Citrus Sinensis ID: 045112

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290------
Protein Sequence
MAGTGNSITPHVIGSTFVELSRSGRTGAPFSVRISTKSHGNGGGGFAAAATMCKNEEGPSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYGSHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLSRRNRRQRWM
Secondary Structure (PSIPRED)
cccccccccccccccEEEEEEccccccccccEEEEEccccccccccHHHHHHcccccccEEEEEccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccccEEEccccEEccccccccccccHHHHHHHHHHHHHHHHHHcccEEEcEEEEEEEEccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEccccccccccHHcccccccccccccccccccccEEEEEcccEEcccccccEEEEEEEEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccEEEEEEEEEcccccccccEEEEEEcccccccccccEcccccccccccccEEEEcccccccHHHHHHHHHHHHHHHHcccccEcHHHHHHHHHHHHHccccEEEEcccccccccEEEccccHcHHHHHHHHHHHHHHHHcccEEEEEcccHEEEEEcccccccEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccEEEEEcccccccccEEEEEEEcccccccccEEEcccccEEEEEEEEEccccccccEEEEEEEEEEEccccccccc
Coil and Loop (DISEMBL)
magtgnsitphviGSTFVElsrsgrtgapfsvristkshgnggggFAAAATMckneegpscifvgpletASKETLEALYRQARDayysgkplivddmFDRVELKLRWygsksvikyprcsirrqstyadaEEDLSQVLALGIIWILILAFgssicfvpIIYTVFLAYQDAFsrgisygshasVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALrgacpncgeEVFAFvnsdqtknsphrsdchvcgslLEFRTKVeqsssrlgrqwVYGRIYLLSRRNRRQRWM
Flexible Loop (DISEMBL)
magtgnsitphviGSTFVELSRSGRTGAPFSVRISTKSHGNGGGGFAAAATMCKNEEGPSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRwygsksvikyprcsirRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYGSHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNsdqtknsphrsDCHVCGSLLEFrtkveqsssrlgrqwvygriyllsrrnrrqrwm
Low Complexity Region (SEG)
MAGTGNSITPHVIGSTFVELSRSGRTGAPFSVRISTKSHgnggggfaaaaTMCKNEEGPSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCSIRRQSTYADAEEDLSQVlalgiiwililaFGSSICFVPIIYTVFLAYQDAFSRGISYGSHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLSRRNRRQRWM
Disordered region (IsUnstruct)
***********VIGSTFV**************************GFAAAATMCKNEEGPSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYGSHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNS**********DCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLS*********
Disordered Region (DISOPRED)
**********HVIGSTFV**********************************CKNEEGPSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYGSHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNS********RSDCHVCGSLLEFRTK********GRQWVYGRIYLLSRRN******
Disordered Region (DISEMBL)
MAGTGNSITPHVIGSTFVELSRSGRTGAPFSVRISTKSHGNGGGGFAAAATMCKNEEGPSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYGSHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNSD**********CHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLSRRNRRQRWM
Disordered Region (DISPRO)
******SITPHVIGSTFVELSRSGRTGAPFSVRISTKSHGN*GGGFAAAATMCKNEEGPSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYGSHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLSRR*******
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAGTGNSITPHVIGSTFVELSRSGRTGAPFSVRISTKSHGNGGGGFAAAATMCKNEEGPSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYGSHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLSRRNRRQRWM
Positional Conservation
no confident homologs detected

---

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	296	2.2.26 [Sep-21-2011]
Q8H112	324	PGR5-like protein 1A, chl	no	no	0.570	0.521	0.276	3e-12
Q8GYC7	313	PGR5-like protein 1B, chl	no	no	0.554	0.523	0.279	4e-12

>sp|Q8H112|PGL1A_ARATH PGR5-like protein 1A, chloroplastic OS=Arabidopsis thaliana GN=PGRL1A PE=1 SV=1

 Score = 72.8 bits (177), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 57/206 (27%), Positives = 97/206 (47%), Gaps = 37/206 (17%)

Query: 76  EALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCSIRRQSTYADAEEDLS 135
           E  + +A  AY SG P++ D+ +D+++LKL+  GS  V + PRCS+R +  Y+D   D  
Sbjct: 140 EQRFLEASMAYVSGNPILNDEEYDKLKLKLKIDGSDIVSEGPRCSLRSKKVYSDLAVDYF 199

Query: 136 QVLALG----IIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYGSHASVSGFLAAVN 191
           ++L L     ++ + +  F   I    I Y + L    +F           +  + AAV 
Sbjct: 200 KMLLLNVPATVVALGLFFFLDDITGFEITYIMELPEPYSF-----------IFTWFAAVP 248

Query: 192 VILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHR 251
           VI+++A+               +  L   D + L+G CPNCG E  +F  +  + +S  +
Sbjct: 249 VIVYLALS--------------ITKLIIKDFLILKGPCPNCGTENTSFFGTILSISSGGK 294

Query: 252 SD---CHVCGSLLEFRTKVEQSSSRL 274
           ++   C  CG+ +     V  S SRL
Sbjct: 295 TNTVKCTNCGTAM-----VYDSGSRL 315

Involved in cyclic electron flow (CEF) around photosystem I.
Arabidopsis thaliana (taxid: 3702)

>sp|Q8GYC7|PGL1B_ARATH PGR5-like protein 1B, chloroplastic OS=Arabidopsis thaliana GN=PGRL1B PE=1 SV=1

 Score = 72.4 bits (176), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/211 (27%), Positives = 95/211 (45%), Gaps = 47/211 (22%)

Query: 76  EALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCSIRRQSTYADAEEDL- 134
           E  + +A  AY SG P++ D+ +D++++KL+  GS+ V + PRCS+R +  Y+D   D  
Sbjct: 129 EQRFLEASMAYVSGNPILSDEEYDKLKMKLKMDGSEIVCEGPRCSLRSKKVYSDLAIDYF 188

Query: 135 --------SQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYGSHASVSGF 186
                   + V+ALG+ + L    G  I       T  L   + FS   ++         
Sbjct: 189 KMFLLNVPATVVALGLFFFLDDITGFEI-------TYLLELPEPFSFIFTW--------- 232

Query: 187 LAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAF---VNSD 243
            AAV  I+++A+               L  L   D + L+G CPNCG E  +F   + S 
Sbjct: 233 FAAVPAIVYLALS--------------LTKLILKDFLILKGPCPNCGTENVSFFGTILSI 278

Query: 244 QTKNSPHRSDCHVCGSLLEFRTKVEQSSSRL 274
              ++ +   C  CG+ +     V  S SRL
Sbjct: 279 PNDSNTNNVKCSGCGTEM-----VYDSGSRL 304

Involved in cyclic electron flow (CEF) around photosystem I.

Arabidopsis thaliana (taxid: 3702)

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	296
255584751	287	conserved hypothetical protein [Ricinus	0.959	0.989	0.750	1e-121
224059484	294	predicted protein [Populus trichocarpa]	0.942	0.948	0.686	1e-114
147818033	1059	hypothetical protein VITISV_021080 [Viti	0.935	0.261	0.727	1e-113
225434915	293	PREDICTED: PGR5-like protein 1B, chlorop	0.935	0.945	0.724	1e-113
449455102	291	PREDICTED: PGR5-like protein 1A, chlorop	0.979	0.996	0.663	1e-110
224104421	286	predicted protein [Populus trichocarpa]	0.959	0.993	0.696	1e-109
30697213	299	uncharacterized protein [Arabidopsis tha	0.986	0.976	0.651	1e-104
356542431	280	PREDICTED: uncharacterized protein LOC10	0.942	0.996	0.659	1e-104
297793495	299	hypothetical protein ARALYDRAFT_496067 [	0.986	0.976	0.647	1e-104
21554137	299	unknown [Arabidopsis thaliana]	0.986	0.976	0.644	1e-103

>gi|255584751|ref|XP_002533094.1| conserved hypothetical protein [Ricinus communis] gi|223527106|gb|EEF29286.1| conserved hypothetical protein [Ricinus communis]

 Score =  441 bits (1135), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 223/297 (75%), Positives = 244/297 (82%), Gaps = 13/297 (4%)

Query: 1   MAGTGNSITPHVIGSTFVELSR-SGRTG-APFSVRISTKSHGNGGGGFAAAATMCKNEEG 58
           MAG   SI+ HVIGST VELSR S R G A FS RIS KS+G      A         EG
Sbjct: 1   MAGACTSISRHVIGSTTVELSRPSNRNGVASFSARISLKSNGASASPVA---------EG 51

Query: 59  PSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPR 118
           PSCI+VGP+ETASKETLEALYRQARDAYYSG+PLIVDDMFDRVELKLRWYGSKSV+KYPR
Sbjct: 52  PSCIYVGPVETASKETLEALYRQARDAYYSGQPLIVDDMFDRVELKLRWYGSKSVVKYPR 111

Query: 119 CSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYG 178
           CSIRRQSTYADAE+D+SQV AL  IWI+ L  GSS+C  PIIY+  LAYQDA S  IS G
Sbjct: 112 CSIRRQSTYADAEDDISQVFALASIWIVFLTIGSSLCVGPIIYSFVLAYQDAISSKISQG 171

Query: 179 SHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFA 238
           S AS+  FLA VN ILFMAVG+LIGYPIAS+SV+VLQGLWRNDLVAL+GACPNCGEEVFA
Sbjct: 172 SQASMVQFLATVNGILFMAVGTLIGYPIASSSVKVLQGLWRNDLVALKGACPNCGEEVFA 231

Query: 239 FVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLSRRNRRQRW 295
           FV SDQ+ NSPHR+DCHVC SLLEFRTKVE++ SRLGR WVYGRIYL+SR  RRQRW
Sbjct: 232 FVKSDQSNNSPHRADCHVCESLLEFRTKVERTDSRLGRNWVYGRIYLVSR--RRQRW 286

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224059484|ref|XP_002299869.1| predicted protein [Populus trichocarpa] gi|222847127|gb|EEE84674.1| predicted protein [Populus trichocarpa]

 Score =  418 bits (1075), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 212/309 (68%), Positives = 241/309 (77%), Gaps = 30/309 (9%)

Query: 1   MAGTGNSITPHVIGSTFVELSRSGRTGAPFSVRISTKSHGNGGG--------------GF 46
           MAGT   I+ HVI     ELS   R         ++++ G GGG              G 
Sbjct: 1   MAGTCTFISRHVI-----ELSSKNR---------ASRTWGGGGGASFCWPRISAMNSNGV 46

Query: 47  AAAATMCKNEEGPSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLR 106
           ++   +  + EGPSCIFVGP+ETAS++TLEALY QARDAYYSGKPLIVDDMFDRVELKLR
Sbjct: 47  SSTREVALSPEGPSCIFVGPIETASQDTLEALYCQARDAYYSGKPLIVDDMFDRVELKLR 106

Query: 107 WYGSKSVIKYPRCSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLA 166
           WYGSKSV+KYPRCS+RRQSTY+DAEED+SQ  AL  IW+L L  GSS C  PIIYTV LA
Sbjct: 107 WYGSKSVVKYPRCSLRRQSTYSDAEEDISQAFALASIWVLFLTIGSSACAFPIIYTVGLA 166

Query: 167 YQDAFSRGISYGSHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALR 226
           YQDAF  GI++GS A + GFLA VN ILFMAVGSLIGYPIASASV+VLQGLWRNDLVAL+
Sbjct: 167 YQDAFGSGIAHGSQAPIIGFLATVNGILFMAVGSLIGYPIASASVKVLQGLWRNDLVALK 226

Query: 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLL 286
           GACPNCGEEVFAFV SDQ+ +SPHR+DCHVC SLLEFRTKVEQ++SR+GRQWVYGRIYL+
Sbjct: 227 GACPNCGEEVFAFVKSDQSNDSPHRADCHVCESLLEFRTKVEQTTSRVGRQWVYGRIYLV 286

Query: 287 SRRNRRQRW 295
           SR  RRQRW
Sbjct: 287 SR--RRQRW 293

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147818033|emb|CAN64889.1| hypothetical protein VITISV_021080 [Vitis vinifera]

 Score =  415 bits (1066), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 211/290 (72%), Positives = 230/290 (79%), Gaps = 13/290 (4%)

Query: 1    MAGTGNSITPHVIGSTFVELSRSGRTGAPFSVRISTKSHG----NGGGGFAAAATMCKNE 56
            MA T  SI+PHVIGST  ELSR+ R+GAPF VRIS KS+G    N     A A       
Sbjct: 767  MAVTSPSISPHVIGSTITELSRTFRSGAPFMVRISAKSNGVSTCNDRNDLALA------- 819

