GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citE in Sphingomonas koreensis DSMZ 15582

Align citrate (pro-3S)-lyase (EC 4.1.3.6) (characterized)
to candidate Ga0059261_0896 Ga0059261_0896 Citrate lyase beta subunit

Query= BRENDA::Q037K5
         (292 letters)



>FitnessBrowser__Korea:Ga0059261_0896
          Length = 272

 Score =  123 bits (309), Expect = 4e-33
 Identities = 92/283 (32%), Positives = 140/283 (49%), Gaps = 25/283 (8%)

Query: 6   RTMMFVPGANPGMLRDAPIYGADAIMFDLEDAVSLKEKDTARMLVYSALKTFDYSSVETV 65
           RT +F+P +NP  +  A    AD I+ DLEDAV   +KD AR    SA     +      
Sbjct: 10  RTALFLPASNPRAIEKARTLAADMIILDLEDAVKAGDKDAAREAAQSAE---GFGDRLFG 66

Query: 66  VRVNALD-AGGDQDIEAMVLGGINVVRLPKTETAQDIIDVDAVITAVEEKYGIQNGTTHM 124
           +RVNA D A   +D+EA+       V +PK E A+ I+                +    +
Sbjct: 67  IRVNAEDSAHWIEDLEAVRKSAATHVIVPKVEKAETIVRAAF------------HSERPV 114

Query: 125 MAAIESAEGVLNAREIAQASS---RMIGIALGAEDYLTSQHTHRSTDGAELSFARNYILH 181
           +A IE+A GV++A  IA A+     M G+  G  D   S     +    ++  +   I+ 
Sbjct: 115 LAMIETAAGVMHAGAIAGATGSGVEMAGLIAGTNDLAASLRLPPAAGRTQMQLSLQLIVL 174

Query: 182 AAREAGIAAIDTVYTQVDNEEGLRHETALIKQLGFDGKSVINPRQIPVINGVFAPALAEV 241
           AAR A I  +D V+ ++D+ +GL  E A  + LGFDGKS+I+P QI ++   F P+ AE+
Sbjct: 175 AARAAEIWVLDGVFNRLDDGDGLAAEAAEGRLLGFDGKSLIHPNQIDIVRAAFDPSPAEL 234

Query: 242 QKAREIVAGLKEAEAKGAGVVSVNGQMVDKPVVERAQYTIALA 284
             AR ++A      A G G      +M++   VE+A+  +A A
Sbjct: 235 DDARALIA------AAGGGAERYKDRMIEDMHVEQAKLLLARA 271


Lambda     K      H
   0.316    0.132    0.355 

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: 176
Number of extensions: 9
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: 292
Length of database: 272
Length adjustment: 26
Effective length of query: 266
Effective length of database: 246
Effective search space:    65436
Effective search space used:    65436
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 (21.6 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