Psyllid ID: psy15303

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--
Protein Sequence
MATRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTIGCLGFLF
Secondary Structure (PSIPRED)
ccccccccccEEEEEEcccccccHHHHHHHHHHHHHHHHccccccEEEEEEcccccEEEEEEcccEEEEEEc
Secondary Structure Prediction (SSPRO)
cccHccHHHHEEEEEEcccccccHHHHHHHHHHHHHHHHHcccccEEEEEccccccEEEEEccccccccccc
Coil and Loop (DISEMBL)
matrfgskLKELRIHLCqkggsssgvRDFLAQHyvplkqanpkfpilvrecsgvtpvvwariptigclgflf
Flexible Loop (DISEMBL)
matrfgsklkELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTIGCLGFLF
Low Complexity Region (SEG)
MATRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTIGCLGFLF
Disordered region (IsUnstruct)
***********LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTIGCLGFL*
Disordered Region (DISOPRED)
*******KLKELRIHLCQKGG*****RDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTIGCLGFLF
Disordered Region (DISEMBL)
MATRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTIGCLGFLF
Disordered Region (DISPRO)
**TRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTIGCLGFLF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MATRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTIGCLGFLF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	72	2.2.26 [Sep-21-2011]
Q02370	99	NADH dehydrogenase [ubiqu	yes	N/A	0.736	0.535	0.622	6e-15
P0CB80	103	NADH dehydrogenase [ubiqu	N/A	N/A	0.736	0.514	0.622	6e-15
P0CB79	103	NADH dehydrogenase [ubiqu	yes	N/A	0.736	0.514	0.622	6e-15
O43678	99	NADH dehydrogenase [ubiqu	yes	N/A	0.736	0.535	0.622	7e-15
Q4R5E2	99	NADH dehydrogenase [ubiqu	N/A	N/A	0.736	0.535	0.622	8e-15
Q9CQ75	99	NADH dehydrogenase [ubiqu	yes	N/A	0.736	0.535	0.603	2e-14
Q0MQ92	99	NADH dehydrogenase [ubiqu	N/A	N/A	0.736	0.535	0.603	6e-14
Q9FIJ2	97	NADH dehydrogenase [ubiqu	yes	N/A	0.736	0.546	0.566	1e-11
Q07842	94	NADH-ubiquinone oxidoredu	N/A	N/A	0.805	0.617	0.448	1e-08

>sp|Q02370|NDUA2_BOVIN NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 OS=Bos taurus GN=NDUFA2 PE=1 SV=2

 Score = 79.3 bits (194), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 33/53 (62%), Positives = 41/53 (77%)

Query: 9  LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          L+E+RIHLCQ+   S GVRDF+ + YV LK+ANP  PIL+RECS V P +WAR
Sbjct: 16 LREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWAR 68

Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.
Bos taurus (taxid: 9913)

>sp|P0CB80|NDUA2_PONPY NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 OS=Pongo pygmaeus GN=NDUFA2 PE=3 SV=1

 Score = 79.3 bits (194), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 33/53 (62%), Positives = 41/53 (77%)

Query: 9  LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          L+E+RIHLCQ+   S GVRDF+ + YV LK+ANP  PIL+RECS V P +WAR
Sbjct: 16 LREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWAR 68

Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Pongo pygmaeus (taxid: 9600)

>sp|P0CB79|NDUA2_PONAB NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 OS=Pongo abelii GN=NDUFA2 PE=3 SV=1

 Score = 79.3 bits (194), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 33/53 (62%), Positives = 41/53 (77%)

Query: 9  LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          L+E+RIHLCQ+   S GVRDF+ + YV LK+ANP  PIL+RECS V P +WAR
Sbjct: 16 LREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWAR 68

Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Pongo abelii (taxid: 9601)

>sp|O43678|NDUA2_HUMAN NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 OS=Homo sapiens GN=NDUFA2 PE=1 SV=3

 Score = 79.0 bits (193), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 33/53 (62%), Positives = 41/53 (77%)

Query: 9  LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          L+E+RIHLCQ+   S GVRDF+ + YV LK+ANP  PIL+RECS V P +WAR
Sbjct: 16 LREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWAR 68

Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Homo sapiens (taxid: 9606)

>sp|Q4R5E2|NDUA2_MACFA NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 OS=Macaca fascicularis GN=NDUFA2 PE=3 SV=3

 Score = 79.0 bits (193), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 33/53 (62%), Positives = 41/53 (77%)

Query: 9  LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          L+E+RIHLCQ+   S GVRDF+ + YV LK+ANP  PIL+RECS V P +WAR
Sbjct: 16 LREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWAR 68

Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Macaca fascicularis (taxid: 9541)

