Citrus Sinensis ID: 038833

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120
Protein Sequence
MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHVLRADHDELETVIPQIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKLA
Secondary Structure (PSIPRED)
cccHHHHHHHccccccEEEcccEEEEEEcccccccEEEEEEEEEEEccccEEEEEccccEEEcccccccEEEEEccccccEEEEEEEEccccEEEEEEccccccccEEEccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHccccccccccccEEEEEEcccccccEEcEEEEEEEEEcccEEEEEcHHHcEEEccccccEEEEEccccccEEEEEEEccccEEEEEEEEcccccccEEEcccHHHHHHcc
Coil and Loop (DISEMBL)
MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFadkgyckqkgivRKVIDKYHVLRADHDELETVIPQIEGLVIVNgayqgsnarllgvdndkfcaktkiekgvndgrvlnaiDYEDICKLA
Flexible Loop (DISEMBL)
mreeekvkekmntqdywlfKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHVLRADHDELETVIPQIEGLVIVNGAYQGSNARLLGVDNDKFCAKTkiekgvndgrvlnaidyedickla
Low Complexity Region (SEG)
MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHVLRADHDELETVIPQIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKLA
Disordered region (IsUnstruct)
**************DYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHVLRADHDELETVIPQIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDIC***
Disordered Region (DISOPRED)
******************FKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHVLRADHDELETVIPQIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKLA
Disordered Region (DISEMBL)
**********MNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHVLRADHDELETVIPQIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKLA
Disordered Region (DISPRO)
***********NTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHVLRADHDELETVIPQIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKLA
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHVLRADHDELETVIPQIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKLA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	120	2.2.26 [Sep-21-2011]
O60870	393	DNA/RNA-binding protein K	yes	no	0.875	0.267	0.401	2e-14
Q8K339	391	DNA/RNA-binding protein K	yes	no	0.975	0.299	0.372	4e-14
Q55D16	445	KIN17-like protein OS=Dic	yes	no	0.816	0.220	0.345	2e-05

>sp|O60870|KIN17_HUMAN DNA/RNA-binding protein KIN17 OS=Homo sapiens GN=KIN PE=1 SV=2

 Score = 78.2 bits (191), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 47/117 (40%), Positives = 66/117 (56%), Gaps = 12/117 (10%)

Query: 15  DYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHV----------LRADHDELETVI 64
           DYWL   IIV++++K   +K Y K+K IV++VIDKY            L+ D   LETVI
Sbjct: 278 DYWLQPEIIVKIITKKLGEK-YHKKKAIVKEVIDKYTAVVKMIDSGDKLKLDQTHLETVI 336

Query: 65  PQI-EGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKLA 120
           P   + ++++NG Y+G+   L  ++   F A   IE G   GR +  I YEDI KLA
Sbjct: 337 PAPGKRILVLNGGYRGNEGTLESINEKTFSATIVIETGPLKGRRVEGIQYEDISKLA 393

Involved in DNA replication and the cellular response to DNA damage. May participate in DNA replication factories and create a bridge between DNA replication and repair mediated by high molecular weight complexes. May play a role in illegitimate recombination and regulation of gene expression. May participate in mRNA processing. Binds, in vitro, to double-stranded DNA. Also shown to bind preferentially to curved DNA in vitro and in vivo (By similarity). Binds via its C-terminal domain to RNA in vitro.
Homo sapiens (taxid: 9606)

>sp|Q8K339|KIN17_MOUSE DNA/RNA-binding protein KIN17 OS=Mus musculus GN=Kin PE=2 SV=1

 Score = 76.6 bits (187), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 48/129 (37%), Positives = 73/129 (56%), Gaps = 12/129 (9%)

Query: 3   EEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHV---------- 52
           E E+ K++    D WL  GI+V++++K   +K Y K+KG+V++VID+Y            
Sbjct: 264 ELEEEKKRTARTDAWLQPGIVVKIITKKLGEK-YHKKKGVVKEVIDRYTAVVKMTDSGDR 322

Query: 53  LRADHDELETVIPQI-EGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAI 111
           L+ D   LETVIP   + ++++NG Y+G+   L  ++   F A   IE G   GR +  I
Sbjct: 323 LKLDQTHLETVIPAPGKRVLVLNGGYRGNEGTLESINEKAFSATIVIETGPLKGRRVEGI 382

Query: 112 DYEDICKLA 120
            YEDI KLA
Sbjct: 383 QYEDISKLA 391

Involved in DNA replication and the cellular response to DNA damage. May participate in DNA replication factories and create a bridge between DNA replication and repair mediated by high molecular weight complexes. May play a role in illegitimate recombination and regulation of gene expression. May participate in mRNA processing. Binds, in vitro, to double-stranded DNA. Also shown to bind preferentially to curved DNA in vitro and in vivo. Binds via its C-terminal domain to RNA in vitro.

Mus musculus (taxid: 10090)

>sp|Q55D16|KIN17_DICDI KIN17-like protein OS=Dictyostelium discoideum GN=DDB_G0269816 PE=3 SV=1

 Score = 48.1 bits (113), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 39/113 (34%), Positives = 59/113 (52%), Gaps = 15/113 (13%)

Query: 17  WLFKGIIVEVMSKAFADKGYCKQKGIV----------RKVIDKYHVLRADHDELETVIPQ 66
           W+ K I+++++ K  A+  Y KQKG +           K++D   +L+ D   LETVIPQ
Sbjct: 335 WIIKDIVIKIIDKELANGKYFKQKGYIVSVENEFLAKVKLLDSGDILKIDQTFLETVIPQ 394

Query: 67  I-EGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118
           I   ++IVNG Y+G  A +  V+ D F AK  I+    D  +   + YE   K
Sbjct: 395 IGSTVIIVNGKYRGKEATIKNVNFDDFNAKLYIK----DNDITITLPYESFSK 443

Dictyostelium discoideum (taxid: 44689)

