GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Sphingomonas koreensis DSMZ 15582

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate Ga0059261_2803 Ga0059261_2803 Enoyl-CoA hydratase/carnithine racemase

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>FitnessBrowser__Korea:Ga0059261_2803
          Length = 266

 Score =  128 bits (322), Expect = 1e-34
 Identities = 82/253 (32%), Positives = 125/253 (49%), Gaps = 10/253 (3%)

Query: 17  LVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNL------- 69
           L+LT+ +P  RNAL P++  A + A      D S+  V++TGA + FCAGGN+       
Sbjct: 15  LILTIDDPATRNALSPELTRALVAACAEANADMSVSCVILTGAGDVFCAGGNIKDMYARA 74

Query: 70  NRLLENRAKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAA 129
           N    N A+        +  +A  +  L +   P IAAV+GAA GAG   A  C + +A+
Sbjct: 75  NHFAGNAAEIRRTYQAGVQTIARALYDLEV---PSIAAVNGAAMGAGMDFATMCTMRIAS 131

Query: 130 DDAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKP 189
           + AKF  S+ ++GLT   GG+WFL +A+    A E+ + G  I AAR  E+G+V+ +   
Sbjct: 132 ERAKFAESFIKLGLTSAAGGAWFLNRAIGASAAAELALTGDTIDAARALEIGLVSGVVPH 191

Query: 190 GTARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEG 249
               D A A A  + +   +S+     L+  +    LS  L              +  E 
Sbjct: 192 AALLDEARALAKRIARHPAHSIRLNTRLLRESARLDLSAALEIASAMQAVVQQTDDQYEA 251

Query: 250 ISAFLEKRAPVYK 262
           ++A +EKR P YK
Sbjct: 252 VAAAVEKRPPAYK 264


Lambda     K      H
   0.317    0.132    0.377 

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: 138
Number of extensions: 5
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: 262
Length of database: 266
Length adjustment: 25
Effective length of query: 237
Effective length of database: 241
Effective search space:    57117
Effective search space used:    57117
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: 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