Query: 57   EGPSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKY 116
            EGPSCIFVGP+ETASKETLEALY QARDAYYSG+PLIVDDMFDRVELKLRWYGSKSV+KY
Sbjct: 820  EGPSCIFVGPIETASKETLEALYCQARDAYYSGEPLIVDDMFDRVELKLRWYGSKSVLKY 879

Query: 117  PRCSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGIS 176
            PRCS+RR  TYADAEED SQV AL  IWIL LAFG S C VPIIYTV  AYQDAF+ G+S
Sbjct: 880  PRCSLRRHYTYADAEEDPSQVFALASIWILFLAFGGSACLVPIIYTVGQAYQDAFNSGLS 939

Query: 177  YGSHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEV 236
            Y S AS    LA  N ILFM +GS+IGYP+ASASV VLQGLWRNDLVAL+GACPNCGEEV
Sbjct: 940  YSSQASALQLLATANGILFMVLGSVIGYPVASASVGVLQGLWRNDLVALKGACPNCGEEV 999

Query: 237  FAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLL 286
            FAFV S Q  +SPH +DCHVC S LEF TKVEQS+  LGR+WVYGRIYL+
Sbjct: 1000 FAFVKSGQPNSSPHSADCHVCESSLEFSTKVEQST--LGRRWVYGRIYLV 1047

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225434915|ref|XP_002280802.1| PREDICTED: PGR5-like protein 1B, chloroplastic [Vitis vinifera] gi|297746060|emb|CBI16116.3| unnamed protein product [Vitis vinifera]

 Score =  413 bits (1061), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 210/290 (72%), Positives = 230/290 (79%), Gaps = 13/290 (4%)

Query: 1   MAGTGNSITPHVIGSTFVELSRSGRTGAPFSVRISTKSHG----NGGGGFAAAATMCKNE 56
           MA T  SI+PHVIGST  ELSR+ R+GAPF VRIS KS+G    N     A A       
Sbjct: 1   MAVTSPSISPHVIGSTITELSRTFRSGAPFMVRISAKSNGVSTCNDRNDLALA------- 53

Query: 57  EGPSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKY 116
           EGPSCIFVGP+ETASKETLEALY QARDAYYSG+PLIVDDMFDRVELKLRWYGSKSV+KY
Sbjct: 54  EGPSCIFVGPIETASKETLEALYCQARDAYYSGEPLIVDDMFDRVELKLRWYGSKSVLKY 113

Query: 117 PRCSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGIS 176
           PRCS+R+  TYADAEED SQV AL  IWIL LAFG S C VPIIYTV  AYQDAF+ G+S
Sbjct: 114 PRCSLRQHYTYADAEEDPSQVFALASIWILFLAFGGSACLVPIIYTVGQAYQDAFNSGLS 173

Query: 177 YGSHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEV 236
           Y S AS    LA  N ILFM +GS+IGYP+ASASV VLQGLWRNDLVAL+GACPNCGEEV
Sbjct: 174 YSSQASALQLLATANGILFMVLGSVIGYPVASASVGVLQGLWRNDLVALKGACPNCGEEV 233

Query: 237 FAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLL 286
           FAFV S Q  +SPH +DCHVC S LEF TKVEQS+  LGR+WVYGRIYL+
Sbjct: 234 FAFVKSGQPNSSPHSADCHVCESSLEFSTKVEQST--LGRRWVYGRIYLV 281

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455102|ref|XP_004145292.1| PREDICTED: PGR5-like protein 1A, chloroplastic-like [Cucumis sativus] gi|449473542|ref|XP_004153911.1| PREDICTED: PGR5-like protein 1A, chloroplastic-like [Cucumis sativus] gi|449515667|ref|XP_004164870.1| PREDICTED: PGR5-like protein 1A, chloroplastic-like [Cucumis sativus]

 Score =  404 bits (1039), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 197/297 (66%), Positives = 230/297 (77%), Gaps = 7/297 (2%)

Query: 1   MAGTGNSITPHVIGSTFVELSRSGRTGAPFS-VRISTKSHGNGGGGFAAAATMCKNEEGP 59
           MAG   S +PH+I ST   L+R+ R   PF  V  STK+  +        A      +GP
Sbjct: 1   MAGASTSFSPHLIKSTVSNLARTIRAATPFHLVPFSTKTPNSPLSSSEDLA------QGP 54

Query: 60  SCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRC 119
           SCIFVGP+ETA++ETLEALY QARDAYYSG+PLI+DDMFDRVELKLRWYGSKSV+KYPRC
Sbjct: 55  SCIFVGPIETATQETLEALYLQARDAYYSGQPLILDDMFDRVELKLRWYGSKSVVKYPRC 114

Query: 120 SIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYGS 179
           S+RRQSTY+DAEEDLSQVLAL  IW+L LA G S C VP+I    L ++D  S G+SY +
Sbjct: 115 SLRRQSTYSDAEEDLSQVLALAGIWLLFLALGCSACLVPLICIADLIFKDPLSLGLSYDT 174

Query: 180 HASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAF 239
           H S  GFL+A+N ILFMA GSLIGYPI +ASV VLQGLWRNDLVAL+GACPNCGEEVFAF
Sbjct: 175 HGSPFGFLSAINAILFMAFGSLIGYPITTASVGVLQGLWRNDLVALKGACPNCGEEVFAF 234

Query: 240 VNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLSRRNRRQRWM 296
           V SD+   SPHRSDCHVC  LLEFR K E+SS++LGRQWVYGRIYL+ R++R QR +
Sbjct: 235 VRSDRANGSPHRSDCHVCECLLEFRIKFEKSSTKLGRQWVYGRIYLVRRKSRHQRLL 291

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224104421|ref|XP_002313431.1| predicted protein [Populus trichocarpa] gi|222849839|gb|EEE87386.1| predicted protein [Populus trichocarpa]

 Score =  401 bits (1031), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 202/290 (69%), Positives = 230/290 (79%), Gaps = 6/290 (2%)

Query: 1   MAGTGNSITPHVIG-STFVELSRSGRTGAPFS-VRISTKSHGNGGGGFAAAATMCKNEEG 58
           MAGT   I+ HVI  S++   SRSGR GA F   R+S  S      G +    +    EG
Sbjct: 1   MAGTCTYISRHVIELSSYNRASRSGREGASFCWARLSAMS----SNGVSRTRKVALAPEG 56

Query: 59  PSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPR 118
           PSC+FVGP+ETAS+ETLEALYRQARDAYYSGKPLI+DDMFDRVELKLR YGSK V+KYPR
Sbjct: 57  PSCLFVGPIETASQETLEALYRQARDAYYSGKPLIIDDMFDRVELKLRCYGSKCVVKYPR 116

Query: 119 CSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYG 178
           CSIRRQSTY+DAE D+SQ  AL  IWIL L  G S C +PIIYT+ LAYQDAF   IS+G
Sbjct: 117 CSIRRQSTYSDAEADISQAFALASIWILFLTVGCSACALPIIYTIGLAYQDAFGSVISHG 176

Query: 179 SHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFA 238
           S   + GFLA VN ILFMAV +LIGYPIASASV+VLQGLWRNDLVAL+GACPNCGEEVFA
Sbjct: 177 SQTPIIGFLATVNGILFMAVSALIGYPIASASVKVLQGLWRNDLVALKGACPNCGEEVFA 236

Query: 239 FVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLSR 288
           FV SDQ+ NS HR+DCHVC SLLEFRT+VEQ+ SR+GR+WV+GRIYL+SR
Sbjct: 237 FVKSDQSNNSTHRADCHVCESLLEFRTEVEQTISRVGRRWVFGRIYLVSR 286

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30697213|ref|NP_851220.1| uncharacterized protein [Arabidopsis thaliana] gi|332009797|gb|AED97180.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  385 bits (988), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 196/301 (65%), Positives = 229/301 (76%), Gaps = 9/301 (2%)

Query: 1   MAGTGNSITPHVIGST-FVELSR-SGRTGAPFSVRISTKSHGNGGGGFAAAATMCKNEEG 58
           MAGT  SI P +IGS+  VELSR   R G PFSVR ST++    GGG  A  +    EEG
Sbjct: 1   MAGTCTSIRPRLIGSSSIVELSRLINRAGVPFSVRFSTRTRALHGGGLTAPTS---REEG 57

Query: 59  PSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPR 118
           PSCIFVGP+++A KETLEALYRQA+DAYY+GKPLIVDDMFDRVELKLRWYGSKSV+KYPR
Sbjct: 58  PSCIFVGPIDSARKETLEALYRQAKDAYYNGKPLIVDDMFDRVELKLRWYGSKSVVKYPR 117

Query: 119 CSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAY-QDAFSRGISY 177
           CS+ RQSTYADAE+D SQVL L  +WI+I  FGSS C +P IY V L Y  D F  G+ Y
Sbjct: 118 CSLLRQSTYADAEDDASQVLLLATVWIMIFLFGSSACVLPTIYGVGLVYGGDPFDSGLVY 177

Query: 178 GSHASVS-GFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEV 236
            S  S S   L+  N IL   +G   GYPIAS++VRVL+GLWRNDL AL+G CPNCGEEV
Sbjct: 178 SSQLSSSVPILSKFNGILLSVLGPAFGYPIASSAVRVLKGLWRNDLTALKGDCPNCGEEV 237

Query: 237 FAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLS--RRNRRQR 294
           FAFV SDQ+  S H++DCHVC   LEFRTKVE+S+SRLGR+WVYGRIYL+S  RR+RR +
Sbjct: 238 FAFVRSDQSNRSAHKADCHVCECTLEFRTKVEKSASRLGRKWVYGRIYLVSRPRRDRRSK 297

Query: 295 W 295
           +
Sbjct: 298 F 298

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356542431|ref|XP_003539670.1| PREDICTED: uncharacterized protein LOC100810752 [Glycine max]

 Score =  384 bits (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 194/294 (65%), Positives = 223/294 (75%), Gaps = 15/294 (5%)

Query: 1   MAGTGNSITPHVIGSTFVELSRSGRTGAPFSVRISTKSHGNGGGGFAAAATMCKNEEGPS 60
           MAGT  S   HVI ST +EL R+ R      VRIS KSH         +AT  +   GP 
Sbjct: 1   MAGTSLS---HVIQSTVLELPRTTR-----HVRISAKSH-------RVSATSDQRPAGPC 45

Query: 61  CIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCS 120
           CI+VGPLETA+KE LEALY QARDAYYSG+PLIVDDMFDRVEL+LRW+GSKSV+KYPRCS
Sbjct: 46  CIYVGPLETANKENLEALYCQARDAYYSGQPLIVDDMFDRVELRLRWFGSKSVVKYPRCS 105

Query: 121 IRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAYQDAFSRGISYGSH 180
           IRRQST+ADAEEDLS V AL   W + LAFGS  C  P+ YTV +AYQ+AF  G+S GS 
Sbjct: 106 IRRQSTFADAEEDLSMVFALASTWAMFLAFGSLACVGPVSYTVGMAYQNAFDSGLSLGSQ 165

Query: 181 ASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFV 240
               GFLA VN ++F+ +G +IGYP+ASAS +VLQGLWRNDLVAL+GACPNCGEEVFAFV
Sbjct: 166 TPGLGFLAVVNSLIFVGLGFVIGYPVASASAKVLQGLWRNDLVALKGACPNCGEEVFAFV 225

Query: 241 NSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLSRRNRRQR 294
             D+   SPHR+DCHVC  +LEFRTKVEQS SR GRQWVYGRIYL+S R R +R
Sbjct: 226 RMDRNIESPHRADCHVCECILEFRTKVEQSVSRFGRQWVYGRIYLVSLRGRSRR 279

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297793495|ref|XP_002864632.1| hypothetical protein ARALYDRAFT_496067 [Arabidopsis lyrata subsp. lyrata] gi|297310467|gb|EFH40891.1| hypothetical protein ARALYDRAFT_496067 [Arabidopsis lyrata subsp. lyrata]

 Score =  382 bits (981), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 195/301 (64%), Positives = 229/301 (76%), Gaps = 9/301 (2%)

Query: 1   MAGTGNSITPHVIGST-FVELSRS-GRTGAPFSVRISTKSHGNGGGGFAAAATMCKNEEG 58
           MAGT  SI P +IGS+  VELSR   R G PFSVRIST++    GGG  A  +    EEG
Sbjct: 1   MAGTCTSIRPRLIGSSSIVELSRLINRAGVPFSVRISTRTRALHGGGLTAPTS---REEG 57

Query: 59  PSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPR 118
           PSCIFVGP+++A KETLEALYRQA+DAYY+GKPLIVDDMFDRVELKLRWYGSKSV+KYPR
Sbjct: 58  PSCIFVGPIDSARKETLEALYRQAKDAYYNGKPLIVDDMFDRVELKLRWYGSKSVVKYPR 117