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	120
125586877	411	hypothetical protein OsJ_11495 [Oryza sa	0.991	0.289	0.661	3e-42
125544570	430	hypothetical protein OsI_12309 [Oryza sa	0.991	0.276	0.661	3e-42
115453837	430	Os03g0570300 [Oryza sativa Japonica Grou	0.991	0.276	0.661	3e-42
226498760	424	antigenic determinant of rec-A protein [	1.0	0.283	0.656	2e-41
242055993	424	hypothetical protein SORBIDRAFT_03g00190	1.0	0.283	0.656	2e-41
357147988	416	PREDICTED: DNA/RNA-binding protein KIN17	1.0	0.288	0.648	8e-41
224098413	396	predicted protein [Populus trichocarpa]	0.925	0.280	0.704	1e-40
224112785	400	predicted protein [Populus trichocarpa]	0.925	0.277	0.704	2e-40
226498332	423	uncharacterized protein LOC100273614 [Ze	1.0	0.283	0.641	3e-40
18405389	411	DNA/RNA-binding protein Kin17 conserved	0.925	0.270	0.688	6e-40

>gi|125586877|gb|EAZ27541.1| hypothetical protein OsJ_11495 [Oryza sativa Japonica Group]

 Score =  175 bits (444), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 86/130 (66%), Positives = 105/130 (80%), Gaps = 11/130 (8%)

Query: 1   MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY---------- 50
           M+EEEK KE+ N +DYWL  GI+V+VMSK+ A+KGYCKQKG+V++VIDKY          
Sbjct: 280 MKEEEKAKERSNRKDYWLCPGIVVKVMSKSLAEKGYCKQKGVVKRVIDKYVGEIEMLESK 339

Query: 51  HVLRADHDELETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLN 109
           HVLR D DELETVIPQI GLV IVNGAY+GSNARLL VD ++FCAK ++EKG+ DG+VL 
Sbjct: 340 HVLRVDQDELETVIPQIGGLVRIVNGAYRGSNARLLSVDTERFCAKVQVEKGLYDGKVLK 399

Query: 110 AIDYEDICKL 119
           AI+YEDICK+
Sbjct: 400 AIEYEDICKI 409

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125544570|gb|EAY90709.1| hypothetical protein OsI_12309 [Oryza sativa Indica Group]

 Score =  175 bits (444), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 86/130 (66%), Positives = 105/130 (80%), Gaps = 11/130 (8%)

Query: 1   MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY---------- 50
           M+EEEK KE+ N +DYWL  GI+V+VMSK+ A+KGYCKQKG+V++VIDKY          
Sbjct: 299 MKEEEKAKERSNRKDYWLCPGIVVKVMSKSLAEKGYCKQKGVVKRVIDKYVGEIEMLESK 358

Query: 51  HVLRADHDELETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLN 109
           HVLR D DELETVIPQI GLV IVNGAY+GSNARLL VD ++FCAK ++EKG+ DG+VL 
Sbjct: 359 HVLRVDQDELETVIPQIGGLVRIVNGAYRGSNARLLSVDTERFCAKVQVEKGLYDGKVLK 418

Query: 110 AIDYEDICKL 119
           AI+YEDICK+
Sbjct: 419 AIEYEDICKI 428

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115453837|ref|NP_001050519.1| Os03g0570300 [Oryza sativa Japonica Group] gi|37700344|gb|AAR00634.1| unknown protein [Oryza sativa Japonica Group] gi|108709401|gb|ABF97196.1| KOW motif family protein, expressed [Oryza sativa Japonica Group] gi|113548990|dbj|BAF12433.1| Os03g0570300 [Oryza sativa Japonica Group] gi|215697417|dbj|BAG91411.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  175 bits (443), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 86/130 (66%), Positives = 105/130 (80%), Gaps = 11/130 (8%)

Query: 1   MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY---------- 50
           M+EEEK KE+ N +DYWL  GI+V+VMSK+ A+KGYCKQKG+V++VIDKY          
Sbjct: 299 MKEEEKAKERSNRKDYWLCPGIVVKVMSKSLAEKGYCKQKGVVKRVIDKYVGEIEMLESK 358

Query: 51  HVLRADHDELETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLN 109
           HVLR D DELETVIPQI GLV IVNGAY+GSNARLL VD ++FCAK ++EKG+ DG+VL 
Sbjct: 359 HVLRVDQDELETVIPQIGGLVRIVNGAYRGSNARLLSVDTERFCAKVQVEKGLYDGKVLK 418

Query: 110 AIDYEDICKL 119
           AI+YEDICK+
Sbjct: 419 AIEYEDICKI 428

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226498760|ref|NP_001150142.1| antigenic determinant of rec-A protein [Zea mays] gi|194707714|gb|ACF87941.1| unknown [Zea mays] gi|195637094|gb|ACG38015.1| antigenic determinant of rec-A protein [Zea mays] gi|413935581|gb|AFW70132.1| hypothetical protein ZEAMMB73_750082 [Zea mays]

 Score =  173 bits (438), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 86/131 (65%), Positives = 105/131 (80%), Gaps = 11/131 (8%)

Query: 1   MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY---------- 50
           M+EEEK KE+ N +DYWL  GI+V+VMSK+ A+KGY KQKG+V+KVIDKY          
Sbjct: 293 MKEEEKAKERSNRKDYWLCPGIVVKVMSKSLAEKGYYKQKGVVKKVIDKYVGEIEMLESK 352

Query: 51  HVLRADHDELETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLN 109
           HVLR D DELETVIPQI GLV IVNGAY+GSNARLL VD +KFCAK ++EKG+ DG+VL 
Sbjct: 353 HVLRVDQDELETVIPQIGGLVRIVNGAYRGSNARLLSVDTEKFCAKVQVEKGLYDGKVLR 412

Query: 110 AIDYEDICKLA 120
           A++YEDICK++
Sbjct: 413 AVEYEDICKIS 423

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242055993|ref|XP_002457142.1| hypothetical protein SORBIDRAFT_03g001900 [Sorghum bicolor] gi|241929117|gb|EES02262.1| hypothetical protein SORBIDRAFT_03g001900 [Sorghum bicolor]

 Score =  172 bits (437), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 86/131 (65%), Positives = 105/131 (80%), Gaps = 11/131 (8%)

