CATH Domain: 3bjdA02

3bjdA02

PDB 3bjd, Chain A, Domain 2

CATH Code	Level Description	Links
1	Mainly Alpha
1.20	Up-down Bundle
1.20.910	Heme Oxygenase; Chain A
1.20.910.10	Heme Oxygenase; Chain A	Gene3D
1.20.910.10.8
1.20.910.10.8.1
1.20.910.10.8.1.1
1.20.910.10.8.1.1.1
1.20.910.10.8.1.1.1.1

Structure
Sequence
History

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Segment boundaries for domain 3bjdA02

Domain	Start PDB Residue	Stop PDB Residue
3bjdA01	6	93
3bjdA02	103	327

What is a Structural Neighbour?

The term "structural neighbour" is used here to describe two CATH domains that share a degree of structural similarity. The SSAP algorithm is used to calculate this similarity and works by generating a structure-based pairwise alignment of the two domains then scoring this alignment using a RMSD score which has been normalised by the length of the larger domain divided by the number of aligned residues (SIMAX).

Structural Neighbourhood (7 entries)

There are 7 matching structural neighberhood comparisons for CATH ID 1.20.910.10.8.1.1.1.1 (SIMAX score < 5)

Match	SSAP score	Match Keywords	Match Superfamily	Length	Sequence Id	Overlap	RMSD	SIMAX
1rcwB00	86.39	Chlamydia trachomatisPqqC-like proteinPyrroloquinoline-quinone synthase [EC:1.3.3.11]	1.20.910.10	210	15	92	2.07	2.23
3hlxA00	81.77	Pyrroloquinoline-quinone synthase [EC:1.3.3.11]Klebsiella pneumoniae subsp. pneumoniae MGH 78578Pyrroloquinoline-quinone synthase	1.20.910.10	247	17	85	2.86	3.36
2qcxA00	80.08	Thiamine metabolismBacillus subtilisThiaminase-2Transcriptional activator TenA [EC:3.5.99.2]	1.20.910.10	222	8	93	3.90	4.18
1uddA00	79.79	Thiamine metabolismPyrococcus horikoshiiTranscriptional activator TenA [EC:3.5.99.2]218aa long hypothetical transcriptional regulator	1.20.910.10	215	11	92	4.07	4.42
1rtwB00	78.72	Pyrococcus furiosusTranscriptional activator, putative	1.20.910.10	204	11	89	3.87	4.31
1sk7A00	77.34	Pseudomonas aeruginosaHeme oxygenaseHeme oxygenase	1.20.910.10	187	11	82	3.17	3.86
2f2gA00	75.80	Seed maturation protein PM36 homologArabidopsis thaliana	1.20.910.10	211	8	89	4.18	4.65

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Domain ATOM Sequence

>pdb|3bjdA02
LSEEDFQKRLEQEIAAQERHPSQYVFSGSASRAQLQVFLRHQWFRTFRLYRDAADLLVNLTDVDEAAALARYLYGELGEE
DEKGSHPRLLAKLLEAIGLEADFQAVSTPEEIAYLNNRARAFRHAEVGWGLAVFYITELVVPGNHEKLYRALLQAGLSED
QAEYYKVHISLVPKREWQLIARRIPDVQFQNAFLTSLSQHFRVERAYYDAIWEEQSV

BLAST against CATH

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Domain COMBS Sequence

>pdb|3bjdA02
LSEEDFQKRLEQEIAAQSRERHPXSQYVFSGSASRAQLQVFLRHQWFRTFRLYRDAADLLVNLTDVDEAAALARYLYGEL
GEEDEKGSHPRLLAKLLEAIGLEADFQAVSTXPEEIAYLNNRARAFRHAEVGWGLAVFYITELVVPGNHEKLYRALLQAG
LSEDQAEYYKVHISLVPPRAKREWQLIARRIPDVQFQNAFLTSLSQHFRVERAYYDAIWEEXQSVKGS

BLAST against CATH

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Domain History Events (46)

Domain assigned by cuff on 06 Feb 2009 16:53

homology match

Domain assignment manual match h by cuff on 06 Feb 2009 16:51

same superfamily

Homcheck allotment by cuff on 06 Feb 2009 16:49

User 'cuff' has allocated a domain to themselves for HomChecking with comment : Grabbed this domain via HomCheck's "Get Me A Domain" button.

Flow stage update by cuff on 06 Feb 2009 16:49

User 'cuff' has allocated a domain to themselves for HomChecking with comment : Grabbed this domain via HomCheck's "Get Me A Domain" button.

Flow stage update by auto on 28 Nov 2008 23:37

Domain "3bjdA02" SCOP scan with no results - no SCOP mapping

Domain scan scop cath by auto on 28 Nov 2008 23:37

Adding scan of type "DOMAIN_SCAN_SCOP_CATH" with 0 results for 3bjdA02

Flow stage update by auto on 28 Nov 2008 23:29

Retrieved PRC_PFAMCATH results for job ID SID5922139213534112 and results inserted.

Domain scan prc pfamcath by auto on 28 Nov 2008 23:28

Adding scan of type "DOMAIN_SCAN_PRC_PFAMCATH" with 10 results for 3bjdA02

Update comment by auto on 28 Nov 2008 21:53

PRC_PFAMCATH job SID5922139213534112 is not yet finished.

Flow stage update by auto on 28 Nov 2008 21:51

The entry "3bjdA02" has been submitted to the PRC_PFAMCATH webservice.

Prc pfamcath submit by auto on 28 Nov 2008 21:51

The entry "3bjdA02" has been submitted to the PRC_PFAMCATH webservice.

Flow stage update by auto on 28 Nov 2008 21:40

Retrieved SSAP results for job ID SID5368592839191808 and results inserted.

Domain scan ssap cath by auto on 28 Nov 2008 21:38

Adding scan of type "DOMAIN_SCAN_SSAP_CATH" with 411 results for 3bjdA02

Update comment by auto on 27 Nov 2008 07:21

SSAP job SID5368592839191808 is not yet finished.

Flow stage update by auto on 27 Nov 2008 07:14

The entry "3bjdA02" has been submitted to the SSAP webservice.

Ssap cath submit by auto on 27 Nov 2008 07:14

The entry "3bjdA02" has been submitted to the SSAP webservice.

Flow stage update by auto on 27 Nov 2008 06:43

Retrieved PRC results for job ID SID1432208590343376 and inserted them into the database.

Domain scan prc cath by auto on 27 Nov 2008 06:43

Adding scan of type "DOMAIN_SCAN_PRC_CATH" with 12 results for 3bjdA02

Flow stage update by auto on 27 Nov 2008 06:29

The entry "3bjdA02" has been submitted to the PRC webservice.

Prc cath submit by auto on 27 Nov 2008 06:29

The entry "3bjdA02" has been submitted to the PRC webservice.

Flow stage update by auto on 27 Nov 2008 05:58

Retrieved HMM(SAM) results for job ID SID5361234312962448 and inserted them into the database.

Domain scan sam cath by auto on 27 Nov 2008 05:58

Adding scan of type "DOMAIN_SCAN_SAM_CATH" with 2 results for 3bjdA02