Query: 119 CSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAY-QDAFSRGISY 177
           CS+ RQSTYADAE+D SQVL L  IWILI  FGSS C +P +Y + L Y  D    G+ Y
Sbjct: 118 CSLLRQSTYADAEDDASQVLLLATIWILIFLFGSSACVLPTMYGLGLVYGGDPVDSGLVY 177

Query: 178 -GSHASVSGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEV 236
            G  +S    L+  N IL   +G   GYPIAS++VRVL+GLWRNDL AL+G CPNCGEEV
Sbjct: 178 SGQLSSSVPLLSKFNGILLAVLGPAFGYPIASSAVRVLKGLWRNDLTALKGDCPNCGEEV 237

Query: 237 FAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLS--RRNRRQR 294
           FAFV SDQ+  S H++DCHVC   LEFRTKVE+S+SRLGR+WVYGRIYL+S  RR+RR +
Sbjct: 238 FAFVRSDQSNRSAHKADCHVCECTLEFRTKVEKSTSRLGRKWVYGRIYLVSRPRRDRRSK 297

Query: 295 W 295
           +
Sbjct: 298 F 298

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21554137|gb|AAM63217.1| unknown [Arabidopsis thaliana]

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 194/301 (64%), Positives = 228/301 (75%), Gaps = 9/301 (2%)

Query: 1   MAGTGNSITPHVIGST-FVELSR-SGRTGAPFSVRISTKSHGNGGGGFAAAATMCKNEEG 58
           MAGT  SI P +IGS+  VELSR   R G PFSVR ST++    GGG  A  +    EEG
Sbjct: 1   MAGTCTSIRPRLIGSSSIVELSRLINRAGVPFSVRFSTRTRALHGGGLTAPTS---REEG 57

Query: 59  PSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPR 118
           PSCIFVGP+++A KETLEALYRQA+DAYY+GKPLIVDDMFDRVELKLRWYGSKSV+KYPR
Sbjct: 58  PSCIFVGPIDSARKETLEALYRQAKDAYYNGKPLIVDDMFDRVELKLRWYGSKSVVKYPR 117

Query: 119 CSIRRQSTYADAEEDLSQVLALGIIWILILAFGSSICFVPIIYTVFLAY-QDAFSRGISY 177
           CS+ RQSTYADAE+D SQVL L  +WI+I  FGSS C +P IY V L Y  D F  G+ Y
Sbjct: 118 CSLLRQSTYADAEDDASQVLLLATVWIMIFLFGSSACVLPTIYGVGLVYGGDPFDSGLVY 177

Query: 178 GSHASVS-GFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEV 236
            +  S S   L+  N IL   +G   GYPIAS++VR L+GLWRNDL AL+G CPNCGEEV
Sbjct: 178 SNQLSSSVPILSKFNGILLSVLGPAFGYPIASSAVRALKGLWRNDLTALKGDCPNCGEEV 237

Query: 237 FAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLS--RRNRRQR 294
           FAFV SDQ+  S H++DCHVC   LEFRTKVE+S+SRLGR+WVYGRIYL+S  RR+RR +
Sbjct: 238 FAFVRSDQSNRSAHKADCHVCECTLEFRTKVEKSASRLGRKWVYGRIYLVSRPRRDRRSK 297

Query: 295 W 295
           +
Sbjct: 298 F 298

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

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	296
TAIR|locus:2148338	301	AT5G59400 "AT5G59400" [Arabido	0.986	0.970	0.617	1.2e-90
TAIR|locus:2118031	313	PGRL1B "AT4G11960" [Arabidopsi	0.195	0.185	0.379	3.8e-08
TAIR|locus:2127233	324	PGR5-LIKE A "AT4G22890" [Arabi	0.195	0.179	0.396	1.3e-07

TAIR|locus:2148338 AT5G59400 "AT5G59400" [Arabidopsis thaliana (taxid:3702)]

 Score = 904 (323.3 bits), Expect = 1.2e-90, P = 1.2e-90
 Identities = 187/303 (61%), Positives = 218/303 (71%)

Query:     1 MAGTGNSITPHVIGST-FVELSRS-GRTGAPFSVRISTKSHXXXXXXXXXXXTMCKNEEG 58
             MAGT  SI P +IGS+  VELSR   R G PFSVR ST++            +    EEG
Sbjct:     1 MAGTCTSIRPRLIGSSSIVELSRLINRAGVPFSVRFSTRTRALHGGGLTAPTS---REEG 57

Query:    59 PSCIFVGPLETASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPR 118
             PSCIFVGP+++A KETLEALYRQA+DAYY+GKPLIVDDMFDRVELKLRWYGSKSV+KYPR
Sbjct:    58 PSCIFVGPIDSARKETLEALYRQAKDAYYNGKPLIVDDMFDRVELKLRWYGSKSVVKYPR 117

Query:   119 CSIRRQSTYADAEEDLSQVXXXXXXXXXXXXFGSSICFVPIIYTVFLAYQ-DAFSRGISY 177
             CS+ RQSTYADAE+D SQV            FGSS C +P IY V L Y  D F  G+ Y
Sbjct:   118 CSLLRQSTYADAEDDASQVLLLATVWIMIFLFGSSACVLPTIYGVGLVYGGDPFDSGLVY 177

Query:   178 GSHASVS-GFLAAVNVILFMAVGSLIGYPIASASVRVLQGLWRNDLVALRGACPNCGEEV 236
              S  S S   L+  N IL   +G   GYPIAS++VRVL+GLWRNDL AL+G CPNCGEEV
Sbjct:   178 SSQLSSSVPILSKFNGILLSVLGPAFGYPIASSAVRVLKGLWRNDLTALKGDCPNCGEEV 237

Query:   237 FAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVE--QSSSRLGRQWVYGRIYLLSR--RNRR 292
             FAFV SDQ+  S H++DCHVC   LEFRTKVE  +S+SRLGR+WVYGRIYL+SR  R+RR
Sbjct:   238 FAFVRSDQSNRSAHKADCHVCECTLEFRTKVEVDKSASRLGRKWVYGRIYLVSRPRRDRR 297

Query:   293 QRW 295
              ++
Sbjct:   298 SKF 300

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2118031 PGRL1B "AT4G11960" [Arabidopsis thaliana (taxid:3702)]

 Score = 119 (46.9 bits), Expect = 3.8e-08, Sum P(2) = 3.8e-08
 Identities = 22/58 (37%), Positives = 38/58 (65%)

Query:    76 EALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCSIRRQSTYADAEED 133
             E  + +A  AY SG P++ D+ +D++++KL+  GS+ V + PRCS+R +  Y+D   D
Sbjct:   129 EQRFLEASMAYVSGNPILSDEEYDKLKMKLKMDGSEIVCEGPRCSLRSKKVYSDLAID 186

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009773 "photosynthetic electron transport in photosystem I" evidence=IGI;RCA

GO:0015979 "photosynthesis" evidence=IGI

GO:0015996 "chlorophyll catabolic process" evidence=RCA

TAIR|locus:2127233 PGR5-LIKE A "AT4G22890" [Arabidopsis thaliana (taxid:3702)]

 Score = 116 (45.9 bits), Expect = 1.3e-07, Sum P(2) = 1.3e-07
 Identities = 23/58 (39%), Positives = 37/58 (63%)

Query:    76 EALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCSIRRQSTYADAEED 133
             E  + +A  AY SG P++ D+ +D+++LKL+  GS  V + PRCS+R +  Y+D   D
Sbjct:   140 EQRFLEASMAYVSGNPILNDEEYDKLKLKLKIDGSDIVSEGPRCSLRSKKVYSDLAVD 197

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009773 "photosynthetic electron transport in photosystem I" evidence=IGI;RCA

GO:0015979 "photosynthesis" evidence=IGI

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0000023 "maltose metabolic process" evidence=RCA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0006364 "rRNA processing" evidence=RCA

GO:0009637 "response to blue light" evidence=RCA

GO:0009657 "plastid organization" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010114 "response to red light" evidence=RCA

GO:0010207 "photosystem II assembly" evidence=RCA

GO:0010218 "response to far red light" evidence=RCA

GO:0010304 "PSII associated light-harvesting complex II catabolic process" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

GO:0019684 "photosynthesis, light reaction" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

GO:0042742 "defense response to bacterium" evidence=RCA

GO:0043085 "positive regulation of catalytic activity" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	296
cd00114	307	LIGANc NAD+ dependent DNA ligase adenylation domai	96.78
PF01653	315	DNA_ligase_aden: NAD-dependent DNA ligase adenylat	96.49
smart00532	441	LIGANc Ligase N family.	96.26
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	96.13
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	95.92
PF13248	26	zf-ribbon_3: zinc-ribbon domain	95.75
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	95.59
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	95.52
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	95.44
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	95.19
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	95.08
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	95.08
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	94.49
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	94.28
PRK05978	148	hypothetical protein; Provisional	93.91
smart00531	147	TFIIE Transcription initiation factor IIE.	93.87
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	93.53
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	93.31
PRK00420	112	hypothetical protein; Validated	93.09
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	92.87
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	92.71
PHA00626	59	hypothetical protein	92.57
PF14255	52	Cys_rich_CPXG: Cysteine-rich CPXCG	92.56
COG5349	126	Uncharacterized protein conserved in bacteria [Fun	92.55
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	92.05
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	91.78
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	91.61
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	91.58
PF14353	128	CpXC: CpXC protein	91.2
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	90.99
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	90.84
PRK09710	64	lar restriction alleviation and modification prote	90.32
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	90.31
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	89.63
PF06044	254	DRP: Dam-replacing family; InterPro: IPR010324 Dam	89.38
PRK06266	178	transcription initiation factor E subunit alpha; V	89.28
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	88.39
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	88.37
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	88.04
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	87.41
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	87.08
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	87.0
PLN00209	86	ribosomal protein S27; Provisional	86.19
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	86.14
PF12773	50	DZR: Double zinc ribbon	86.11
PTZ00083	85	40S ribosomal protein S27; Provisional	84.51
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	83.92
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	83.57
smart00661	52	RPOL9 RNA polymerase subunit 9.	83.18
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	82.61
PRK02935	110	hypothetical protein; Provisional	82.32
COG1326	201	Uncharacterized archaeal Zn-finger protein [Genera	82.28
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	82.11
PRK00432	50	30S ribosomal protein S27ae; Validated	81.94
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	81.51
PRK14714	1337	DNA polymerase II large subunit; Provisional	81.18
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	81.0
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	80.67

>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain

Probab=96.78  E-value=0.0017  Score=61.85  Aligned_cols=36  Identities=28%  Similarity=0.437  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHhH
Q 045112           72 KETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        72 ~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk~  107 (296)
                      ..+|+++-.++..+||. |+|+|||+|||.|..+|+.
T Consensus         3 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~~   39 (307)
T cd00114           3 IAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRA   39 (307)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            67899999999999887 9999999999999999973

DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.

>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose

Probab=96.49  E-value=0.0033  Score=59.94  Aligned_cols=36  Identities=31%  Similarity=0.534  Sum_probs=32.2

Q ss_pred             cHHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHh
Q 045112           71 SKETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLR  106 (296)
Q Consensus        71 t~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk  106 (296)
                      ...+|+++-.++..+||. |+|+|||+|||.|..+|+
T Consensus         6 ~i~~L~~~i~~~~~~YY~~~~p~isD~eYD~l~~~L~   42 (315)
T PF01653_consen    6 RIEELRKEINRHNYAYYNLGEPIISDAEYDQLFRELK   42 (315)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            467888889999999877 899999999999999986

It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....