Query: 1   MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY---------- 50
           M+EEEK KE+ N +DYWL  GI+V+VMSK+ A+KGY KQKG+V+KVIDKY          
Sbjct: 293 MKEEEKAKERSNRKDYWLCPGIVVKVMSKSLAEKGYYKQKGVVKKVIDKYVGEIEMLESK 352

Query: 51  HVLRADHDELETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLN 109
           HVLR D DELETVIPQI GLV IVNGAY+GSNARLL VD +KFCAK ++EKG+ DG+VL 
Sbjct: 353 HVLRVDQDELETVIPQIGGLVWIVNGAYRGSNARLLSVDTEKFCAKVQVEKGLYDGKVLR 412

Query: 110 AIDYEDICKLA 120
           A++YEDICK++
Sbjct: 413 AVEYEDICKIS 423

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357147988|ref|XP_003574577.1| PREDICTED: DNA/RNA-binding protein KIN17-like [Brachypodium distachyon]

 Score =  170 bits (431), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 85/131 (64%), Positives = 104/131 (79%), Gaps = 11/131 (8%)

Query: 1   MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY---------- 50
           M+EEE  KE+ N +DYWL  GI+V+VMSK+ A+KGY KQKG+V++VIDKY          
Sbjct: 286 MKEEENAKERSNRKDYWLCPGIVVKVMSKSLAEKGYYKQKGLVKRVIDKYVGEIEMLESK 345

Query: 51  HVLRADHDELETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLN 109
           HVLR D DELETVIPQI GLV IVNGAY+GSNARLL VD ++FCAK ++EKG+ DG+VL 
Sbjct: 346 HVLRVDQDELETVIPQIGGLVRIVNGAYRGSNARLLAVDTERFCAKLQVEKGLYDGKVLR 405

Query: 110 AIDYEDICKLA 120
           AI+YEDICK+A
Sbjct: 406 AIEYEDICKVA 416

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224098413|ref|XP_002311165.1| predicted protein [Populus trichocarpa] gi|222850985|gb|EEE88532.1| predicted protein [Populus trichocarpa]

 Score =  170 bits (430), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 86/122 (70%), Positives = 99/122 (81%), Gaps = 11/122 (9%)

Query: 10  KMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY----------HVLRADHDE 59
           + N +DYWLF+GIIV+VMSKA A+KGY KQKG+VRKVIDKY          H LR D +E
Sbjct: 275 RTNRKDYWLFEGIIVKVMSKALAEKGYYKQKGVVRKVIDKYVAEIEILENKHKLRVDQEE 334

Query: 60  LETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118
           LETVIPQI GLV IVNGAY+GSNARLLGVD +KFCAK +IEKG+ DGRVL A++YEDICK
Sbjct: 335 LETVIPQIGGLVKIVNGAYRGSNARLLGVDTEKFCAKVQIEKGIYDGRVLKAVEYEDICK 394

Query: 119 LA 120
           LA
Sbjct: 395 LA 396

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224112785|ref|XP_002316291.1| predicted protein [Populus trichocarpa] gi|222865331|gb|EEF02462.1| predicted protein [Populus trichocarpa]

 Score =  169 bits (428), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 86/122 (70%), Positives = 99/122 (81%), Gaps = 11/122 (9%)

Query: 10  KMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY----------HVLRADHDE 59
           + N +DYWLF+GIIV+VMSKA A+KGY KQKG+VRKVIDKY          H LR D +E
Sbjct: 279 RSNRKDYWLFEGIIVKVMSKALAEKGYYKQKGVVRKVIDKYVAEIEMLESKHKLRVDQEE 338

Query: 60  LETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118
           LETVIPQI GLV IVNGAY+GSNARLLGVD +KFCAK +IEKG+ DGRVL A++YEDICK
Sbjct: 339 LETVIPQIGGLVKIVNGAYRGSNARLLGVDTEKFCAKVQIEKGIYDGRVLKAVEYEDICK 398

Query: 119 LA 120
           LA
Sbjct: 399 LA 400

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226498332|ref|NP_001141502.1| uncharacterized protein LOC100273614 [Zea mays] gi|194704844|gb|ACF86506.1| unknown [Zea mays] gi|413926604|gb|AFW66536.1| hypothetical protein ZEAMMB73_911645 [Zea mays]

 Score =  169 bits (427), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 84/131 (64%), Positives = 103/131 (78%), Gaps = 11/131 (8%)

Query: 1   MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY---------- 50
           M+EEE  KE+ N +DYWL  GI+V+VMSK+ A+KGY KQKG+VRKV+DKY          
Sbjct: 292 MKEEEMAKERSNRKDYWLCPGIVVKVMSKSLAEKGYYKQKGVVRKVMDKYVGEIEMLESK 351

Query: 51  HVLRADHDELETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLN 109
           HVLR D DELETVIPQI GLV I+NGAY+GSNARLL VD +KFCAK ++EKG+ DG+VL 
Sbjct: 352 HVLRVDQDELETVIPQIGGLVRILNGAYRGSNARLLSVDTEKFCAKVQVEKGLYDGKVLR 411

Query: 110 AIDYEDICKLA 120
           A+ YEDICK++
Sbjct: 412 AVKYEDICKIS 422

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18405389|ref|NP_564690.1| DNA/RNA-binding protein Kin17 conserved region-containing protein [Arabidopsis thaliana] gi|13430440|gb|AAK25842.1|AF360132_1 unknown protein [Arabidopsis thaliana] gi|4204268|gb|AAD10649.1| Similar to Kin17 protein [Arabidopsis thaliana] gi|15293155|gb|AAK93688.1| unknown protein [Arabidopsis thaliana] gi|332195127|gb|AEE33248.1| DNA/RNA-binding protein Kin17 conserved region-containing protein [Arabidopsis thaliana]

 Score =  167 bits (424), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 84/122 (68%), Positives = 99/122 (81%), Gaps = 11/122 (9%)

Query: 10  KMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY----------HVLRADHDE 59
           +MN +DYWLF+GIIV+VMSKA A+KGY KQKG+V+KVID Y          HVLR D  E
Sbjct: 290 RMNRKDYWLFEGIIVKVMSKALAEKGYYKQKGVVKKVIDNYVGEIKMLDSKHVLRVDQKE 349