>sp|Q9CQ75|NDUA2_MOUSE NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 OS=Mus musculus GN=Ndufa2 PE=1 SV=3

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 32/53 (60%), Positives = 41/53 (77%)

Query: 9  LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          L+E+R+HLCQ+   S GVRDF+ Q YV LK+A+P  PIL+RECS V P +WAR
Sbjct: 16 LREIRVHLCQRSPGSQGVRDFIVQRYVELKKAHPNLPILIRECSEVQPKLWAR 68

Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Mus musculus (taxid: 10090)

>sp|Q0MQ92|NDUA2_GORGO NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 OS=Gorilla gorilla gorilla GN=NDUFA2 PE=3 SV=3

 Score = 75.9 bits (185), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 32/53 (60%), Positives = 40/53 (75%)

Query: 9  LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          L+E+RIHLCQ+   S GVRDF+ + YV LK+AN   PIL+RECS V P +WAR
Sbjct: 16 LREIRIHLCQRSPGSRGVRDFIEKRYVELKKANSDLPILIRECSDVQPKLWAR 68

Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Gorilla gorilla gorilla (taxid: 9595)

>sp|Q9FIJ2|NDUA2_ARATH NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 OS=Arabidopsis thaliana GN=At5g47890 PE=3 SV=1

 Score = 68.2 bits (165), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/53 (56%), Positives = 38/53 (71%)

Query: 9  LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          +KELRI LCQ   +S+  R F+ ++Y  LK  NPK PIL+RECSGV P +WAR
Sbjct: 11 MKELRILLCQSSPASAPTRTFVEKNYKDLKSLNPKLPILIRECSGVQPQMWAR 63

Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Arabidopsis thaliana (taxid: 3702)

>sp|Q07842|NDUA2_NEUCR NADH-ubiquinone oxidoreductase 10.5 kDa subunit OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=nuo-10.5 PE=4 SV=1

 Score = 58.5 bits (140), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 35/58 (60%)

Query: 5  FGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARI 62
          F   LKE+R   CQ G  S+  R FL ++Y  +K+ NP  PIL+R+ SG  P V+AR 
Sbjct: 7  FNKGLKEVRFLFCQTGEHSAATRSFLLRNYPAMKKDNPATPILIRDASGTLPKVYARF 64


  Database: swissprot
    Posted date:  Mar 23, 2013  2:32 AM
  Number of letters in database: 191,569,459
  Number of sequences in database:  539,616
  
Lambda     K      H
   0.328    0.143    0.461 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,627,122
Number of Sequences: 539616
Number of extensions: 900214
Number of successful extensions: 2566
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 2557
Number of HSP's gapped (non-prelim): 9
length of query: 72
length of database: 191,569,459
effective HSP length: 44
effective length of query: 28
effective length of database: 167,826,355
effective search space: 4699137940
effective search space used: 4699137940
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (25.8 bits)

Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	72
91083339	90	PREDICTED: similar to NADH dehydrogenase	0.833	0.666	0.7	3e-19
357622081	89	NADH dehydrogenase [Danaus plexippus]	0.847	0.685	0.688	5e-18
193662265	91	PREDICTED: NADH dehydrogenase [ubiquinon	0.833	0.659	0.683	7e-18
443683732	94	hypothetical protein CAPTEDRAFT_108701 [	0.805	0.617	0.672	2e-17
126290815	100	PREDICTED: NADH dehydrogenase [ubiquinon	0.847	0.61	0.606	5e-17
387019617	101	NADH dehydrogenase (ubiquinone) 1 alpha	0.791	0.564	0.649	8e-17
327270325	100	PREDICTED: NADH dehydrogenase [ubiquinon	0.791	0.57	0.666	8e-17
156717414	100	NADH dehydrogenase (ubiquinone) 1 alpha	0.847	0.61	0.590	8e-17
149580687	99	PREDICTED: NADH dehydrogenase [ubiquinon	0.819	0.595	0.627	1e-16
66773106	101	NADH dehydrogenase [ubiquinone] 1 alpha	0.847	0.603	0.590	1e-16

>gi|91083339|ref|XP_974988.1| PREDICTED: similar to NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa [Tribolium castaneum] gi|270008152|gb|EFA04600.1| hypothetical protein TcasGA2_TC013353 [Tribolium castaneum]

 Score = 99.4 bits (246), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 42/60 (70%), Positives = 49/60 (81%)

Query: 2  ATRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          A RFG++LKELR+HLCQK  SS GVRDF+ QHYV +K  NPK PIL+RECSGV P +WAR
Sbjct: 4  AIRFGARLKELRLHLCQKSASSQGVRDFIEQHYVAIKSNNPKLPILIRECSGVEPKLWAR 63