>smart00532 LIGANc Ligase N family

Probab=96.26  E-value=0.0049  Score=61.53  Aligned_cols=36  Identities=28%  Similarity=0.497  Sum_probs=32.6

Q ss_pred             cHHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHh
Q 045112           71 SKETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLR  106 (296)
Q Consensus        71 t~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk  106 (296)
                      ...+|.++-.++..+||. |+|+|||+|||+|..||+
T Consensus         4 ~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~   40 (441)
T smart00532        4 EISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELK   40 (441)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHH
Confidence            367888889999999886 999999999999999997

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=96.13  E-value=0.0059  Score=63.62  Aligned_cols=36  Identities=31%  Similarity=0.383  Sum_probs=32.8

Q ss_pred             cHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHh
Q 045112           71 SKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLR  106 (296)
Q Consensus        71 t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk  106 (296)
                      ...+|.++-.++..+|| .|+|+|||+|||+|..+|+
T Consensus         8 ~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~   44 (665)
T PRK07956          8 RIEELREELNHHAYAYYVLDAPSISDAEYDRLYRELV   44 (665)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            36788888888999988 9999999999999999997

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=95.92  E-value=0.01  Score=62.31  Aligned_cols=36  Identities=28%  Similarity=0.548  Sum_probs=30.3

Q ss_pred             cHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHh
Q 045112           71 SKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLR  106 (296)
Q Consensus        71 t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk  106 (296)
                      ..++|.++-.++..+|| .|+|+|||+|||+|.++|+
T Consensus        35 ~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~   71 (689)
T PRK14351         35 QAEQLREAIREHDHRYYVEADPVIADRAYDALFARLQ   71 (689)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            45666777777777887 6899999999999999998

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=95.75  E-value=0.0041  Score=39.45  Aligned_cols=24  Identities=46%  Similarity=1.036  Sum_probs=18.6

Q ss_pred             cCCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112          227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL  261 (296)
Q Consensus       227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L  261 (296)
                      -.|||||+++           +....-|++||++|
T Consensus         3 ~~Cp~Cg~~~-----------~~~~~fC~~CG~~L   26 (26)
T PF13248_consen    3 MFCPNCGAEI-----------DPDAKFCPNCGAKL   26 (26)
T ss_pred             CCCcccCCcC-----------CcccccChhhCCCC
Confidence            3699999976           33466799999875

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=95.59  E-value=0.0074  Score=40.36  Aligned_cols=35  Identities=26%  Similarity=0.507  Sum_probs=22.9

Q ss_pred             ecCCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112          226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE  262 (296)
Q Consensus       226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~  262 (296)
                      +-.||+|++.+..  ....-.....+++|++|+..+.
T Consensus         2 ~~~CP~C~~~~~v--~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         2 RIQCPNCKTSFRV--VDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             EEECCCCCCEEEe--CHHHcCCCCCEEECCCCCCEEE
Confidence            4579999998542  2211112334899999999875

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=95.52  E-value=0.015  Score=59.93  Aligned_cols=35  Identities=29%  Similarity=0.523  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHh
Q 045112           72 KETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLR  106 (296)
Q Consensus        72 ~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk  106 (296)
                      ..+|.++-.++..+||. |+|+|||+|||+|..||+
T Consensus        34 i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~   69 (562)
T PRK08097         34 IAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLT   69 (562)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            55677777777788775 999999999999999997

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=95.44  E-value=0.014  Score=40.88  Aligned_cols=31  Identities=32%  Similarity=0.702  Sum_probs=22.7

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT  265 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds  265 (296)
                      -|||||+++-.    +.   .....+|+.||+.+.|..
T Consensus         5 ~C~~CG~~~~~----~~---~~~~~~Cp~CG~~~~~~~   35 (46)
T PRK00398          5 KCARCGREVEL----DE---YGTGVRCPYCGYRILFKE   35 (46)
T ss_pred             ECCCCCCEEEE----CC---CCCceECCCCCCeEEEcc
Confidence            59999997643    11   112789999999999864

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=95.19  E-value=0.02  Score=60.00  Aligned_cols=38  Identities=26%  Similarity=0.447  Sum_probs=31.7

Q ss_pred             cccHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHh
Q 045112           69 TASKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLR  106 (296)
Q Consensus        69 ~~t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk  106 (296)
                      ++..++|.++-.+.-.+|| .|+|+|||+|||+|..||+
T Consensus         6 ~~~i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~   44 (669)
T PRK14350          6 QDEILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQ   44 (669)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            3456777777778888877 5899999999999999996

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=95.08  E-value=0.019  Score=59.74  Aligned_cols=32  Identities=31%  Similarity=0.473  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHhhc-CCCccchhhhHHHHHHHhH
Q 045112           76 EALYRQARDAYYS-GKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        76 E~~flqA~~AY~~-GkPimsDeeFD~LK~kLk~  107 (296)
                      .++-.++..+||. |+|+|||+|||+|.++|+.
T Consensus         2 ~~~l~~~~~~YY~~~~p~IsD~eYD~L~~~L~~   34 (652)
T TIGR00575         2 RKLIRHHDYRYYVLDEPSISDAEYDRLYRELQE   34 (652)
T ss_pred             HHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            3445667788886 9999999999999999984

The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=95.08  E-value=0.017  Score=43.09  Aligned_cols=34  Identities=29%  Similarity=0.604  Sum_probs=24.4

Q ss_pred             ecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112          226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR  264 (296)
Q Consensus       226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd  264 (296)
                      +..||.||+++--     .....-..++|++||..++--
T Consensus         2 ~~~CP~CG~~iev-----~~~~~GeiV~Cp~CGaeleVv   35 (54)
T TIGR01206         2 QFECPDCGAEIEL-----ENPELGELVICDECGAELEVV   35 (54)
T ss_pred             ccCCCCCCCEEec-----CCCccCCEEeCCCCCCEEEEE
Confidence            5689999998732     222223478999999998864

This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=94.49  E-value=0.016  Score=44.51  Aligned_cols=36  Identities=28%  Similarity=0.583  Sum_probs=23.3

Q ss_pred             eeeeecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112          222 LVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS  259 (296)
Q Consensus       222 ~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t  259 (296)
                      --..+=+||||||+.-  .+-..--.-.|..+|++||=
T Consensus        23 e~~v~F~CPnCGe~~I--~Rc~~CRk~g~~Y~Cp~CGF   58 (61)
T COG2888          23 ETAVKFPCPNCGEVEI--YRCAKCRKLGNPYRCPKCGF   58 (61)
T ss_pred             CceeEeeCCCCCceee--ehhhhHHHcCCceECCCcCc
Confidence            3457889999996543  12222223457899999983

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=94.28  E-value=0.021  Score=35.76  Aligned_cols=22  Identities=45%  Similarity=1.029  Sum_probs=16.3

Q ss_pred             CCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112          229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL  261 (296)
Q Consensus       229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L  261 (296)
                      |||||+|+.           .+..-|++||++|
T Consensus         2 Cp~CG~~~~-----------~~~~fC~~CG~~l   23 (23)
T PF13240_consen    2 CPNCGAEIE-----------DDAKFCPNCGTPL   23 (23)
T ss_pred             CcccCCCCC-----------CcCcchhhhCCcC
Confidence            999999873           2233499999875

>PRK05978 hypothetical protein; Provisional

Probab=93.91  E-value=0.026  Score=49.48  Aligned_cols=32  Identities=38%  Similarity=0.937  Sum_probs=23.4

Q ss_pred             eecCCCCCccccc--eeeccCCCCCCCCccccCCCCcceEEe
Q 045112          225 LRGACPNCGEEVF--AFVNSDQTKNSPHRSDCHVCGSLLEFR  264 (296)
Q Consensus       225 LKGpCPNCGeEv~--sFfgtv~s~~~~n~vkChvC~t~L~fd  264 (296)
                      |+|-||+||+.-.  .|++        -+-.|++||..+++.
T Consensus        32 l~grCP~CG~G~LF~g~Lk--------v~~~C~~CG~~~~~~   65 (148)
T PRK05978         32 FRGRCPACGEGKLFRAFLK--------PVDHCAACGEDFTHH   65 (148)
T ss_pred             HcCcCCCCCCCcccccccc--------cCCCccccCCccccC
Confidence            5899999999743  3333        344699999988753

>smart00531 TFIIE Transcription initiation factor IIE

Probab=93.87  E-value=0.028  Score=47.82  Aligned_cols=53  Identities=23%  Similarity=0.452  Sum_probs=30.5

Q ss_pred             HHhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecc
Q 045112          213 VLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTK  266 (296)
Q Consensus       213 ~Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~  266 (296)
                      .|..-+..+.--..=-|||||.. |+|--...-...+.+..|++||..|+++..
T Consensus        86 ~L~~~l~~e~~~~~Y~Cp~C~~~-y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn  138 (147)
T smart00531       86 RLEDKLEDETNNAYYKCPNCQSK-YTFLEANQLLDMDGTFTCPRCGEELEEDDN  138 (147)
T ss_pred             HHHHHHhcccCCcEEECcCCCCE-eeHHHHHHhcCCCCcEECCCCCCEEEEcCc
Confidence            34443333332233459999944 445322211123566999999999988653

>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]

Probab=93.53  E-value=0.057  Score=42.26  Aligned_cols=36  Identities=36%  Similarity=0.782  Sum_probs=29.6

Q ss_pred             eeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112          224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT  265 (296)
Q Consensus       224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds  265 (296)
                      -|+--||.||+|-..|      +.+...+.|.+||+.|..-|
T Consensus        17 Fl~VkCpdC~N~q~vF------shast~V~C~~CG~~l~~PT   52 (67)
T COG2051          17 FLRVKCPDCGNEQVVF------SHASTVVTCLICGTTLAEPT   52 (67)
T ss_pred             EEEEECCCCCCEEEEe------ccCceEEEecccccEEEecC
Confidence            4677799999998877      25677899999999997654

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=93.31  E-value=0.024  Score=41.02  Aligned_cols=32  Identities=22%  Similarity=0.549  Sum_probs=22.8

Q ss_pred             CCCCCccccceeeccCCCCCCC-CccccCCCCc
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSP-HRSDCHVCGS  259 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~-n~vkChvC~t  259 (296)
                      |||=||.+..........+... ..+.|++||.
T Consensus         5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga   37 (61)
T PF14354_consen    5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA   37 (61)
T ss_pred             CCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence            8999998887665533322111 7899999998

>PRK00420 hypothetical protein; Validated

Probab=93.09  E-value=0.063  Score=45.27  Aligned_cols=44  Identities=23%  Similarity=0.441  Sum_probs=30.5

Q ss_pred             HhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112          214 LQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT  265 (296)
Q Consensus       214 Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds  265 (296)
                      +..++.+=...|-..||.||.+.|.+   .     ...+-|++||..+.=..
T Consensus        11 ~a~~Ll~Ga~ml~~~CP~Cg~pLf~l---k-----~g~~~Cp~Cg~~~~v~~   54 (112)
T PRK00420         11 AAELLLKGAKMLSKHCPVCGLPLFEL---K-----DGEVVCPVHGKVYIVKS   54 (112)
T ss_pred             HHHHHHhHHHHccCCCCCCCCcceec---C-----CCceECCCCCCeeeecc
Confidence            44444454555789999999888765   1     23678999999766433

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=92.87  E-value=0.047  Score=41.75  Aligned_cols=33  Identities=30%  Similarity=0.819  Sum_probs=21.8

Q ss_pred             eeecCCCCCccc-cceeeccCCCCCCCCccccCCCCc
Q 045112          224 ALRGACPNCGEE-VFAFVNSDQTKNSPHRSDCHVCGS  259 (296)
Q Consensus       224 iLKGpCPNCGeE-v~sFfgtv~s~~~~n~vkChvC~t  259 (296)
                      ..+=+|||||++ +.-   -.+--.-.|.++|++||-
T Consensus        23 ~~~F~CPnCG~~~I~R---C~~CRk~~~~Y~CP~CGF   56 (59)
T PRK14890         23 AVKFLCPNCGEVIIYR---CEKCRKQSNPYTCPKCGF   56 (59)
T ss_pred             cCEeeCCCCCCeeEee---chhHHhcCCceECCCCCC
Confidence            456689999998 432   111113458899999984

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=92.71  E-value=0.072  Score=40.68  Aligned_cols=34  Identities=35%  Similarity=0.779  Sum_probs=28.1

Q ss_pred             eeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112          224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF  263 (296)
Q Consensus       224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f  263 (296)
                      -|+--||.|++|...|      +.+...++|.+||+.|.-
T Consensus         9 F~~VkCp~C~n~q~vF------sha~t~V~C~~Cg~~L~~   42 (59)
T PRK00415          9 FLKVKCPDCGNEQVVF------SHASTVVRCLVCGKTLAE   42 (59)
T ss_pred             EEEEECCCCCCeEEEE------ecCCcEEECcccCCCccc
Confidence            4677899999999888      256778999999999853

>PHA00626 hypothetical protein

Probab=92.57  E-value=0.073  Score=40.73  Aligned_cols=42  Identities=21%  Similarity=0.325  Sum_probs=28.5

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeecc
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSS  271 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s~  271 (296)
                      .||+||..+..==+.+.  .-+++.+|+.||-...=|+-=|+-+
T Consensus         2 ~CP~CGS~~Ivrcg~cr--~~snrYkCkdCGY~ft~~~~~~~~~   43 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMR--GWSDDYVCCDCGYNDSKDAFGERGK   43 (59)
T ss_pred             CCCCCCCceeeeeceec--ccCcceEcCCCCCeechhhhhhccc
Confidence            49999997655223322  2478999999998776665555443

>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG

Probab=92.56  E-value=0.093  Score=38.87  Aligned_cols=42  Identities=26%  Similarity=0.680  Sum_probs=33.2

