLVSGPSKTADIEQVLAYGAHGPRELIVLVL 220
           WA G+PTN LL+SGPSKTADIEQ LAYG HGP+ L+V+++
Sbjct: 183 WADGMPTNALLISGPSKTADIEQTLAYGVHGPKRLVVVIV 222


Lambda     K      H
   0.317    0.133    0.406 

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: 178
Number of extensions: 7
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: 223
Length of database: 223
Length adjustment: 22
Effective length of query: 201
Effective length of database: 201
Effective search space:    40401
Effective search space used:    40401
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 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