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357622081|gb|EHJ73687.1| NADH dehydrogenase [Danaus plexippus]

 Score = 95.1 bits (235), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/61 (68%), Positives = 48/61 (78%)

Query: 1  MATRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWA 60
          MA RF   LKELRIHLCQ    S+GVRDF+ ++YV LK+ NPKFPIL+RECSGV P VWA
Sbjct: 1  MAVRFAGALKELRIHLCQTNQQSAGVRDFIQKYYVGLKKENPKFPILIRECSGVQPRVWA 60

Query: 61 R 61
          R
Sbjct: 61 R 61

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193662265|ref|XP_001950727.1| PREDICTED: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2-like [Acyrthosiphon pisum]

 Score = 94.4 bits (233), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 41/60 (68%), Positives = 50/60 (83%)

Query: 2  ATRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          A +FGS LKELR+HLCQ   SS GVR F+ ++Y+P+K+ANPKFPILVRECSGV P V+AR
Sbjct: 3  AIKFGSHLKELRLHLCQSSSSSKGVRQFIEKYYIPMKKANPKFPILVRECSGVEPKVFAR 62

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

>gi|443683732|gb|ELT87889.1| hypothetical protein CAPTEDRAFT_108701 [Capitella teleta]

 Score = 93.2 bits (230), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 47/58 (81%)

Query: 4  RFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          +F + L+ELRIHLCQK  SS GVR+F+ Q+YV +KQ NPKFPIL+RECS V P VWAR
Sbjct: 8  KFAAPLRELRIHLCQKSASSQGVREFIEQNYVTIKQNNPKFPILIRECSSVQPRVWAR 65

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|126290815|ref|XP_001377022.1| PREDICTED: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2-like [Monodelphis domestica]

 Score = 91.7 bits (226), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 37/61 (60%), Positives = 48/61 (78%)

Query: 1  MATRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWA 60
          +A++ G  L+E+RIHLCQ+  SS GVRDF+ +HYV LK+ANP FPIL+RECS V P +W 
Sbjct: 9  IASKVGKNLREIRIHLCQRSASSQGVRDFIEKHYVELKKANPDFPILIRECSEVQPKLWV 68

Query: 61 R 61
          R
Sbjct: 69 R 69

Source: Monodelphis domestica

Species: Monodelphis domestica

Genus: Monodelphis

Family: Didelphidae

Order: Didelphimorphia

Class: Mammalia

Phylum: Chordata

>gi|387019617|gb|AFJ51926.1| NADH dehydrogenase (ubiquinone) 1 alpha subcomplex subunit 2-like [Crotalus adamanteus]

 Score = 90.9 bits (224), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 44/57 (77%)

Query: 5  FGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
           G  LKE+RIHLCQ   +S GVRDF+ QHYV LK+ANP FPIL+RECS V P++W R
Sbjct: 14 LGQNLKEIRIHLCQHSAASQGVRDFIEQHYVTLKKANPNFPILIRECSNVHPMLWGR 70

Source: Crotalus adamanteus

Species: Crotalus adamanteus

Genus: Crotalus

Family: Viperidae

Order: Squamata

Phylum: Chordata

Superkingdom: Eukaryota

>gi|327270325|ref|XP_003219940.1| PREDICTED: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2-like [Anolis carolinensis]

 Score = 90.9 bits (224), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 46/57 (80%)

Query: 5  FGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
           G  LKE+RIHLCQ+  +S GVRDF+ QHYV LK+ANP+FPIL+RECS V P +WAR
Sbjct: 13 LGRNLKEIRIHLCQRSPASQGVRDFIEQHYVSLKKANPEFPILIRECSDVQPKLWAR 69

Source: Anolis carolinensis

Species: Anolis carolinensis

Genus: Anolis

Family: Iguanidae

Order: Squamata

Class: N/A

Phylum: Chordata

>gi|156717414|ref|NP_001096247.1| NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa [Xenopus (Silurana) tropicalis] gi|301631843|ref|XP_002945004.1| PREDICTED: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2-like [Xenopus (Silurana) tropicalis] gi|134023821|gb|AAI35401.1| LOC100124807 protein [Xenopus (Silurana) tropicalis]

 Score = 90.9 bits (224), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 36/61 (59%), Positives = 48/61 (78%)

Query: 1  MATRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWA 60
          + ++    ++E+RIHLCQ   +S GVRDF+ QHYV LK+ANP+FPIL+RECSGV P +WA
Sbjct: 9  VGSKLSRNVREIRIHLCQSSAASQGVRDFIEQHYVELKKANPEFPILIRECSGVQPKLWA 68

