GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Sphingomonas koreensis DSMZ 15582

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate Ga0059261_2840 Ga0059261_2840 Enoyl-CoA hydratase/carnithine racemase

Query= CharProtDB::CH_091794
         (261 letters)



>FitnessBrowser__Korea:Ga0059261_2840
          Length = 263

 Score =  140 bits (353), Expect = 3e-38
 Identities = 85/247 (34%), Positives = 137/247 (55%), Gaps = 5/247 (2%)

Query: 11  EGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAGADISE 70
           +G + + TINRP  +NA++ + +   + +   ++ D E   +ILTGAG ++F AGAD+  
Sbjct: 10  DGGIVIATINRPARMNAIDRNLIASFEALFDRLDADREARVLILTGAG-RAFCAGADLKS 68

Query: 71  --MKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDIRIASSNA 128
             ++     E     +   ++  R+  L +PVIAAVNG A GGG    ++ DIRIA  +A
Sbjct: 69  DFVESAGPEESLASQLRLARLMERIANLRQPVIAAVNGAAAGGGFAFTLAADIRIAGRSA 128

Query: 129 RFGQPEVGLGITPGFGGTQ-RLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNKVVEPSE 187
            F      LG++ G  G    L RL+G+  A +L+ T +   A+EA RIG V + V    
Sbjct: 129 HFSIANARLGLSAGECGISWLLPRLIGLSRAFELMLTGRKFDAEEAERIGYVVRTVADDV 188

Query: 188 LMNTAKEIANKIVSNAPVAVKLSKQAINRGMQ-CDIDTALAFESEAFGECFSTEDQKDAM 246
           L++TA E A  I +NAP  V ++K  + R ++   +  A+A E+     C  + D ++A+
Sbjct: 189 LLDTALETARLIAANAPFGVAMTKDVVRRNLETASMQAAIALEARTQLLCGGSGDFREAV 248

Query: 247 TAFIEKR 253
           +AF+EKR
Sbjct: 249 SAFLEKR 255


Lambda     K      H
   0.317    0.134    0.365 

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: 150
Number of extensions: 13
Number of successful extensions: 4
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: 261
Length of database: 263
Length adjustment: 25
Effective length of query: 236
Effective length of database: 238
Effective search space:    56168
Effective search space used:    56168
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