Query: 60  LETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118
           LETV+PQI G+V IVNGAY+GSNARLLGVD +KFCAK +IEKGV DGRV+ +I+YEDICK
Sbjct: 350 LETVLPQIGGMVKIVNGAYRGSNARLLGVDTEKFCAKVQIEKGVYDGRVIKSIEYEDICK 409

Query: 119 LA 120
           LA
Sbjct: 410 LA 411

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	120
TAIR|locus:2193859	411	AT1G55460 [Arabidopsis thalian	1.0	0.291	0.694	9.3e-43
TAIR|locus:504954922	347	AT5G51795 "AT5G51795" [Arabido	0.958	0.331	0.603	2.9e-32
WB|WBGene00013128	404	Y52B11A.9 [Caenorhabditis eleg	0.958	0.284	0.409	1.4e-19
FB|FBgn0024887	390	kin17 "kin17" [Drosophila mela	0.983	0.302	0.4	2e-19
UNIPROTKB|E1BND1	392	E1BND1 "Uncharacterized protei	0.958	0.293	0.418	1e-15
RGD|1596107	392	Kin "antigenic determinant of	0.958	0.293	0.410	2.2e-15
UNIPROTKB|E1C8B5	396	KIN "Uncharacterized protein"	0.975	0.295	0.379	3.8e-15
UNIPROTKB|O60870	393	KIN "DNA/RNA-binding protein K	0.958	0.292	0.410	4.8e-15
MGI|MGI:96676	391	Kin "antigenic determinant of	0.958	0.294	0.395	6e-15
UNIPROTKB|E2RNV7	391	KIN "Uncharacterized protein"	0.975	0.299	0.379	1.3e-14

TAIR|locus:2193859 AT1G55460 [Arabidopsis thaliana (taxid:3702)]

 Score = 452 (164.2 bits), Expect = 9.3e-43, P = 9.3e-43
 Identities = 91/131 (69%), Positives = 107/131 (81%)

Query:     1 MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY---------- 50
             M+EEEK KE+MN +DYWLF+GIIV+VMSKA A+KGY KQKG+V+KVID Y          
Sbjct:   281 MKEEEKKKERMNRKDYWLFEGIIVKVMSKALAEKGYYKQKGVVKKVIDNYVGEIKMLDSK 340

Query:    51 HVLRADHDELETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLN 109
             HVLR D  ELETV+PQI G+V IVNGAY+GSNARLLGVD +KFCAK +IEKGV DGRV+ 
Sbjct:   341 HVLRVDQKELETVLPQIGGMVKIVNGAYRGSNARLLGVDTEKFCAKVQIEKGVYDGRVIK 400

Query:   110 AIDYEDICKLA 120
             +I+YEDICKLA
Sbjct:   401 SIEYEDICKLA 411

GO:0005622 "intracellular" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000226 "microtubule cytoskeleton organization" evidence=RCA

TAIR|locus:504954922 AT5G51795 "AT5G51795" [Arabidopsis thaliana (taxid:3702)]

 Score = 353 (129.3 bits), Expect = 2.9e-32, P = 2.9e-32
 Identities = 73/121 (60%), Positives = 94/121 (77%)

Query:     1 MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHVLRADHDEL 60
             M+EEEK KE+MN +DYWLF+GIIV+ + K   DK Y    G + ++++  HVLR D  EL
Sbjct:   232 MKEEEKKKERMNRKDYWLFEGIIVKGVVKRVIDK-YV---GEI-EMLESKHVLRVDQVEL 286

Query:    61 ETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119
             +TV+PQI G+V IVNGAY+GSN RLL +D +KFCAK +IEKGV DGRV+ +I+YEDICKL
Sbjct:   287 KTVLPQIGGMVKIVNGAYRGSNTRLLDLDTEKFCAKVQIEKGVYDGRVIKSIEYEDICKL 346

Query:   120 A 120
             A
Sbjct:   347 A 347

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

WB|WBGene00013128 Y52B11A.9 [Caenorhabditis elegans (taxid:6239)]

 Score = 237 (88.5 bits), Expect = 1.4e-19, P = 1.4e-19
 Identities = 52/127 (40%), Positives = 79/127 (62%)

Query:     4 EEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYH---------VLR 54
             EE+ KE+ N +DYW+ +GI+V+V++K+   + Y K KG+VRKV+D Y          V++
Sbjct:   280 EERKKERKNRKDYWMREGIVVKVITKSLGSE-YYKAKGVVRKVVDDYTAQVKLDDGTVVK 338

Query:    55 ADHDELETVIPQI-EGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDY 113
              D + +ETVIP +   ++IVNGAY+G  A L  +D  +F  + KI  G   GR ++ + Y
Sbjct:   339 LDQEHVETVIPSLGRQMMIVNGAYRGQEATLESIDEKRFSLRLKIASGPTRGRQID-VPY 397

Query:   114 EDICKLA 120
             ED  KLA
Sbjct:   398 EDASKLA 404

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0002009 "morphogenesis of an epithelium" evidence=IMP

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

GO:0010171 "body morphogenesis" evidence=IMP

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0007281 "germ cell development" evidence=IMP

GO:0005730 "nucleolus" evidence=IDA

FB|FBgn0024887 kin17 "kin17" [Drosophila melanogaster (taxid:7227)]

 Score = 235 (87.8 bits), Expect = 2.0e-19, P = 2.0e-19
 Identities = 52/130 (40%), Positives = 80/130 (61%)

Query:     1 MREEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYH--------- 51
             +++EE  KE+ N +DYWL KGI+V+ +SK+  +K + KQK +V  VID+Y          
Sbjct:   259 IKQEESKKERANRKDYWLHKGIVVKFISKSMGEK-FFKQKAVVLDVIDRYQGKIKFLETG 317

Query:    52 -VLRADHDELETVIPQIEG-LVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLN 109
               L+ D   LETVIP ++  +++VNGAY+GS A L  +D  ++    +I  G   GR+++
Sbjct:   318 EKLKVDQAHLETVIPALDKPVMVVNGAYRGSEALLRKLDERRYSVSVEILHGPLKGRIVD 377