Query: 61 R 61
          R
Sbjct: 69 R 69

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|149580687|ref|XP_001512375.1| PREDICTED: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2-like isoform 1 [Ornithorhynchus anatinus] gi|345317498|ref|XP_003429887.1| PREDICTED: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2-like isoform 2 [Ornithorhynchus anatinus]

 Score = 90.5 bits (223), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 37/59 (62%), Positives = 45/59 (76%)

Query: 3  TRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
           R G  L+ELRIHLCQ+   S GVRDF+ +HYV LK+ANP FP+L+RECS V P +WAR
Sbjct: 9  ARLGPALRELRIHLCQRSAESRGVRDFIEKHYVALKKANPTFPVLIRECSAVQPKLWAR 67

Source: Ornithorhynchus anatinus

Species: Ornithorhynchus anatinus

Genus: Ornithorhynchus

Family: Ornithorhynchidae

Order: Monotremata

Class: Mammalia

Phylum: Chordata

>gi|66773106|ref|NP_001019591.1| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 [Danio rerio] gi|66267534|gb|AAH95772.1| Zgc:112340 [Danio rerio] gi|182889660|gb|AAI65480.1| Zgc:112340 protein [Danio rerio]

 Score = 90.1 bits (222), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 36/61 (59%), Positives = 47/61 (77%)

Query: 1  MATRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWA 60
          + +     L+E+R+HLCQ   +S G RDF+ QHYV LK+ANP+FPIL+RECSGV PV+WA
Sbjct: 10 IGSNLSKNLREIRLHLCQISAASQGTRDFIEQHYVTLKKANPQFPILIRECSGVQPVLWA 69

Query: 61 R 61
          R
Sbjct: 70 R 70

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	72
UNIPROTKB|F1NDF3	101	NDUFA2 "NADH dehydrogenase [ub	0.777	0.554	0.660	2e-17
ZFIN|ZDB-GENE-050522-377	101	ndufa2 "NADH dehydrogenase (ub	0.847	0.603	0.590	2e-17
UNIPROTKB|E2R503	99	NDUFA2 "Uncharacterized protei	0.805	0.585	0.583	9.8e-16
UNIPROTKB|O43678	99	NDUFA2 "NADH dehydrogenase [ub	0.777	0.565	0.603	1.1e-14
UNIPROTKB|Q02370	99	NDUFA2 "NADH dehydrogenase [ub	0.736	0.535	0.622	1.4e-14
MGI|MGI:1343103	99	Ndufa2 "NADH dehydrogenase (ub	0.777	0.565	0.586	1.4e-14
RGD|1309997	97	Ndufa2 "NADH dehydrogenase (ub	0.777	0.577	0.603	1.8e-14
WB|WBGene00013406	92	Y63D3A.7 [Caenorhabditis elega	0.847	0.663	0.548	4.9e-14
TAIR|locus:2160882	97	AT5G47890 "AT5G47890" [Arabido	0.847	0.628	0.523	6.4e-12
FB|FBgn0040705	95	CG15434 [Drosophila melanogast	0.791	0.6	0.578	8.2e-12

UNIPROTKB|F1NDF3 NDUFA2 "NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2" [Gallus gallus (taxid:9031)]

 Score = 213 (80.0 bits), Expect = 2.0e-17, P = 2.0e-17
 Identities = 37/56 (66%), Positives = 44/56 (78%)

Query:     6 GSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
             G  L+ELR+HLCQ+   S G R+F+ QHYV LKQANP FPIL+RECSGV P +WAR
Sbjct:    15 GRSLRELRVHLCQRSAGSRGAREFIEQHYVTLKQANPDFPILIRECSGVQPRLWAR 70

GO:0022900 "electron transport chain" evidence=IEA

GO:0005747 "mitochondrial respiratory chain complex I" evidence=IEA

ZFIN|ZDB-GENE-050522-377 ndufa2 "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2" [Danio rerio (taxid:7955)]

 Score = 213 (80.0 bits), Expect = 2.0e-17, P = 2.0e-17
 Identities = 36/61 (59%), Positives = 47/61 (77%)

Query:     1 MATRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWA 60
             + +     L+E+R+HLCQ   +S G RDF+ QHYV LK+ANP+FPIL+RECSGV PV+WA
Sbjct:    10 IGSNLSKNLREIRLHLCQISAASQGTRDFIEQHYVTLKKANPQFPILIRECSGVQPVLWA 69

Query:    61 R 61
             R
Sbjct:    70 R 70

GO:0003674 "molecular_function" evidence=ND

UNIPROTKB|E2R503 NDUFA2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 197 (74.4 bits), Expect = 9.8e-16, P = 9.8e-16
 Identities = 35/60 (58%), Positives = 46/60 (76%)

