GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_0896 Ga0059261_0896 Citrate
           lyase beta subunit
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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