Query:   110 AIDYEDICKL 119
              + YEDI KL
Sbjct:   378 NVQYEDISKL 387

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC

UNIPROTKB|E1BND1 E1BND1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 202 (76.2 bits), Expect = 1.0e-15, P = 1.0e-15
 Identities = 54/129 (41%), Positives = 73/129 (56%)

Query:     3 EEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHV---------- 52
             EEEK K    T DYWL   IIV++++K   +K Y K+KGIV++VIDKY            
Sbjct:   267 EEEK-KRTART-DYWLQPEIIVKIITKKLGEK-YHKKKGIVKEVIDKYTAVVKMIDSGDK 323

Query:    53 LRADHDELETVIPQI-EGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAI 111
             L+ D   LETVIP   + ++++NG Y+G+   L  ++   F A   IE G   GR +  I
Sbjct:   324 LKLDQTHLETVIPAPGKRILVLNGGYRGNEGTLESINEKTFSATIVIETGPLKGRRVEGI 383

Query:   112 DYEDICKLA 120
              YEDI KLA
Sbjct:   384 QYEDISKLA 392

GO:0016363 "nuclear matrix" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003690 "double-stranded DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

RGD|1596107 Kin "antigenic determinant of rec-A protein homolog (mouse)" [Rattus norvegicus (taxid:10116)]

 Score = 199 (75.1 bits), Expect = 2.2e-15, P = 2.2e-15
 Identities = 53/129 (41%), Positives = 73/129 (56%)

Query:     3 EEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHV---------- 52
             EEEK K    T D WL  GIIV++++K   +K Y K+KG+V++VID+Y            
Sbjct:   267 EEEK-KRTART-DSWLQPGIIVKIITKKLGEK-YHKKKGVVKEVIDRYTAVVKMTDSGDR 323

Query:    53 LRADHDELETVIPQI-EGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAI 111
             L+ D   LETVIP   + ++++NG Y+G+   L  ++   F A   IE G   GR L  I
Sbjct:   324 LKLDQTHLETVIPAPGKRVLVLNGGYRGNEGTLESINEKTFSATIVIETGPLKGRRLEGI 383

Query:   112 DYEDICKLA 120
              YEDI KLA
Sbjct:   384 QYEDISKLA 392

GO:0003690 "double-stranded DNA binding" evidence=IEA;ISO

GO:0003723 "RNA binding" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=ISO

GO:0006260 "DNA replication" evidence=IEA;ISO

GO:0006974 "response to DNA damage stimulus" evidence=IEA;ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA;ISO

UNIPROTKB|E1C8B5 KIN "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 197 (74.4 bits), Expect = 3.8e-15, P = 3.8e-15
 Identities = 49/129 (37%), Positives = 74/129 (57%)

Query:     3 EEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHV---------- 52
             E E+ K++ +  DYWL   IIV++++K   +K Y K+K +V++VIDKY            
Sbjct:   269 ELEEEKKRTSRTDYWLQPEIIVKIVTKKLGEK-YHKKKAVVKEVIDKYTAVVKMIDSGDK 327

Query:    53 LRADHDELETVIPQI-EGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAI 111
             L+ D   LETVIP   + ++++NG Y+G+   L  ++  KF A   I+ G   GR +  I
Sbjct:   328 LKLDQTHLETVIPAPGKKVMVLNGGYRGNEGILESINEKKFSATIIIDSGPLKGRRVEGI 387

Query:   112 DYEDICKLA 120
              YEDI KLA
Sbjct:   388 QYEDISKLA 396

GO:0003690 "double-stranded DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

UNIPROTKB|O60870 KIN "DNA/RNA-binding protein KIN17" [Homo sapiens (taxid:9606)]

 Score = 196 (74.1 bits), Expect = 4.8e-15, P = 4.8e-15
 Identities = 53/129 (41%), Positives = 72/129 (55%)

Query:     3 EEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHV---------- 52
             EEEK K    T DYWL   IIV++++K   +K Y K+K IV++VIDKY            
Sbjct:   268 EEEK-KRTART-DYWLQPEIIVKIITKKLGEK-YHKKKAIVKEVIDKYTAVVKMIDSGDK 324

Query:    53 LRADHDELETVIPQI-EGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAI 111
             L+ D   LETVIP   + ++++NG Y+G+   L  ++   F A   IE G   GR +  I
Sbjct:   325 LKLDQTHLETVIPAPGKRILVLNGGYRGNEGTLESINEKTFSATIVIETGPLKGRRVEGI 384

Query:   112 DYEDICKLA 120
              YEDI KLA
Sbjct:   385 QYEDISKLA 393

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006260 "DNA replication" evidence=IDA

GO:0006974 "response to DNA damage stimulus" evidence=IEP

GO:0006397 "mRNA processing" evidence=TAS

GO:0016363 "nuclear matrix" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0003690 "double-stranded DNA binding" evidence=ISS

GO:0003677 "DNA binding" evidence=TAS

GO:0005634 "nucleus" evidence=TAS

MGI|MGI:96676 Kin "antigenic determinant of rec-A protein" [Mus musculus (taxid:10090)]

 Score = 195 (73.7 bits), Expect = 6.0e-15, P = 6.0e-15
 Identities = 51/129 (39%), Positives = 73/129 (56%)

Query:     3 EEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHV---------- 52
             EEEK K    T D WL  GI+V++++K   +K Y K+KG+V++VID+Y            
Sbjct:   266 EEEK-KRTART-DAWLQPGIVVKIITKKLGEK-YHKKKGVVKEVIDRYTAVVKMTDSGDR 322

Query:    53 LRADHDELETVIPQI-EGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAI 111
             L+ D   LETVIP   + ++++NG Y+G+   L  ++   F A   IE G   GR +  I
Sbjct:   323 LKLDQTHLETVIPAPGKRVLVLNGGYRGNEGTLESINEKAFSATIVIETGPLKGRRVEGI 382