Query:     4 RFGSK--LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
             R G+K  L+E+R+HLCQ+   S GVR+F+ +HYV LK+ANP  PIL+RECS V P +WAR
Sbjct:     9 RIGAKVGLREIRVHLCQRSSGSQGVREFIEKHYVELKKANPDLPILIRECSDVQPKLWAR 68

GO:0005747 "mitochondrial respiratory chain complex I" evidence=IEA

UNIPROTKB|O43678 NDUFA2 "NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2" [Homo sapiens (taxid:9606)]

 Score = 187 (70.9 bits), Expect = 1.1e-14, P = 1.1e-14
 Identities = 35/58 (60%), Positives = 44/58 (75%)

Query:     6 GSKL--KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
             G+KL  +E+RIHLCQ+   S GVRDF+ + YV LK+ANP  PIL+RECS V P +WAR
Sbjct:    11 GAKLGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWAR 68

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=NAS

GO:0006120 "mitochondrial electron transport, NADH to ubiquinone" evidence=NAS

GO:0005747 "mitochondrial respiratory chain complex I" evidence=IDA;NAS

GO:0031966 "mitochondrial membrane" evidence=IDA

GO:0005743 "mitochondrial inner membrane" evidence=TAS

GO:0022904 "respiratory electron transport chain" evidence=TAS

GO:0044281 "small molecule metabolic process" evidence=TAS

UNIPROTKB|Q02370 NDUFA2 "NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2" [Bos taurus (taxid:9913)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 33/53 (62%), Positives = 41/53 (77%)

Query:     9 LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
             L+E+RIHLCQ+   S GVRDF+ + YV LK+ANP  PIL+RECS V P +WAR
Sbjct:    16 LREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWAR 68

GO:0031966 "mitochondrial membrane" evidence=ISS

GO:0005747 "mitochondrial respiratory chain complex I" evidence=ISS

GO:0022900 "electron transport chain" evidence=IEA

MGI|MGI:1343103 Ndufa2 "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2" [Mus musculus (taxid:10090)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 34/58 (58%), Positives = 44/58 (75%)

Query:     6 GSKL--KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
             G+KL  +E+R+HLCQ+   S GVRDF+ Q YV LK+A+P  PIL+RECS V P +WAR
Sbjct:    11 GAKLGLREIRVHLCQRSPGSQGVRDFIVQRYVELKKAHPNLPILIRECSEVQPKLWAR 68

GO:0005739 "mitochondrion" evidence=IDA

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0005747 "mitochondrial respiratory chain complex I" evidence=ISO;TAS

GO:0006810 "transport" evidence=IEA

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=TAS

GO:0016020 "membrane" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

GO:0031966 "mitochondrial membrane" evidence=ISO

GO:0055114 "oxidation-reduction process" evidence=TAS

GO:0070469 "respiratory chain" evidence=IEA

RGD|1309997 Ndufa2 "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2" [Rattus norvegicus (taxid:10116)]

 Score = 185 (70.2 bits), Expect = 1.8e-14, P = 1.8e-14
 Identities = 35/58 (60%), Positives = 44/58 (75%)

Query:     6 GSK--LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
             G+K  L+E+RIHLCQ+   S GVRDF+ Q YV LK+A+P  PIL+RECS V P +WAR
Sbjct:     9 GAKQVLREIRIHLCQRSPGSQGVRDFIQQRYVELKKAHPDLPILIRECSEVQPKLWAR 66

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005739 "mitochondrion" evidence=ISO

GO:0005747 "mitochondrial respiratory chain complex I" evidence=ISO

GO:0008150 "biological_process" evidence=ND

GO:0031966 "mitochondrial membrane" evidence=ISO

WB|WBGene00013406 Y63D3A.7 [Caenorhabditis elegans (taxid:6239)]

 Score = 181 (68.8 bits), Expect = 4.9e-14, P = 4.9e-14
 Identities = 34/62 (54%), Positives = 48/62 (77%)

Query:     1 MATRF-GSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVW 59
             M+ R  G+ L+E+RIH+CQK  +S+GVR F+   YV +K+ANP+FPIL+RE SG+ P V+
Sbjct:     1 MSVRLAGTALREIRIHVCQKSPASAGVRAFIENDYVGIKKANPQFPILIREASGIVPRVF 60

Query:    60 AR 61
             AR
Sbjct:    61 AR 62

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

TAIR|locus:2160882 AT5G47890 "AT5G47890" [Arabidopsis thaliana (taxid:3702)]

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 33/63 (52%), Positives = 41/63 (65%)