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeec
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQS  270 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s  270 (296)
                      .||.||+.+-.....-.+ .-.---+|.+|-+++.+.-.+...
T Consensus         2 ~CPyCge~~~~~iD~s~~-~Q~yiEDC~vCC~PI~~~v~~d~~   43 (52)
T PF14255_consen    2 QCPYCGEPIEILIDPSAG-DQEYIEDCQVCCRPIEVQVTVDED   43 (52)
T ss_pred             CCCCCCCeeEEEEecCCC-CeeEEeehhhcCCccEEEEEECCC
Confidence            599999999887766555 444556899999999999877643

>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.55  E-value=0.041  Score=47.52  Aligned_cols=31  Identities=42%  Similarity=0.977  Sum_probs=23.2

Q ss_pred             eecCCCCCccccc--eeeccCCCCCCCCccccCCCCcceEE
Q 045112          225 LRGACPNCGEEVF--AFVNSDQTKNSPHRSDCHVCGSLLEF  263 (296)
Q Consensus       225 LKGpCPNCGeEv~--sFfgtv~s~~~~n~vkChvC~t~L~f  263 (296)
                      |+|-||||||--.  .|.+..+        .|.+||-.+-|
T Consensus        20 l~grCP~CGeGrLF~gFLK~~p--------~C~aCG~dyg~   52 (126)
T COG5349          20 LRGRCPRCGEGRLFRGFLKVVP--------ACEACGLDYGF   52 (126)
T ss_pred             hcCCCCCCCCchhhhhhcccCc--------hhhhccccccC
Confidence            6899999999643  5555444        49999987765

>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]

Probab=92.05  E-value=0.18  Score=53.41  Aligned_cols=38  Identities=24%  Similarity=0.372  Sum_probs=31.9

Q ss_pred             ccHHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHhH
Q 045112           70 ASKETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        70 ~t~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk~  107 (296)
                      +..++|.++-.+-...||- ++|+|+|+|||+|.+||..
T Consensus         9 ~~i~~L~~~L~~~~~~Yyv~d~P~VsD~eYD~L~reL~~   47 (667)
T COG0272           9 EEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQE   47 (667)
T ss_pred             HHHHHHHHHHHHHHHHHhccCCCCCChHHHHHHHHHHHH
Confidence            4567777777777788776 9999999999999999974

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=91.78  E-value=0.14  Score=37.05  Aligned_cols=36  Identities=22%  Similarity=0.481  Sum_probs=25.3

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF  263 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f  263 (296)
                      |||-||.+...|...........-.+|..|+.....
T Consensus         3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~   38 (53)
T TIGR03655         3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV   38 (53)
T ss_pred             CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence            899999998877532222234445699999988765

Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.

>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins

Probab=91.61  E-value=0.38  Score=41.10  Aligned_cols=34  Identities=26%  Similarity=0.637  Sum_probs=25.5

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeec
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQS  270 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s  270 (296)
                      .|||||.+....=+.         --|..|+++|+-|-..|--
T Consensus        71 ~CP~C~K~TKmLGr~---------D~CM~C~~pLTLd~~legk  104 (114)
T PF11023_consen   71 ECPNCGKQTKMLGRV---------DACMHCKEPLTLDPSLEGK  104 (114)
T ss_pred             ECCCCCChHhhhchh---------hccCcCCCcCccCchhhcc
Confidence            399999987643111         2699999999999887753

; GO: 0005887 integral to plasma membrane

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=91.58  E-value=0.17  Score=34.98  Aligned_cols=38  Identities=29%  Similarity=0.542  Sum_probs=25.6

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeecc
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSS  271 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s~  271 (296)
                      -||+||... ..+-     ..+.+.-|.+||.-++.+.-.+..+
T Consensus         2 ~Cp~Cg~~~-~~~D-----~~~g~~vC~~CG~Vl~e~~i~~~~e   39 (43)
T PF08271_consen    2 KCPNCGSKE-IVFD-----PERGELVCPNCGLVLEENIIDEGPE   39 (43)
T ss_dssp             SBTTTSSSE-EEEE-----TTTTEEEETTT-BBEE-TTBSCCCS
T ss_pred             CCcCCcCCc-eEEc-----CCCCeEECCCCCCEeecccccCCcc
Confidence            499999977 3332     3456789999999998776655443

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>PF14353 CpXC: CpXC protein

Probab=91.20  E-value=0.15  Score=41.88  Aligned_cols=41  Identities=27%  Similarity=0.495  Sum_probs=27.8

Q ss_pred             CCCCCccccceee-ccCCC-----------CCCCCccccCCCCcceEEeccee
Q 045112          228 ACPNCGEEVFAFV-NSDQT-----------KNSPHRSDCHVCGSLLEFRTKVE  268 (296)
Q Consensus       228 pCPNCGeEv~sFf-gtv~s-----------~~~~n~vkChvC~t~L~fds~ve  268 (296)
                      .||+||++...=+ ..+..           +++-+.+.|+.||.....+...-
T Consensus         3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~l   55 (128)
T PF14353_consen    3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLL   55 (128)
T ss_pred             CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEE
Confidence            6999999765332 22222           25778999999999876655443

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=90.99  E-value=0.12  Score=33.43  Aligned_cols=23  Identities=39%  Similarity=0.912  Sum_probs=17.8

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL  261 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L  261 (296)
                      .||+|+++|           ..+..+|+.||-..
T Consensus         2 ~CP~C~~~V-----------~~~~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEV-----------PESAKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCc-----------hhhcCcCCCCCCCC
Confidence            499999998           34556899998653

Several members are annotated as putative helicases.

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=90.84  E-value=0.096  Score=45.49  Aligned_cols=33  Identities=27%  Similarity=0.619  Sum_probs=23.9

Q ss_pred             cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112          227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT  265 (296)
Q Consensus       227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds  265 (296)
                      =-||||+.. ++|--...     +...|++||..|+++.
T Consensus       110 Y~Cp~c~~r-~tf~eA~~-----~~F~Cp~Cg~~L~~~d  142 (158)
T TIGR00373       110 FICPNMCVR-FTFNEAME-----LNFTCPRCGAMLDYLD  142 (158)
T ss_pred             EECCCCCcE-eeHHHHHH-----cCCcCCCCCCEeeecc
Confidence            349999943 45543322     5899999999999864

This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=90.32  E-value=0.18  Score=39.22  Aligned_cols=33  Identities=24%  Similarity=0.518  Sum_probs=23.5

Q ss_pred             cCCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112          227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF  263 (296)
Q Consensus       227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f  263 (296)
                      -|||.||++....=-+    ...-.++|+.|++.-.|
T Consensus         7 KPCPFCG~~~~~v~~~----~g~~~v~C~~CgA~~~~   39 (64)
T PRK09710          7 KPCPFCGCPSVTVKAI----SGYYRAKCNGCESRTGY   39 (64)
T ss_pred             cCCCCCCCceeEEEec----CceEEEEcCCCCcCccc
Confidence            3999999998765321    23446999999996443

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=90.31  E-value=0.23  Score=35.46  Aligned_cols=29  Identities=28%  Similarity=0.605  Sum_probs=23.5

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR  264 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd  264 (296)
                      -|.+||+|+..-        ....++|+.||..+.|-
T Consensus         4 ~C~~Cg~~~~~~--------~~~~irC~~CG~rIlyK   32 (44)
T smart00659        4 ICGECGRENEIK--------SKDVVRCRECGYRILYK   32 (44)
T ss_pred             ECCCCCCEeecC--------CCCceECCCCCceEEEE
Confidence            499999997632        45679999999999985

present in RNA polymerase I, II and III

>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=89.63  E-value=0.27  Score=37.03  Aligned_cols=35  Identities=29%  Similarity=0.611  Sum_probs=23.5

Q ss_pred             eecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112          225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT  265 (296)
Q Consensus       225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds  265 (296)
                      |+--||.|++|...|      +.+...+.|.+|++.|.--|
T Consensus         6 m~VkCp~C~~~q~vF------Sha~t~V~C~~Cg~~L~~Pt   40 (55)
T PF01667_consen    6 MDVKCPGCYNIQTVF------SHAQTVVKCVVCGTVLAQPT   40 (55)
T ss_dssp             EEEE-TTT-SEEEEE------TT-SS-EE-SSSTSEEEEE-
T ss_pred             EEEECCCCCCeeEEE------ecCCeEEEcccCCCEecCCC
Confidence            556799999999887      36778899999999986543

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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.

>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements

Probab=89.38  E-value=0.091  Score=49.88  Aligned_cols=58  Identities=29%  Similarity=0.515  Sum_probs=27.7

Q ss_pred             hhhhhhhhHHHHhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecce
Q 045112          203 GYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKV  267 (296)
Q Consensus       203 gyplasa~v~~Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~v  267 (296)
                      +|-=.+-.+++||..|.    .=...|||||.+..+=|+   .|+...+..|++|+...+-.|+=
T Consensus        12 ~YkS~sQ~aRVltE~Wv----~~n~yCP~Cg~~~L~~f~---NN~PVaDF~C~~C~eeyELKSk~   69 (254)
T PF06044_consen   12 GYKSNSQIARVLTEDWV----AENMYCPNCGSKPLSKFE---NNRPVADFYCPNCNEEYELKSKK   69 (254)
T ss_dssp             HTTT-TTHHHHHHHHHH----HHH---TTT--SS-EE-----------EEE-TTT--EEEEEEEE
T ss_pred             hccChhhhhHHHHHHHH----HHCCcCCCCCChhHhhcc---CCCccceeECCCCchHHhhhhhc
Confidence            44444555666776654    445789999999776664   34557789999999987766653

The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=89.28  E-value=0.15  Score=45.22  Aligned_cols=47  Identities=26%  Similarity=0.412  Sum_probs=29.7

Q ss_pred             HHhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112          213 VLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT  265 (296)
Q Consensus       213 ~Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds  265 (296)
                      .|..-+..+.--.-=-||||+.. |+|.-..     .+...|++||..|++..
T Consensus       104 klk~~l~~e~~~~~Y~Cp~C~~r-ytf~eA~-----~~~F~Cp~Cg~~L~~~d  150 (178)
T PRK06266        104 KLKEQLEEEENNMFFFCPNCHIR-FTFDEAM-----EYGFRCPQCGEMLEEYD  150 (178)
T ss_pred             HHHHHhhhccCCCEEECCCCCcE-EeHHHHh-----hcCCcCCCCCCCCeecc
Confidence            34444443333333459999944 4554322     35899999999999864

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=88.39  E-value=0.45  Score=31.60  Aligned_cols=29  Identities=21%  Similarity=0.556  Sum_probs=20.5

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL  260 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~  260 (296)
                      .||+||.+.-.....    .+.....|+.||..
T Consensus         7 ~C~~Cg~~fe~~~~~----~~~~~~~CP~Cg~~   35 (41)
T smart00834        7 RCEDCGHTFEVLQKI----SDDPLATCPECGGD   35 (41)
T ss_pred             EcCCCCCEEEEEEec----CCCCCCCCCCCCCc
Confidence            699999965544332    22567889999984

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=88.37  E-value=0.31  Score=33.62  Aligned_cols=33  Identities=24%  Similarity=0.573  Sum_probs=21.6

Q ss_pred             CCCCCccccceeec--cCCCC-CCCCccccCCCCcc
Q 045112          228 ACPNCGEEVFAFVN--SDQTK-NSPHRSDCHVCGSL  260 (296)
Q Consensus       228 pCPNCGeEv~sFfg--tv~s~-~~~n~vkChvC~t~  260 (296)
                      +||+||.+.-.||-  +.++. ..+--..|-+|+..
T Consensus         2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~   37 (39)
T PF01096_consen    2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR   37 (39)
T ss_dssp             --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred             CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence            69999999998883  33332 35667889999853

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=88.04  E-value=0.54  Score=33.11  Aligned_cols=39  Identities=23%  Similarity=0.547  Sum_probs=24.9

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeeccccCC
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLG  275 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s~s~~~  275 (296)
                      -|++||.+.-.....    .+.....|++||+     .++++-.|+++
T Consensus         7 ~C~~Cg~~fe~~~~~----~~~~~~~CP~Cg~-----~~~~r~~s~~~   45 (52)
T TIGR02605         7 RCTACGHRFEVLQKM----SDDPLATCPECGG-----EKLRRLLSAVG   45 (52)
T ss_pred             EeCCCCCEeEEEEec----CCCCCCCCCCCCC-----CceeEEecccc
Confidence            499999765444322    1245678999998     35566666553

This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=87.41  E-value=0.33  Score=33.16  Aligned_cols=28  Identities=29%  Similarity=0.669  Sum_probs=15.9

Q ss_pred             CCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112          229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS  259 (296)
Q Consensus       229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t  259 (296)
                      ||+||.++--   .+..+.++.+.-|+.||.
T Consensus         3 C~~CG~~l~~---~ip~gd~r~R~vC~~Cg~   30 (34)
T PF14803_consen    3 CPQCGGPLER---RIPEGDDRERLVCPACGF   30 (34)
T ss_dssp             -TTT--B-EE---E--TT-SS-EEEETTTTE
T ss_pred             cccccChhhh---hcCCCCCccceECCCCCC
Confidence            9999999632   344557889999999985

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=87.08  E-value=0.4  Score=32.38  Aligned_cols=28  Identities=29%  Similarity=0.687  Sum_probs=19.9

Q ss_pred             CCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112          229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR  264 (296)
Q Consensus       229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd  264 (296)
                      |.+||+||.     ++   ....++|..||..+.|-
T Consensus         3 C~~Cg~~~~-----~~---~~~~irC~~CG~RIlyK   30 (32)
T PF03604_consen    3 CGECGAEVE-----LK---PGDPIRCPECGHRILYK   30 (32)
T ss_dssp             ESSSSSSE------BS---TSSTSSBSSSS-SEEBE
T ss_pred             CCcCCCeeE-----cC---CCCcEECCcCCCeEEEe
Confidence            889999987     22   23458999999988773

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins

Probab=87.00  E-value=0.39  Score=35.42  Aligned_cols=32  Identities=28%  Similarity=0.595  Sum_probs=24.6

Q ss_pred             cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecce
Q 045112          227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKV  267 (296)
Q Consensus       227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~v  267 (296)
                      -.||.||..+..       ........|++||..  +|.++
T Consensus        29 q~C~~CG~~~~~-------~~~~r~~~C~~Cg~~--~~rD~   60 (69)
T PF07282_consen   29 QTCPRCGHRNKK-------RRSGRVFTCPNCGFE--MDRDV   60 (69)
T ss_pred             cCccCccccccc-------ccccceEEcCCCCCE--ECcHH
Confidence            359999999887       356678999999976  45444

More information about these proteins can be found at Protein of the Month: Transposase [].