Query:   112 DYEDICKLA 120
              YEDI KLA
Sbjct:   383 QYEDISKLA 391

GO:0003677 "DNA binding" evidence=IEA

GO:0003690 "double-stranded DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=ISO

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006260 "DNA replication" evidence=ISO;IDA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006950 "response to stress" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016363 "nuclear matrix" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|E2RNV7 KIN "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 192 (72.6 bits), Expect = 1.3e-14, P = 1.3e-14
 Identities = 49/129 (37%), Positives = 73/129 (56%)

Query:     3 EEEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHV---------- 52
             E E+ K++    D+WL   IIV++++K   +K Y K+KG+V++VIDKY            
Sbjct:   264 EIEEEKKRTARIDHWLQPEIIVKIITKKLGEK-YHKKKGVVKEVIDKYTAVVKMIDSGDK 322

Query:    53 LRADHDELETVIPQI-EGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAI 111
             L+ D   LETVIP   + ++++NG Y+G+   L  ++   F A   IE G   GR +  I
Sbjct:   323 LKLDQTHLETVIPAPGKRILVLNGGYRGNEGTLESINEKTFSATIIIETGPLKGRRVEGI 382

Query:   112 DYEDICKLA 120
              YEDI KLA
Sbjct:   383 QYEDISKLA 391

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

---

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

Your Input: OsI_12309 Os03g0570300 (430 aa) (Oryza sativa Indica)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	120
cd13155	54	cd13155, KOW_KIN17, KOW_Kin17 is a RNA-binding mot	7e-17

>gnl|CDD|240519 cd13155, KOW_KIN17, KOW_Kin17 is a RNA-binding motif

 Score = 68.3 bits (168), Expect = 7e-17
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 71  VIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119
           ++VNGAY+G  A L  +D DKF A  +++ G   GRV+  + YEDI KL
Sbjct: 6   LVVNGAYRGCEATLESIDEDKFSATVRLDSGPLKGRVVEGVPYEDISKL 54

KOW domain of the KIN17protein contributes to the RNA-binding properties of the whole protein. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KIN17 is conserved from yeast to human that ubiquitously expressed at low levels in mammals tissue and have functions in DNA replication, DNA repair and cell cycle control. Length = 54

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	120
KOG4315	455	consensus G-patch nucleic acid binding protein [Ge	99.77
KOG2837	309	consensus Protein containing a U1-type Zn-finger a	99.2
KOG1999	1024	consensus RNA polymerase II transcription elongati	97.92
PF00467	32	KOW: KOW motif; InterPro: IPR005824 Ribosomes are	97.77
smart00739	28	KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif i	97.37
PRK12281	76	rplX 50S ribosomal protein L24; Reviewed	97.22
CHL00141	83	rpl24 ribosomal protein L24; Validated	97.22
TIGR00405	145	L26e_arch ribosomal protein L24p/L26e, archaeal. T	97.09
PRK00004	105	rplX 50S ribosomal protein L24; Reviewed	96.91
TIGR01079	104	rplX_bact ribosomal protein L24, bacterial/organel	96.66
PRK08559	153	nusG transcription antitermination protein NusG; V	96.58
TIGR00922	172	nusG transcription termination/antitermination fac	96.51
TIGR01080	114	rplX_A_E ribosomal protein L24p/L26e, archaeal/euk	96.5
PRK01191	120	rpl24p 50S ribosomal protein L24P; Validated	96.49
PRK05609	181	nusG transcription antitermination protein NusG; V	96.45
PTZ00194	143	60S ribosomal protein L26; Provisional	96.39
COG0250	178	NusG Transcription antiterminator [Transcription]	96.19
PRK09014	162	rfaH transcriptional activator RfaH; Provisional	95.32
TIGR01955	159	RfaH transcriptional activator RfaH. This model re	95.23
COG0198	104	RplX Ribosomal protein L24 [Translation, ribosomal	94.87
TIGR01956	258	NusG_myco NusG family protein. This model represen	94.69
PF15591	74	Imm17: Immunity protein 17	91.84
PF11623	53	DUF3252: Protein of unknown function (DUF3252); In	90.85
COG5164	607	SPT5 Transcription elongation factor [Transcriptio	90.73
PRK04313	237	30S ribosomal protein S4e; Validated	86.63
PLN00036	261	40S ribosomal protein S4; Provisional	86.32
COG1471	241	RPS4A Ribosomal protein S4E [Translation, ribosoma	85.72
KOG1999	1024	consensus RNA polymerase II transcription elongati	82.67
PTZ00118	262	40S ribosomal protein S4; Provisional	82.2
PRK04333	84	50S ribosomal protein L14e; Validated	81.68
PTZ00065	130	60S ribosomal protein L14; Provisional	81.4
PTZ00223	273	40S ribosomal protein S4; Provisional	81.08

>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]

Probab=99.77  E-value=6.1e-20  Score=153.88  Aligned_cols=100  Identities=23%  Similarity=0.341  Sum_probs=89.6

Q ss_pred             CcccCCcEEEEEeccCCCccceeeeEEEEEecCCc-----------eEE-EeecCceeeecCC-CCCeE-EEecCCCCce
Q 038833           16 YWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY-----------HVL-RADHDELETVIPQ-IEGLV-IVNGAYQGSN   81 (120)
Q Consensus        16 ~Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~-----------~~~-~v~q~~LETViP~-~G~~V-Vv~G~~rG~~   81 (120)
                      .|++.+|.|||+|+.++.|+||++|++|.||.+..           .+. +++|++|||++|. .|.+| |+.|.|.|..
T Consensus       332 ~wlR~dl~VR~is~d~Kgg~ly~~K~~i~dv~gp~scd~r~Dedq~~~qg~irq~~lET~~pr~~Ge~vmvv~gkhkg~~  411 (455)
T KOG4315|consen  332 SWLRSDLKVRFISKDVKGGRLYEKKVRIVDVVGPTSCDIRMDEDQELVQGNIRQELLETALPRRGGEKVMVVSGKHKGVY  411 (455)
T ss_pred             hhhhcceeEEeeccccccchhhhcccceecccCCCccceeccccccccccchHHHHHhhhcccccCceeEEEecccccch
Confidence            89999999999999999999999999999999843           122 4999999999995 67779 9999999999