Query:     1 MATR--FGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVV 58
             MA R      +KELRI LCQ   +S+  R F+ ++Y  LK  NPK PIL+RECSGV P +
Sbjct:     1 MAWRGSISKSMKELRILLCQSSPASAPTRTFVEKNYKDLKSLNPKLPILIRECSGVQPQM 60

Query:    59 WAR 61
             WAR
Sbjct:    61 WAR 63

GO:0005739 "mitochondrion" evidence=ISS;IDA

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0016655 "oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor" evidence=ISS

GO:0005747 "mitochondrial respiratory chain complex I" evidence=IDA

GO:0009853 "photorespiration" evidence=RCA

FB|FBgn0040705 CG15434 [Drosophila melanogaster (taxid:7227)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 33/57 (57%), Positives = 42/57 (73%)

Query:     5 FGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
             F  KLKELRI L  KG +S GVR+++ + Y  LK++NP  PILVRECSGV P ++AR
Sbjct:    11 FTPKLKELRIILDPKGDTSKGVREYVERFYPNLKKSNPDLPILVRECSGVQPRLYAR 67

GO:0003954 "NADH dehydrogenase activity" evidence=ISS

GO:0005747 "mitochondrial respiratory chain complex I" evidence=ISS

GO:0006120 "mitochondrial electron transport, NADH to ubiquinone" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q02370	NDUA2_BOVIN	No assigned EC number	0.6226	0.7361	0.5353	yes	N/A
Q9FIJ2	NDUA2_ARATH	No assigned EC number	0.5660	0.7361	0.5463	yes	N/A
O43678	NDUA2_HUMAN	No assigned EC number	0.6226	0.7361	0.5353	yes	N/A
Q9CQ75	NDUA2_MOUSE	No assigned EC number	0.6037	0.7361	0.5353	yes	N/A
P0CB79	NDUA2_PONAB	No assigned EC number	0.6226	0.7361	0.5145	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	72
smart00916	70	smart00916, L51_S25_CI-B8, Mitochondrial ribosomal	6e-18
pfam05047	52	pfam05047, L51_S25_CI-B8, Mitochondrial ribosomal	2e-13

>gnl|CDD|197984 smart00916, L51_S25_CI-B8, Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain

 Score = 69.5 bits (171), Expect = 6e-18
 Identities = 22/41 (53%), Positives = 25/41 (60%)

Query: 21 GSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          GSS+G R FL  +   LK  NP  PILVRE SGV P + A 
Sbjct: 1  GSSAGARKFLESNLPTLKFKNPDVPILVRERSGVVPKLTAE 41

Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25. This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) . It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins. Length = 70

>gnl|CDD|191176 pfam05047, L51_S25_CI-B8, Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain

 Score = 57.6 bits (140), Expect = 2e-13
 Identities = 19/36 (52%), Positives = 23/36 (63%)

Query: 26 VRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
           RDFL ++   LK  NP+ PILVRE SG  P + AR
Sbjct: 1  ARDFLEKNLPTLKYKNPQVPILVRERSGKHPRLLAR 36

The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins. Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	72
KOG3445|consensus	145		99.93
KOG3446|consensus	97		99.88
PF05047	52	L51_S25_CI-B8: Mitochondrial ribosomal protein L51	99.58
KOG4079|consensus	169		98.25
PF10780	51	MRP_L53: 39S ribosomal protein L53/MRP-L53; InterP	96.76

>KOG3445|consensus

Probab=99.93  E-value=2.2e-26  Score=152.83  Aligned_cols=63  Identities=30%  Similarity=0.518  Sum_probs=61.3

Q ss_pred             cccccCceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEEecCC
Q psy15303          3 TRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTI   65 (72)
Q Consensus         3 ~~f~~qLk~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n~   65 (72)
                      -+|++||++|+|+||+|||||+|||+||++.|++|+++||+|+|++..++|+||.|+|+|.|+
T Consensus        17 gryv~ql~rit~sfCnwggSSrGmR~Fle~~L~~~a~enP~v~i~v~~rrg~hP~lraeY~NG   79 (145)
T KOG3445|consen   17 GRYVWQLRRITVSFCNWGGSSRGMREFLESELPDLARENPGVVIYVEPRRGQHPLLRAEYLNG   79 (145)
T ss_pred             hhhhheeeEEEEEEecCCCccHHHHHHHHHHHHHHHhhCCCeEEEEeccCCCCceEEEEecCC
Confidence            379999999999999999999999999999999999999999999999999999999999994

>KOG3446|consensus

Probab=99.88  E-value=7.1e-24  Score=132.18  Aligned_cols=64  Identities=59%  Similarity=0.992  Sum_probs=60.2