>PLN00209 ribosomal protein S27; Provisional

Probab=86.19  E-value=0.49  Score=38.67  Aligned_cols=36  Identities=19%  Similarity=0.327  Sum_probs=29.9

Q ss_pred             eeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112          223 VALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR  264 (296)
Q Consensus       223 liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd  264 (296)
                      --|+--||.|++|...|      +.+...|.|.+|++.|.--
T Consensus        33 ~Fm~VkCp~C~n~q~VF------ShA~t~V~C~~Cg~~L~~P   68 (86)
T PLN00209         33 FFMDVKCQGCFNITTVF------SHSQTVVVCGSCQTVLCQP   68 (86)
T ss_pred             EEEEEECCCCCCeeEEE------ecCceEEEccccCCEeecc
Confidence            56788899999999887      2567789999999998643

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=86.14  E-value=0.58  Score=32.47  Aligned_cols=32  Identities=25%  Similarity=0.603  Sum_probs=23.6

Q ss_pred             CCCCCccccceeecc--CCCC-CCCCccccCCCCc
Q 045112          228 ACPNCGEEVFAFVNS--DQTK-NSPHRSDCHVCGS  259 (296)
Q Consensus       228 pCPNCGeEv~sFfgt--v~s~-~~~n~vkChvC~t  259 (296)
                      +||+||...-.||-.  .++. ..+--.+|-+|+-
T Consensus         2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~   36 (40)
T smart00440        2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGH   36 (40)
T ss_pred             cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCC
Confidence            699999888888752  2222 3567889999984

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>PF12773 DZR: Double zinc ribbon

Probab=86.11  E-value=0.36  Score=33.68  Aligned_cols=18  Identities=17%  Similarity=0.294  Sum_probs=11.7

Q ss_pred             CCCCccccCCCCcceEEe
Q 045112          247 NSPHRSDCHVCGSLLEFR  264 (296)
Q Consensus       247 ~~~n~vkChvC~t~L~fd  264 (296)
                      .......|++||+.+.=+
T Consensus        25 ~~~~~~~C~~Cg~~~~~~   42 (50)
T PF12773_consen   25 PDQSKKICPNCGAENPPN   42 (50)
T ss_pred             ccCCCCCCcCCcCCCcCC
Confidence            455567788888865433

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=84.51  E-value=0.67  Score=37.82  Aligned_cols=35  Identities=23%  Similarity=0.413  Sum_probs=29.4

Q ss_pred             eeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112          223 VALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF  263 (296)
Q Consensus       223 liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f  263 (296)
                      --|+--||.|+++...|      +.+...|.|.+|++.|.-
T Consensus        32 ~Fm~VkCp~C~n~q~VF------ShA~t~V~C~~Cg~~L~~   66 (85)
T PTZ00083         32 YFMDVKCPGCSQITTVF------SHAQTVVLCGGCSSQLCQ   66 (85)
T ss_pred             eEEEEECCCCCCeeEEE------ecCceEEEccccCCEeec
Confidence            56788899999999887      266778999999999854

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=83.92  E-value=0.57  Score=31.90  Aligned_cols=34  Identities=26%  Similarity=0.613  Sum_probs=20.8

Q ss_pred             ecCCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112          226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL  261 (296)
Q Consensus       226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L  261 (296)
                      +-.||||++.-.  +...+=....-+++|++|+...
T Consensus         2 ~i~CP~C~~~f~--v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    2 IITCPNCQTRFR--VPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EEECCCCCceEE--cCHHHcccCCcEEECCCCCcEe
Confidence            346999997521  1121111344599999999764

>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2

Probab=83.57  E-value=0.64  Score=31.93  Aligned_cols=33  Identities=30%  Similarity=0.580  Sum_probs=23.0

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT  265 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds  265 (296)
                      -||+||+--...|.     .....-+|.+||..|+=|.
T Consensus         3 ~C~~Cg~~Yh~~~~-----pP~~~~~Cd~cg~~L~qR~   35 (36)
T PF05191_consen    3 ICPKCGRIYHIEFN-----PPKVEGVCDNCGGELVQRK   35 (36)
T ss_dssp             EETTTTEEEETTTB-------SSTTBCTTTTEBEBEEG
T ss_pred             CcCCCCCccccccC-----CCCCCCccCCCCCeeEeCC
Confidence            39999986554443     2456679999999887654

7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=83.18  E-value=0.9  Score=31.65  Aligned_cols=28  Identities=29%  Similarity=0.720  Sum_probs=18.3

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL  260 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~  260 (296)
                      -||+||+-+  +....   ...+...|+.||-.
T Consensus         2 FCp~Cg~~l--~~~~~---~~~~~~vC~~Cg~~   29 (52)
T smart00661        2 FCPKCGNML--IPKEG---KEKRRFVCRKCGYE   29 (52)
T ss_pred             CCCCCCCcc--ccccC---CCCCEEECCcCCCe
Confidence            399999944  22221   22358899999954

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=82.61  E-value=0.74  Score=47.16  Aligned_cols=50  Identities=28%  Similarity=0.448  Sum_probs=36.5

Q ss_pred             ccceeeeecCCCCCccccceeecc---CCC-CCCCCccccCCCCcceEEeccee
Q 045112          219 RNDLVALRGACPNCGEEVFAFVNS---DQT-KNSPHRSDCHVCGSLLEFRTKVE  268 (296)
Q Consensus       219 ~~D~liLKGpCPNCGeEv~sFfgt---v~s-~~~~n~vkChvC~t~L~fds~ve  268 (296)
                      ..|----.-|||+||++..-=|..   ... ...+....|+.||+.+.-.-+-.
T Consensus       193 ~sdqr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~  246 (557)
T PF05876_consen  193 ESDQRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRR  246 (557)
T ss_pred             hCCceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhh
Confidence            466677889999999987633443   222 46788899999999998665544

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>PRK02935 hypothetical protein; Provisional

Probab=82.32  E-value=3.2  Score=35.34  Aligned_cols=35  Identities=23%  Similarity=0.512  Sum_probs=25.8

Q ss_pred             cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeec
Q 045112          227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQS  270 (296)
Q Consensus       227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s  270 (296)
                      -.||||+.+..--=+.|         -|-.|+++|+-|...|.-
T Consensus        71 V~CP~C~K~TKmLGrvD---------~CM~C~~PLTLd~~legk  105 (110)
T PRK02935         71 VICPSCEKPTKMLGRVD---------ACMHCNQPLTLDRSLEGK  105 (110)
T ss_pred             eECCCCCchhhhcccee---------ecCcCCCcCCcCcccccc
Confidence            38999998875321111         599999999998877753

>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]

Probab=82.28  E-value=0.48  Score=43.82  Aligned_cols=34  Identities=32%  Similarity=0.678  Sum_probs=20.2

Q ss_pred             eecCCCCCc-cccceeeccCCCCCCCCccccCCCCcc
Q 045112          225 LRGACPNCG-EEVFAFVNSDQTKNSPHRSDCHVCGSL  260 (296)
Q Consensus       225 LKGpCPNCG-eEv~sFfgtv~s~~~~n~vkChvC~t~  260 (296)
                      ..-+||+|| +|+..=+-.-.  ...-.+.|.+||+-
T Consensus         5 iy~~Cp~Cg~eev~hEVik~~--g~~~lvrC~eCG~V   39 (201)
T COG1326           5 IYIECPSCGSEEVSHEVIKER--GREPLVRCEECGTV   39 (201)
T ss_pred             EEEECCCCCcchhhHHHHHhc--CCceEEEccCCCcE
Confidence            456899999 44421111111  12268999999973

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=82.11  E-value=0.57  Score=30.15  Aligned_cols=11  Identities=55%  Similarity=1.074  Sum_probs=8.4

Q ss_pred             eeecCCCCCcc
Q 045112          224 ALRGACPNCGE  234 (296)
Q Consensus       224 iLKGpCPNCGe  234 (296)
                      ...=+|||||+
T Consensus        14 ~v~f~CPnCG~   24 (24)
T PF07754_consen   14 AVPFPCPNCGF   24 (24)
T ss_pred             CceEeCCCCCC
Confidence            44568999996

It is likely to bind zinc via its four well-conserved cysteine residues.

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=81.94  E-value=0.82  Score=33.38  Aligned_cols=29  Identities=31%  Similarity=0.726  Sum_probs=20.2

Q ss_pred             eeecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112          224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL  260 (296)
Q Consensus       224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~  260 (296)
                      .++--||+||.+   |....     ..+..|..||-.
T Consensus        18 ~~~~fCP~Cg~~---~m~~~-----~~r~~C~~Cgyt   46 (50)
T PRK00432         18 RKNKFCPRCGSG---FMAEH-----LDRWHCGKCGYT   46 (50)
T ss_pred             EccCcCcCCCcc---hhecc-----CCcEECCCcCCE
Confidence            456699999987   32221     157899999864

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=81.51  E-value=0.89  Score=38.55  Aligned_cols=23  Identities=43%  Similarity=1.061  Sum_probs=16.8

Q ss_pred             CCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112          229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE  262 (296)
Q Consensus       229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~  262 (296)
                      ||.||.+..           ..+.+|++|++.++
T Consensus         1 CPvCg~~l~-----------vt~l~C~~C~t~i~   23 (113)
T PF09862_consen    1 CPVCGGELV-----------VTRLKCPSCGTEIE   23 (113)
T ss_pred             CCCCCCceE-----------EEEEEcCCCCCEEE
Confidence            888887754           34678888888765

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=81.18  E-value=1.1  Score=50.79  Aligned_cols=44  Identities=23%  Similarity=0.443  Sum_probs=27.3

Q ss_pred             ceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112          221 DLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR  264 (296)
Q Consensus       221 D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd  264 (296)
                      ++.+-.--||+||++++.+|=..=+........|+.||..+..+
T Consensus       662 eVEV~~rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~~d  705 (1337)
T PRK14714        662 EVEVGRRRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVPPD  705 (1337)
T ss_pred             EEEEEEEECCCCCCccccccCcccCCcCCCceeCccCCCccCCC
Confidence            35677788999999998876433332222334566666655444

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=81.00  E-value=0.75  Score=40.02  Aligned_cols=39  Identities=28%  Similarity=0.608  Sum_probs=29.6

Q ss_pred             HHHhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112          212 RVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS  259 (296)
Q Consensus       212 ~~Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t  259 (296)
                      +.+..|+.+=+..|--.||-||.+.|.         .+-++-|++||.
T Consensus        14 k~iA~lLl~GAkML~~hCp~Cg~PLF~---------KdG~v~CPvC~~   52 (131)
T COG1645          14 KKIAELLLQGAKMLAKHCPKCGTPLFR---------KDGEVFCPVCGY   52 (131)
T ss_pred             HHHHHHHHhhhHHHHhhCcccCCccee---------eCCeEECCCCCc
Confidence            344456666667777889999999986         345788999996

>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria

Probab=80.67  E-value=1.7  Score=30.28  Aligned_cols=28  Identities=29%  Similarity=0.667  Sum_probs=20.2