Q ss_pred             EEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833           82 ARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL  119 (120)
Q Consensus        82 g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~  119 (120)
                      |.|+++|.++.++++++...   ++.+ .+.||+||+|
T Consensus       412 g~llskd~~Ke~~~v~~~a~---ndvv-~~~~D~v~ey  445 (455)
T KOG4315|consen  412 GSLLSKDLDKETGVVRLVAT---NDVV-TVYLDQVCEY  445 (455)
T ss_pred             hhhhhhhhhhhhcceecccc---cchh-hhhHHHHHHh
Confidence            99999999999999999873   5655 4999999987

>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]

Probab=99.20  E-value=1.6e-13  Score=110.58  Aligned_cols=54  Identities=61%  Similarity=1.000  Sum_probs=49.6

Q ss_pred             EEEEEeccCCCccceeeeEEEEEecCCc---------eEEEeecCceeeecCCCCCeEEEecCCCCceE
Q 038833           23 IVEVMSKAFADKGYCKQKGIVRKVIDKY---------HVLRADHDELETVIPQIEGLVIVNGAYQGSNA   82 (120)
Q Consensus        23 ~Vkii~k~~~~gk~y~~KgvV~~V~~~~---------~~~~v~q~~LETViP~~G~~VVv~G~~rG~~g   82 (120)
                      +|++++++++. + |++||||.+|++.|         .++++||+|||||||+    .||+|.|||..|
T Consensus       247 ~vk~~sk~l~~-k-~K~K~vv~~vid~y~~~~Kld~g~~lk~dq~~lEtvip~----~~vng~yRg~~~  309 (309)
T KOG2837|consen  247 VVKVISKSLGE-K-YKQKGVVKKVIDDYTGQIKLDSGTVLKVDQEHLETVIPQ----MIVNGAYRGSEA  309 (309)
T ss_pred             EEEeehhhhhH-H-hccccHHHHHHHhhhhheeccCCceecccHHHHHHHhHH----HHhhhhhccCCC
Confidence            99999999998 6 99999999999988         6889999999999998    479999999753

>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]

Probab=97.92  E-value=5.8e-06  Score=75.88  Aligned_cols=96  Identities=20%  Similarity=0.189  Sum_probs=80.1

Q ss_pred             CcccCCcEEEEEeccCCCccceeeeEEEEEecCCc---------eEEEeecCceeeecCCCCCeE-EEecCCCCceEEEE
Q 038833           16 YWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY---------HVLRADHDELETVIPQIEGLV-IVNGAYQGSNARLL   85 (120)
Q Consensus        16 ~Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~---------~~~~v~q~~LETViP~~G~~V-Vv~G~~rG~~g~L~   85 (120)
                      +| ..++.+.+-+ ++.++...++.++|++|.++.         ..+.+..++|+++.|..|+.+ ++.|.++|.+|+++
T Consensus       916 ~~-~~~~~~~~~d-~~~~~~~~G~~~~ir~v~~G~~sv~~~de~~~~~~s~~~~a~~~p~~~d~~k~~~g~~~g~~~~~~  993 (1024)
T KOG1999|consen  916 NG-GDGNSSWGPD-TSLDTQLVGQTGIIRSVADGGCSVWLGDEGETISNSKPHLAPAPPCKGDDVKSIWGDDRGSTGKLV  993 (1024)
T ss_pred             CC-CccceEeccc-ccccceecccccceeeccCCceeeecCCCCcccccccccCccCCCCCCCCcccccccccccccccc
Confidence            56 6677887765 566779999999999999876         377899999999999999999 99999999999999


Q ss_pred             EEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833           86 GVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL  119 (120)
Q Consensus        86 ~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~  119 (120)
                      +.|..++.+.+...++      ++.+.+--+||+
T Consensus       994 ~~dg~~g~~~~d~~~~------~k~l~~~~~~k~ 1021 (1024)
T KOG1999|consen  994 GNDGWDGIVRIDETSD------IKILNLGLLCKM 1021 (1024)
T ss_pred             CCCcccceeccccccc------chhhhhhhhhhc
Confidence            9999996665544232      456888889987

>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.77  E-value=5.2e-05  Score=42.48  Aligned_cols=30  Identities=17%  Similarity=0.511  Sum_probs=27.1

Q ss_pred             CCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           67 IEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        67 ~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      +|+.| |+.|+|+|..|++++++.++..+.|
T Consensus         1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~v   31 (32)
T PF00467_consen    1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTV   31 (32)
T ss_dssp             TTSEEEESSSTTTTEEEEEEEEETTTTEEEE
T ss_pred             CCCEEEEeEcCCCCceEEEEEEECCCCEEEE
Confidence            58999 9999999999999999999976654

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 [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....

>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif

Probab=97.37  E-value=0.0004  Score=36.74  Aligned_cols=26  Identities=23%  Similarity=0.586  Sum_probs=23.6

Q ss_pred             CCCCCeE-EEecCCCCceEEEEEEeCC
Q 038833           65 PQIEGLV-IVNGAYQGSNARLLGVDND   90 (120)
Q Consensus        65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~   90 (120)
                      |.+|+.| |+.|+++|..|++++++.+
T Consensus         2 ~~~G~~V~I~~G~~~g~~g~i~~i~~~   28 (28)
T smart00739        2 FEVGDTVRVIAGPFKGKVGKVLEVDGE   28 (28)
T ss_pred             CCCCCEEEEeECCCCCcEEEEEEEcCC
Confidence            5789999 9999999999999999853

Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.