Q ss_pred             ccccCceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEEecCCcc
Q psy15303          4 RFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTIGC   67 (72)
Q Consensus         4 ~f~~qLk~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n~~~   67 (72)
                      .|...||||||+.|+.|+.|+|+|+||+++|+++|+.||++||+||+|.|..|+++|+|+++-+
T Consensus        10 s~~~~lkElRI~lcqkspaSagvR~fvEk~Y~~lKkaNP~lPILIREcSgVqPrl~ARY~~G~E   73 (97)
T KOG3446|consen   10 SFTLKLKELRIHLCQKSPASAGVREFVEKFYVNLKKANPDLPILIRECSGVQPRLWARYGNGVE   73 (97)
T ss_pred             ccchhhhhheeeecCCCCcchhHHHHHHHhhhhhhhcCCCCcEeehhhcCCchHHHHHhcCCce
Confidence            4566799999999999999999999999999999999999999999999999999999999433

>PF05047 L51_S25_CI-B8: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain ; InterPro: IPR007741 Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25

Probab=99.58  E-value=5e-15  Score=82.70  Aligned_cols=40  Identities=33%  Similarity=0.403  Sum_probs=32.5

Q ss_pred             HHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEEecCC
Q psy15303         26 VRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTI   65 (72)
Q Consensus        26 vR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n~   65 (72)
                      ||+|++++||+||++||+|+|+|+++++.||.++|+|.|+
T Consensus         1 ~R~F~~~~lp~l~~~NP~v~~~v~~~~~~~P~~~~~y~~G   40 (52)
T PF05047_consen    1 ARDFLKNNLPTLKYHNPQVQFEVRRRRGRHPFLTAEYLNG   40 (52)
T ss_dssp             HHHHHHHTHHHHHHHSTT--EEEE---SSS-EEEEEESS-
T ss_pred             CHhHHHHhHHHHHHHCCCcEEEEEECCCCCCEEEEEEcCC
Confidence            7999999999999999999999999999999999999994

This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) 1.6.5.3 from EC. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.; PDB: 1S3A_A.

>KOG4079|consensus

Probab=98.25  E-value=2.6e-07  Score=62.49  Aligned_cols=61  Identities=18%  Similarity=0.317  Sum_probs=57.8

Q ss_pred             ccccCceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEEecC
Q psy15303          4 RFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPT   64 (72)
Q Consensus         4 ~f~~qLk~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n   64 (72)
                      .|...++-.++.|..+++...|+|+|+--|+|+++.+||.|+++........|++++..+.
T Consensus        23 vlkD~V~vfsvnynt~g~~~~GARdFVfwNipQiQykNP~VQ~~~~knmtpsPF~R~Yldd   83 (169)
T KOG4079|consen   23 VLKDNVNVFSVNYNTNGPEQSGARDFVFWNIPQIQYKNPKVQLVKHKNMTPSPFARAYLDD   83 (169)
T ss_pred             EEeccceEEEEeccCCCccccCccceEEecchhhcccCCceEEEeeccCCCChHHHheecC
Confidence            5778899999999999999999999999999999999999999999999999999998877

>PF10780 MRP_L53: 39S ribosomal protein L53/MRP-L53; InterPro: IPR019716 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.76  E-value=0.0023  Score=36.01  Aligned_cols=48  Identities=17%  Similarity=0.137  Sum_probs=40.9

Q ss_pred             ecCCCCCCHHHHHHHHhC--HHHHHHhCCCCeEEEEEcCCCCCEEEEEecC
Q psy15303         16 LCQKGGSSSGVRDFLAQH--YVPLKQANPKFPILVRECSGVTPVVWARIPT   64 (72)
Q Consensus        16 yC~~~~sS~GvR~Fl~~~--l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n   64 (72)
                      ||..++.++.+|+||..-  -.....-||+.++..+.. ...|.|...|.+
T Consensus         1 FnPF~~~aksaR~FL~~ip~s~k~~~tni~~~vl~~~~-~~~P~v~V~fkd   50 (51)
T PF10780_consen    1 FNPFSPNAKSARLFLSLIPPSAKARGTNINCEVLPRVS-RSEPSVTVTFKD   50 (51)
T ss_pred             CCCCCcccHHHHHHHHhcCCccccccCCCceEEecCCC-CCCCeEEEEecc
Confidence            688999999999999864  445566899999999888 679999999988

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Mitochondrial ribosomal protein L53 (also known as L44) is part of the 39S ribosome [].

