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_RS01625 AZOBR_RS01625 hypothetical protein

Query= uniprot:E4PLR7
         (223 letters)



>FitnessBrowser__azobra:AZOBR_RS01625
          Length = 228

 Score = 81.3 bits (199), Expect = 1e-20
 Identities = 74/240 (30%), Positives = 106/240 (44%), Gaps = 36/240 (15%)

Query: 2   SARANILGKLRNSLAGTTPRPDEFDERLVTAPWRYAPEDRIERLRSLMEAVHTEVHPCRS 61
           SARA ILG +R +L  +    +E   RL T P            R+L+ A     H    
Sbjct: 6   SARAQILGGIRKAL-NSAEGSEEARRRLATHP------------RNLIPARAQRPH---- 48

Query: 62  DNWPELVAELLNKRNLTNLLCAPSKEHGRALQAYFEATEQKVEL-LAYDQPVEA--WKEE 118
           D   EL A +  + + T  L     E   A+  Y        E+ +A D  ++   W + 
Sbjct: 49  DEQVELFAAMATEVSATVELLGGMAEVPGAVADYLAGLNLPAEVRVAPDAALDPIPWDQR 108

Query: 119 LFWSVE---------ASLTGTLGGIAATGTLVLWPDCHEPRLMSLVPPVHIALLKASEIH 169
              +V          ASLTG   G+A TGTL+L      P  ++ +P  HI +L+  +I 
Sbjct: 109 ATLTVTKGRARDSDGASLTGAFAGVAETGTLMLLSGAERPTTLNFLPDTHIVVLRRGQIV 168

Query: 170 DNLYDMMV------AQDWAAG-LPTNVLLVSGPSKTADIEQVLAYGAHGPRELIVLVLED 222
             + D         A D   G LP  V  ++GPS+T DIE  +  GAHGPR L +L++ED
Sbjct: 169 GTMEDAWDRLRAAGATDGGKGALPRTVNFITGPSRTGDIEMRIELGAHGPRRLHILLVED 228


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: 123
Number of extensions: 4
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: 228
Length adjustment: 22
Effective length of query: 201
Effective length of database: 206
Effective search space:    41406
Effective search space used:    41406
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