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS  259 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t  259 (296)
                      -|++||.+--.+..    ..+...+.|+.||.
T Consensus         7 ~C~~Cg~~fe~~~~----~~~~~~~~CP~Cg~   34 (42)
T PF09723_consen    7 RCEECGHEFEVLQS----ISEDDPVPCPECGS   34 (42)
T ss_pred             EeCCCCCEEEEEEE----cCCCCCCcCCCCCC
Confidence            49999977555543    22367889999998

The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	296
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	3e-04

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 15/71 (21%), Positives = 22/71 (30%), Gaps = 18/71 (25%)

Query: 206 IASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSD--CHVCGSLL-- 261
           +   S+    G    +L  +   CP C       V            D  C +CG +L  
Sbjct: 2   MTRESIDKRAGRRGPNL-NIVLTCPECKVYPPKIVE-R-----FSEGDVVCALCGLVLSD 54

Query: 262 -------EFRT 265
                  E+RT
Sbjct: 55  KLVDTRSEWRT 65

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	296
4glw_A	305	DNA ligase; inhibitor, ligase-ligase inhibitor com	96.18
3jsl_A	318	DNA ligase; NAD+-dependent, DNA damage, DNA repair	96.06
3uq8_A	322	DNA ligase; adenylated protein, ATP-grAsp, rossman	96.02
1zau_A	328	DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu	95.9
1ta8_A	332	DNA ligase, NAD-dependent; nucleotidyl transferase	95.86
1b04_A	318	Protein (DNA ligase); DNA replication; 2.80A {Geob	95.85
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	95.54
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	94.35
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	94.16
4esj_A	257	Type-2 restriction enzyme DPNI; restriction endonu	93.73
3sgi_A	615	DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub	92.97
1nui_A	255	DNA primase/helicase; zinc-biding domain, toprim f	92.79
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	89.68
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	89.31
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	87.93
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	87.21
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	85.08
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	83.86
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	83.67
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	83.64
3flo_B	206	DNA polymerase alpha catalytic subunit A; protein-	83.34
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	83.26

>4glw_A DNA ligase; inhibitor, ligase-ligase inhibitor complex; HET: DNA 0XT NMN; 2.00A {Streptococcus pneumoniae}

Probab=96.18  E-value=0.00073  Score=62.78  Aligned_cols=37  Identities=30%  Similarity=0.420  Sum_probs=6.3

Q ss_pred             cHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHhH
Q 045112           71 SKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        71 t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk~  107 (296)
                      .++||.++-.++..+|| .|+|+|||+|||.|..+|+.
T Consensus         4 ri~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~~   41 (305)
T 4glw_A            4 RMNELVALLNRYATEYYTSDNPSVSDSEYDRLYRELVE   41 (305)
T ss_dssp             HHHC-----------------------------CHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            46778888888889987 59999999999999998874

>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA replication, magnesium, manganese, metal-binding, NAD, zinc; HET: DNA; 1.80A {Staphylococcus aureus} SCOP: d.142.2.2 PDB: 3jsn_A*

Probab=96.06  E-value=0.0051  Score=57.94  Aligned_cols=38  Identities=24%  Similarity=0.355  Sum_probs=32.3

Q ss_pred             ccHHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHhH
Q 045112           70 ASKETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        70 ~t~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk~  107 (296)
                      ...++|.++-.++..+||. |+|+|||+|||+|..+|+.
T Consensus         6 ~~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~   44 (318)
T 3jsl_A            6 SRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIK   44 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHTSCCCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHH
Confidence            3567888888888888775 9999999999999999873

>3uq8_A DNA ligase; adenylated protein, ATP-grAsp, rossman fold, adenylation; HET: DNA NAD AMP; 1.70A {Haemophilus influenzae} PDB: 3pn1_A* 3bac_A*

Probab=96.02  E-value=0.0053  Score=57.82  Aligned_cols=37  Identities=24%  Similarity=0.338  Sum_probs=32.1

Q ss_pred             cHHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHhH
Q 045112           71 SKETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        71 t~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk~  107 (296)
                      ..++|.++-.++..+||. ++|+|||+|||+|..||+.
T Consensus         5 ~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~   42 (322)
T 3uq8_A            5 QLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKA   42 (322)
T ss_dssp             HHHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            467788888888899885 9999999999999999874

>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis}

Probab=95.90  E-value=0.007  Score=57.12  Aligned_cols=38  Identities=26%  Similarity=0.385  Sum_probs=33.1

Q ss_pred             ccHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHhH
Q 045112           70 ASKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        70 ~t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk~  107 (296)
                      +..++|.++-.++..+|| .|+|+|||+|||+|..+|+.
T Consensus        15 ~~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~   53 (328)
T 1zau_A           15 RQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEA   53 (328)
T ss_dssp             TTHHHHHHHHHHHHHHHTTTCCCSSCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            357888888888888877 69999999999999999984

>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA NMN; 1.80A {Enterococcus faecalis} SCOP: d.142.2.2 PDB: 3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A*

Probab=95.86  E-value=0.0069  Score=57.27  Aligned_cols=37  Identities=24%  Similarity=0.374  Sum_probs=32.0

Q ss_pred             cHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHhH
Q 045112           71 SKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        71 t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk~  107 (296)
                      ..++|.++--++..+|| .|+|+|||+|||+|..+|+.
T Consensus        14 ~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~   51 (332)
T 1ta8_A           14 RAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVD   51 (332)
T ss_dssp             HHHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            46778888888888877 79999999999999999884

>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus stearothermophilus} SCOP: d.142.2.2

Probab=95.85  E-value=0.0066  Score=57.06  Aligned_cols=37  Identities=24%  Similarity=0.370  Sum_probs=31.9

Q ss_pred             cHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHhH
Q 045112           71 SKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        71 t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk~  107 (296)
                      ..++|.++--++..+|| .|+|+|||+|||+|..+|+.
T Consensus         9 ~~~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~   46 (318)
T 1b04_A            9 RAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIA   46 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSCCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            46778888888888876 79999999999999999883

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=95.54  E-value=0.0083  Score=60.43  Aligned_cols=37  Identities=27%  Similarity=0.309  Sum_probs=31.9

Q ss_pred             cHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHhH
Q 045112           71 SKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        71 t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk~  107 (296)
                      ..++|.++-.++..+|| .|+|+|||+|||+|..||+.
T Consensus         7 ~i~~L~~~i~~~~~~Yy~~~~p~IsD~eYD~L~~eL~~   44 (586)
T 4glx_A            7 QLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRE   44 (586)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCSSBCCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            46678888888888887 59999999999999999874

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=94.35  E-value=0.03  Score=57.26  Aligned_cols=37  Identities=27%  Similarity=0.309  Sum_probs=32.0

Q ss_pred             cHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHhH
Q 045112           71 SKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        71 t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk~  107 (296)
                      ..++|.++-.++..+|| .++|+|||+|||+|..+|+.
T Consensus         7 ~~~~L~~~l~~~~~~YY~~d~p~isD~eYD~L~~eL~~   44 (671)
T 2owo_A            7 QLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRE   44 (671)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCSSBCCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            46788888888888876 69999999999999999884

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*

Probab=94.16  E-value=0.032  Score=57.04  Aligned_cols=37  Identities=30%  Similarity=0.403  Sum_probs=31.6

Q ss_pred             cHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHhH
Q 045112           71 SKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        71 t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk~  107 (296)
                      ..++|.++-.++..+|| .++|+|||+|||+|..+|+.
T Consensus         9 ~~~~L~~~l~~~~~~YY~~d~p~isD~eYD~l~~eL~~   46 (667)
T 1dgs_A            9 RINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKE   46 (667)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCCSCSSSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            45677777778888877 69999999999999999985

>4esj_A Type-2 restriction enzyme DPNI; restriction endonuclease-DNA complex, type IIM, type IIE, RE enzyme, DPNI; HET: DNA 6MA; 2.05A {Streptococcus pneumoniae}

Probab=93.73  E-value=0.035  Score=51.35  Aligned_cols=58  Identities=24%  Similarity=0.555  Sum_probs=41.0

Q ss_pred             hhhhhhhhHHHHhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecce
Q 045112          203 GYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKV  267 (296)
Q Consensus       203 gyplasa~v~~Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~v  267 (296)
                      +|-=.|-.+++||..|...    .+.|||||.+..+=|+...+   ..+.-|++|....|.-|+=
T Consensus        15 ~YkS~SQ~aRVLTE~Wv~~----n~yCPnCG~~~l~~f~nN~P---VaDF~C~~C~EeyELKSk~   72 (257)
T 4esj_A           15 TYKSNSQKARILTEDWVYR----QSYCPNCGNNPLNHFENNRP---VADFYCNHCSEEFELKSKK   72 (257)
T ss_dssp             HTTTCTTHHHHHHHHHHHH----HCCCTTTCCSSCEEC----C---CCEEECTTTCCEEEEEEEE
T ss_pred             hccChhheehhhhHHHHHH----CCcCCCCCChhhhhccCCCc---ccccccCCcchhheecccc
Confidence            4555566677788777654    57899999988777765444   5678999999988877653

>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}

Probab=92.97  E-value=0.017  Score=58.63  Aligned_cols=37  Identities=27%  Similarity=0.401  Sum_probs=31.3

Q ss_pred             cHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHhH
Q 045112           71 SKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        71 t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk~  107 (296)
                      ..++|.++-.++..+|| .++|+|||+|||+|..||+.
T Consensus        16 ~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~~   53 (615)
T 3sgi_A           16 QWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEA   53 (615)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCCCSSCCSSCSSSSHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHH
Confidence            46677777778888888 79999999999999988873

>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2

Probab=92.79  E-value=0.046  Score=47.79  Aligned_cols=34  Identities=21%  Similarity=0.416  Sum_probs=23.5

Q ss_pred             eeeecCCCCCcc-ccceeeccCCCCCCCCccccCCCCcceEE
Q 045112          223 VALRGACPNCGE-EVFAFVNSDQTKNSPHRSDCHVCGSLLEF  263 (296)
Q Consensus       223 liLKGpCPNCGe-Ev~sFfgtv~s~~~~n~vkChvC~t~L~f  263 (296)
                      ..-+++||+||- .-+.||.  .+     ...||+||..-.+
T Consensus        11 ~~~~~~CP~Cg~~d~~~~~~--dg-----~~~C~~Cg~~~~~   45 (255)
T 1nui_A           11 FLYHIPCDNCGSSDGNSLFS--DG-----HTFCYVCEKWTAG   45 (255)
T ss_dssp             EEEEECCSSSCCSSCEEEET--TS-----CEEETTTCCEEC-
T ss_pred             eecCCcCCCCCCCCCceEeC--CC-----CeecccCCCcCCC
Confidence            345999999998 4456562  22     3999999976443

>3j20_W 30S ribosomal protein S27E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=89.68  E-value=0.2  Score=37.71  Aligned_cols=37  Identities=32%  Similarity=0.671  Sum_probs=29.8

Q ss_pred             eeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112          223 VALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT  265 (296)
Q Consensus       223 liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds  265 (296)
                      --++--||.|+++...|      +.+...+.|.+|++.|.--|
T Consensus        12 ~Fm~VkCp~C~~~q~VF------Sha~t~V~C~~Cgt~L~~PT   48 (63)
T 3j20_W           12 RFLRVKCIDCGNEQIVF------SHPATKVRCLICGATLVEPT   48 (63)
T ss_dssp             CEEEEECSSSCCEEEEE------SSCSSCEECSSSCCEEEECC
T ss_pred             cEEEEECCCCCCeeEEE------ecCCeEEEccCcCCEEecCC
Confidence            45677799999999887      26677899999999986543

>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4

Probab=89.31  E-value=0.22  Score=37.81  Aligned_cols=34  Identities=24%  Similarity=0.656  Sum_probs=28.4

Q ss_pred             eecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112          225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR  264 (296)
Q Consensus       225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd  264 (296)
                      |+--||.|+++...|      +.+...+.|.+|++.|.--
T Consensus         6 m~VKCp~C~niq~VF------ShA~tvV~C~~Cg~~L~~P   39 (66)
T 1qxf_A            6 VKVKCPDCEHEQVIF------DHPSTIVKCIICGRTVAEP   39 (66)
T ss_dssp             EEEECTTTCCEEEEE------SSCSSCEECSSSCCEEEEC
T ss_pred             EEEECCCCCCceEEE------ecCceEEEcccCCCEEeec
Confidence            677799999999888      3677789999999998643

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=87.93  E-value=0.24  Score=34.01  Aligned_cols=29  Identities=24%  Similarity=0.699  Sum_probs=20.9