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	72
1s3a_A	102	Nmr Solution Structure Of Subunit B8 From Human Nad		7e-16

>pdb|1S3A|A Chain A, Nmr Solution Structure Of Subunit B8 From Human Nadh- Ubiquinone Oxidoreductase Complex I (Ci-B8) Length = 102

Iteration: 1
 Score = 79.0 bits (193), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 33/53 (62%), Positives = 41/53 (77%)
Query: 9  LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          L+E+RIHLCQ+   S GVRDF+ + YV LK+ANP  PIL+RECS V P +WAR
Sbjct: 19 LREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWAR 71
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	72
1s3a_A	102	NADH-ubiquinone oxidoreductase B8 subunit; CI-B8,	2e-26

>1s3a_A NADH-ubiquinone oxidoreductase B8 subunit; CI-B8, ndufa2, complex I; NMR {Homo sapiens} SCOP: c.47.1.22 Length = 102

 Score = 91.8 bits (228), Expect = 2e-26
 Identities = 33/53 (62%), Positives = 41/53 (77%)

Query: 9  LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          L+E+RIHLCQ+   S GVRDF+ + YV LK+ANP  PIL+RECS V P +WAR
Sbjct: 19 LREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWAR 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	72
1s3a_A	102	NADH-ubiquinone oxidoreductase B8 subunit; CI-B8,	99.94

>1s3a_A NADH-ubiquinone oxidoreductase B8 subunit; CI-B8, ndufa2, complex I; NMR {Homo sapiens} SCOP: c.47.1.22

Probab=99.94  E-value=1e-26  Score=145.28  Aligned_cols=63  Identities=56%  Similarity=1.021  Sum_probs=56.1

Q ss_pred             cccccC--ceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEEecCC
Q psy15303          3 TRFGSK--LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTI   65 (72)
Q Consensus         3 ~~f~~q--Lk~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n~   65 (72)
                      .+|.+.  ||+|+|+||++++||+|+|+||+.+||+||++||+++|+|++++++||+|+|+|+|+
T Consensus        11 ~~l~~~~qlk~l~~~yc~~~~sS~G~R~Fl~~~l~~~k~~NP~v~i~v~~~~~~~P~i~a~Y~~G   75 (102)
T 1s3a_A           11 RGVGAKLGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYAFG   75 (102)
T ss_dssp             -------CEEEEEEECCSSSCCCHHHHHHHHHTHHHHHHHSTTCCEEEECCCSSSCEEEEEESSC
T ss_pred             hcCCCCCceeEEEEEEcCCCCCchhHHHHHHHhhHHHHHHCCCceEEEEECCCCCCEEEEEECCC
Confidence            367776  999999999999999999999999999999999999999999999999999999993

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	72
d1s3aa1	85	c.47.1.22 (A:15-99) NADH-ubiquinone oxidoreductase	4e-25

>d1s3aa1 c.47.1.22 (A:15-99) NADH-ubiquinone oxidoreductase b8 subunit, CI-B8 {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Mitochondrial ribosomal protein L51/S25/CI-B8 domain
domain: NADH-ubiquinone oxidoreductase b8 subunit, CI-B8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 86.7 bits (215), Expect = 4e-25
 Identities = 33/53 (62%), Positives = 41/53 (77%)

Query: 9  LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61
          L+E+RIHLCQ+   S GVRDF+ + YV LK+ANP  PIL+RECS V P +WAR
Sbjct: 2  LREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWAR 54

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	72
d1s3aa1	85	NADH-ubiquinone oxidoreductase b8 subunit, CI-B8 {	99.95

>d1s3aa1 c.47.1.22 (A:15-99) NADH-ubiquinone oxidoreductase b8 subunit, CI-B8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Mitochondrial ribosomal protein L51/S25/CI-B8 domain
domain: NADH-ubiquinone oxidoreductase b8 subunit, CI-B8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=7e-28  Score=145.25  Aligned_cols=57  Identities=58%  Similarity=1.071  Sum_probs=56.0

Q ss_pred             ceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEEecCC
Q psy15303          9 LKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTI   65 (72)
Q Consensus         9 Lk~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n~   65 (72)
                      ||+|+|+||++|+||+|+|+||+++|++||++||+++|+++++++.||+|+|+|+|+
T Consensus         2 Lk~l~~~yc~~~~sS~G~R~Fi~~~l~~~~~~NP~v~i~v~~~~~~~P~l~a~y~nG   58 (85)
T d1s3aa1           2 LREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYAFG   58 (85)
T ss_dssp             EEEEEEECCSSSCCCHHHHHHHHHTHHHHHHHSTTCCEEEECCCSSSCEEEEEESSC
T ss_pred             ceEEEEEEcCCCCCcHHHHHHHHHhHHHHHHHCCCceEEEEEcCCCCCEEEEEEcCC
Confidence            899999999999999999999999999999999999999999999999999999994