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE  262 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~  262 (296)
                      .||+||.+...|      .....+..|..||..+.
T Consensus         7 ~CP~C~~~~l~~------d~~~gelvC~~CG~v~~   35 (50)
T 1pft_A            7 VCPACESAELIY------DPERGEIVCAKCGYVIE   35 (50)
T ss_dssp             SCTTTSCCCEEE------ETTTTEEEESSSCCBCC
T ss_pred             eCcCCCCcceEE------cCCCCeEECcccCCccc
Confidence            599999865544      13456899999987543

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=87.21  E-value=0.26  Score=34.84  Aligned_cols=35  Identities=23%  Similarity=0.554  Sum_probs=24.5

Q ss_pred             ecCCCCCccccceeecc-CCCC--CCCCccccCCCCcc
Q 045112          226 RGACPNCGEEVFAFVNS-DQTK--NSPHRSDCHVCGSL  260 (296)
Q Consensus       226 KGpCPNCGeEv~sFfgt-v~s~--~~~n~vkChvC~t~  260 (296)
                      .-+||.||.+...|+-. ..+.  ..+--.+|.+||..
T Consensus        15 ~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~   52 (57)
T 1qyp_A           15 KITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHT   52 (57)
T ss_dssp             ECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCE
T ss_pred             EeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCE
Confidence            67899999977777642 2222  34566899999874

>3u5c_b RP61, YS20, 40S ribosomal protein S27-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_X 3u5g_b

Probab=85.08  E-value=0.48  Score=37.31  Aligned_cols=39  Identities=23%  Similarity=0.443  Sum_probs=31.0

Q ss_pred             ceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112          221 DLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT  265 (296)
Q Consensus       221 D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds  265 (296)
                      +---++--||.|+++...|      +.+...+.|.+|++.|.--|
T Consensus        29 nS~Fm~VkCp~C~~~q~VF------Sha~t~V~C~~Cg~~L~~PT   67 (82)
T 3u5c_b           29 RSYFLDVKCPGCLNITTVF------SHAQTAVTCESCSTILCTPT   67 (82)
T ss_dssp             CCCEEEEECTTSCSCEEEE------SBCSSCCCCSSSCCCCEECC
T ss_pred             CCcEEEEECCCCCCeeEEE------ecCCeEEEccccCCEEeccC
Confidence            3356777899999999888      25677899999999986543

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=83.86  E-value=0.44  Score=33.70  Aligned_cols=32  Identities=31%  Similarity=0.690  Sum_probs=22.5

Q ss_pred             eeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112          222 LVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL  260 (296)
Q Consensus       222 ~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~  260 (296)
                      ..-+.--||+||.+++-.  .     ...+..|..||-.
T Consensus        15 v~~~~k~CP~CG~~~fm~--~-----~~~R~~C~kCG~t   46 (50)
T 3j20_Y           15 VIRKNKFCPRCGPGVFMA--D-----HGDRWACGKCGYT   46 (50)
T ss_dssp             EECSSEECSSSCSSCEEE--E-----CSSEEECSSSCCE
T ss_pred             EEEecccCCCCCCceEEe--c-----CCCeEECCCCCCE
Confidence            344677899999987533  1     1367899999853

>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6

Probab=83.67  E-value=0.66  Score=36.41  Aligned_cols=37  Identities=22%  Similarity=0.424  Sum_probs=30.1

Q ss_pred             eeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112          223 VALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT  265 (296)
Q Consensus       223 liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds  265 (296)
                      --|+--||.|+++...|      +.+...|.|.+|++.|.--|
T Consensus        29 ~Fm~VkCp~C~n~q~VF------ShA~t~V~C~~Cg~~L~~PT   65 (81)
T 2xzm_6           29 YFMDVKCAQCQNIQMIF------SNAQSTIICEKCSAILCKPT   65 (81)
T ss_dssp             CEEEEECSSSCCEEEEE------TTCSSCEECSSSCCEEEEEC
T ss_pred             cEEEeECCCCCCeeEEE------ecCccEEEccCCCCEEeecC
Confidence            44778899999998887      26777899999999987544

>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A

Probab=83.64  E-value=0.55  Score=33.82  Aligned_cols=29  Identities=21%  Similarity=0.509  Sum_probs=21.4

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE  262 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~  262 (296)
                      .||+||.+...|      .....+..|.+||.-++
T Consensus        13 ~Cp~C~~~~lv~------D~~~ge~vC~~CGlVl~   41 (58)
T 1dl6_A           13 TCPNHPDAILVE------DYRAGDMICPECGLVVG   41 (58)
T ss_dssp             SBTTBSSSCCEE------CSSSCCEECTTTCCEEC
T ss_pred             cCcCCCCCceeE------eCCCCeEEeCCCCCEEe
Confidence            599999876444      13456799999987664

>3flo_B DNA polymerase alpha catalytic subunit A; protein-protein complex, phosphoesterase fold, OB fold, zinc motif, DNA replication, nucleus; HET: DNA; 2.50A {Saccharomyces cerevisiae}

Probab=83.34  E-value=0.54  Score=41.70  Aligned_cols=45  Identities=22%  Similarity=0.364  Sum_probs=33.5

Q ss_pred             hhhhccceeeeecCCCCCccccceeeccCCCC----CCCCccccCCCCcce
Q 045112          215 QGLWRNDLVALRGACPNCGEEVFAFVNSDQTK----NSPHRSDCHVCGSLL  261 (296)
Q Consensus       215 t~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~----~~~n~vkChvC~t~L  261 (296)
                      +...++|..=|+=.||.|++++.  |+++...    -..+...|++|+..+
T Consensus        11 DeeRfr~c~~l~l~Cp~C~~~~~--F~gv~~~~~~~~~~sg~~C~~C~~~~   59 (206)
T 3flo_B           11 DVERFKDTVTLELSCPSCDKRFP--FGGIVSSNYYRVSYNGLQCKHCEQLF   59 (206)
T ss_dssp             CTTTTTTCCCEEEECTTTCCEEE--ECSSSCCSSEEEETTEEEETTTCCBC
T ss_pred             HHHHhCcCceeEEECCCCCCccC--CCCcccCCCcccccccccCCCCCCcC
Confidence            34667999999999999999864  5554432    145678899999864

>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=83.26  E-value=0.68  Score=36.72  Aligned_cols=37  Identities=19%  Similarity=0.310  Sum_probs=28.9

Q ss_pred             ceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112          221 DLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF  263 (296)
Q Consensus       221 D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f  263 (296)
                      +---++--||.|+++...|      +.+...+.|.+|++.|.-
T Consensus        31 nS~Fm~VkCp~C~~~~~VF------ShA~t~V~C~~CgtvL~~   67 (86)
T 3iz6_X           31 NSFFMDVKCQGCFNITTVF------SHSQTVVVCPGCQTVLCQ   67 (86)
T ss_dssp             --CEEEEECTTTCCEEEEE------TTCSSCCCCSSSCCCCSC
T ss_pred             CCcEeEEECCCCCCeeEEE------ecCCcEEEccCCCCEeec
Confidence            3355777899999999888      366778999999998854

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	296
d1ta8a_	313	Adenylation domain of NAD+-dependent DNA ligase {E	97.7
d1b04a_	312	Adenylation domain of NAD+-dependent DNA ligase {B	97.69
d1dgsa3	314	Adenylation domain of NAD+-dependent DNA ligase {T	97.36
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	92.13
d1pfva3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch	85.86
d1rqga3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro	84.35
d1s3ga2	35	Microbial and mitochondrial ADK, insert "zinc fing	82.79

>d1ta8a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Enterococcus faecalis [TaxId: 1351]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Enterococcus faecalis [TaxId: 1351]

Probab=97.70  E-value=1.4e-05  Score=70.09  Aligned_cols=37  Identities=24%  Similarity=0.374  Sum_probs=33.7

Q ss_pred             cHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHhH
Q 045112           71 SKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        71 t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk~  107 (296)
                      ..++|+++-.++..+|| .|+|+|||+|||.|+.+|+.
T Consensus        10 ~~~~L~~~i~~~~~~Yy~~~~p~iSD~eYD~L~~~L~~   47 (313)
T d1ta8a_          10 RAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVD   47 (313)
T ss_dssp             HHHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            46789999999999998 59999999999999999975

>d1b04a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.69  E-value=1.2e-05  Score=71.21  Aligned_cols=38  Identities=24%  Similarity=0.364  Sum_probs=34.2

Q ss_pred             ccHHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHhH
Q 045112           70 ASKETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        70 ~t~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk~  107 (296)
                      +.++||+++-.++..+||. |+|+|||+|||.|+++|+.
T Consensus         7 ~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~   45 (312)
T d1b04a_           7 RRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIA   45 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCSCCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            3567999999999999986 9999999999999999974

>d1dgsa3 d.142.2.2 (A:1-314) Adenylation domain of NAD+-dependent DNA ligase {Thermus filiformis [TaxId: 276]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Thermus filiformis [TaxId: 276]

Probab=97.36  E-value=4.8e-05  Score=67.56  Aligned_cols=38  Identities=29%  Similarity=0.397  Sum_probs=33.7

Q ss_pred             ccHHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHhH
Q 045112           70 ASKETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLRW  107 (296)
Q Consensus        70 ~t~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk~  107 (296)
                      +-+++|+++-.++..+||. |+|+|||+|||.|+.+|+.
T Consensus         8 ~~i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~~   46 (314)
T d1dgsa3           8 RRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKE   46 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCCCSCSSSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            3567888888999999985 9999999999999999985

>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27e
domain: Ribosomal protein S27e
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=92.13  E-value=0.045  Score=38.85  Aligned_cols=35  Identities=26%  Similarity=0.661  Sum_probs=28.9

Q ss_pred             eecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112          225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT  265 (296)
Q Consensus       225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds  265 (296)
                      ||=.||.|++|...|      +.+...+.|.+|++.|.--|
T Consensus         6 ~~VkC~~C~n~~ivF------sha~t~V~C~~Cg~~L~~Pt   40 (58)
T d1qxfa_           6 VKVKCPDCEHEQVIF------DHPSTIVKCIICGRTVAEPT   40 (58)
T ss_dssp             EEEECTTTCCEEEEE------SSCSSCEECSSSCCEEEECC
T ss_pred             EEeECCCCCCeEEEE------ecCceEEEccccCCEEeccC
Confidence            566799999999888      36778899999999986443

>d1pfva3 g.41.1.1 (A:141-175) Methionyl-tRNA synthetase (MetRS), Zn-domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Escherichia coli [TaxId: 562]

Probab=85.86  E-value=0.13  Score=33.12  Aligned_cols=26  Identities=31%  Similarity=0.916  Sum_probs=19.3

Q ss_pred             eecCCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112          225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE  262 (296)
Q Consensus       225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~  262 (296)
                      ++|.||.|+.|.            ..--.|.+||+.+.
T Consensus         1 V~G~CP~C~~~~------------a~GDqCe~CG~~~~   26 (35)
T d1pfva3           1 VKGTCPKCKSPD------------QYGDNCEVCGATYS   26 (35)
T ss_dssp             EEEECTTTCCSS------------EETTBCTTTCCBCC
T ss_pred             CeeECCCCCCcc------------cccccHHHcCCcCC
Confidence            589999999763            23357999998763

>d1rqga3 g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyrococcus abyssi [TaxId: 29292]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Pyrococcus abyssi [TaxId: 29292]

Probab=84.35  E-value=0.2  Score=32.18  Aligned_cols=26  Identities=42%  Similarity=1.008  Sum_probs=18.7

Q ss_pred             eecCCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112          225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE  262 (296)
Q Consensus       225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~  262 (296)
                      ++|.||.||.|.            ..--.|.+||+.+.
T Consensus         1 V~G~CP~C~~~~------------a~GDqCe~CG~~~~   26 (35)
T d1rqga3           1 VIGTCPYCGAED------------QKGDQCEVCGRPLT   26 (35)
T ss_dssp             CCSBCSSSCCSC------------CCTTTCSSSCCCCC
T ss_pred             CeEECCCCCCCc------------ccCcchhhcCCccC
Confidence            479999999753            22346999998653

>d1s3ga2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus globisporus [TaxId: 1459]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus globisporus [TaxId: 1459]

Probab=82.79  E-value=0.24  Score=31.49  Aligned_cols=30  Identities=23%  Similarity=0.453  Sum_probs=22.5

Q ss_pred             CCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112          228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE  262 (296)
Q Consensus       228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~  262 (296)
                      -||+||+--..+|.     ....+-+|.+||.+|+
T Consensus         4 ~C~~CG~~Yh~~~~-----pPk~~g~CD~cg~~L~   33 (35)
T d1s3ga2           4 ICKVCGTSYHLLFN-----PPQVEGKCDKDGGELY   33 (35)
T ss_dssp             EETTTCCEEETTTB-----CCSBTTBCTTTCCBEE
T ss_pred             CCcCcCchhccccC-----CCCCCCccCCCCCCce
Confidence            49999986555553     3556779999999885