>PRK12281 rplX 50S ribosomal protein L24; Reviewed

Probab=97.22  E-value=0.00075  Score=45.06  Aligned_cols=32  Identities=19%  Similarity=0.299  Sum_probs=29.3

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTK   97 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~   97 (120)
                      +.||+| |+.|.++|..|++++++.++..+.|+
T Consensus         8 ~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve   40 (76)
T PRK12281          8 KKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVE   40 (76)
T ss_pred             cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence            689999 99999999999999999999877763

>CHL00141 rpl24 ribosomal protein L24; Validated

Probab=97.22  E-value=0.00074  Score=45.77  Aligned_cols=31  Identities=19%  Similarity=0.256  Sum_probs=29.1

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      +.|++| |+.|+++|..|++++++.++..+.|
T Consensus        10 ~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~V   41 (83)
T CHL00141         10 KIGDTVKIISGSDKGKIGEVLKIIKKSNKVIV   41 (83)
T ss_pred             cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEE
Confidence            679999 9999999999999999999988877

>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal

Probab=97.09  E-value=0.0018  Score=46.88  Aligned_cols=50  Identities=16%  Similarity=0.318  Sum_probs=41.6

Q ss_pred             CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCce--Eeeeccccccc
Q 038833           65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRV--LNAIDYEDICK  118 (120)
Q Consensus        65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~--v~~~~yddvck  118 (120)
                      +.+|+.| |+.|+++|..|.+.++|..+..+.|.|..   .+..  ++ ++++++-+
T Consensus        87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~---~~~~~~v~-v~~~~l~~  139 (145)
T TIGR00405        87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIE---AAVPIPVT-VKGDQVRI  139 (145)
T ss_pred             cCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEE---cCccceEE-EeeeEEEE
Confidence            5799999 99999999999999999888899998886   2343  53 77777754

This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.

>PRK00004 rplX 50S ribosomal protein L24; Reviewed

Probab=96.91  E-value=0.0021  Score=45.25  Aligned_cols=32  Identities=19%  Similarity=0.231  Sum_probs=29.5

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTK   97 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~   97 (120)
                      +.|++| |+.|.++|..|++++++.++..+.|+
T Consensus         6 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve   38 (105)
T PRK00004          6 KKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVE   38 (105)
T ss_pred             cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence            689999 99999999999999999999888773

>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle

Probab=96.66  E-value=0.004  Score=43.85  Aligned_cols=32  Identities=16%  Similarity=0.211  Sum_probs=29.3

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTK   97 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~   97 (120)
                      +.|++| |+.|.++|..|++++++.++..+.|+
T Consensus         5 kkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve   37 (104)
T TIGR01079         5 KKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVE   37 (104)
T ss_pred             cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEC
Confidence            579999 99999999999999999999888763

This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.

>PRK08559 nusG transcription antitermination protein NusG; Validated

Probab=96.58  E-value=0.0087  Score=44.17  Aligned_cols=49  Identities=16%  Similarity=0.337  Sum_probs=40.4

Q ss_pred             CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCce--Eeeecccccc
Q 038833           65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRV--LNAIDYEDIC  117 (120)
Q Consensus        65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~--v~~~~yddvc  117 (120)
                      ..+|+.| |+.|+++|..|++.++|.++..++|.+..-   ...  + .++.++++
T Consensus        95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~---~~~~pv-~v~~~~~~  146 (153)
T PRK08559         95 IKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEA---AVPIPV-TVRGDQVR  146 (153)
T ss_pred             CCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECC---cceeeE-EEeccEEE
Confidence            4799999 999999999999999999999999988762   222  4 37777764

>TIGR00922 nusG transcription termination/antitermination factor NusG

Probab=96.51  E-value=0.01  Score=43.85  Aligned_cols=49  Identities=12%  Similarity=0.218  Sum_probs=37.5

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccc
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDI  116 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddv  116 (120)
                      ..|++| |+.|++.|..|.+..+|.++..|.|.++-=. ....+ .+++++|
T Consensus       121 ~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~~g-~~~~v-~v~~~~l  170 (172)
T TIGR00922       121 EVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFG-RETPV-ELEFSQV  170 (172)
T ss_pred             CCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEECC-CceEE-EEcHHHe
Confidence            579999 9999999999999999988878888776511 12234 3776665

Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).

>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic

Probab=96.50  E-value=0.0056  Score=43.91  Aligned_cols=31  Identities=19%  Similarity=0.390  Sum_probs=28.6

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      ..|+.| |+.|.++|..|++++++..+..+.|
T Consensus        43 kkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~V   74 (114)
T TIGR01080        43 RKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYV   74 (114)
T ss_pred             ecCCEEEEecCCCCCCEEEEEEEEcCCCEEEE
Confidence            789999 9999999999999999999987766

This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.

>PRK01191 rpl24p 50S ribosomal protein L24P; Validated

Probab=96.49  E-value=0.0064  Score=44.03  Aligned_cols=31  Identities=16%  Similarity=0.328  Sum_probs=29.0

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      ..|+.| |+.|.++|..|++++++.++..+.|
T Consensus        47 kkGD~V~VisG~~KGk~GkV~~V~~~~~~V~V   78 (120)
T PRK01191         47 RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYV   78 (120)
T ss_pred             eCCCEEEEeecCCCCceEEEEEEEcCCCEEEE
Confidence            679999 9999999999999999999988876

>PRK05609 nusG transcription antitermination protein NusG; Validated

Probab=96.45  E-value=0.012  Score=43.72  Aligned_cols=53  Identities=15%  Similarity=0.263  Sum_probs=39.5

Q ss_pred             CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833           65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL  119 (120)
Q Consensus        65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~  119 (120)
                      ...|++| |+.|+++|..|++.++|.++..|.|.++-=. ....+ .++++++-++
T Consensus       127 ~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~~~G-~~~~v-~l~~~~l~~~  180 (181)
T PRK05609        127 FEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFG-RETPV-ELEFSQVEKI  180 (181)
T ss_pred             CCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEEECC-CceEE-EEchHHEEEc
Confidence            3689999 9999999999999999987777877766411 12234 4777777553

>PTZ00194 60S ribosomal protein L26; Provisional

Probab=96.39  E-value=0.0066  Score=45.18  Aligned_cols=32  Identities=19%  Similarity=0.364  Sum_probs=29.5

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTK   97 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~   97 (120)
                      ..|+.| |+.|.++|..|++++++..++.+.|.
T Consensus        48 kkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVE   80 (143)
T PTZ00194         48 RKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIE   80 (143)
T ss_pred             ecCCEEEEecCCCCCCceEEEEEEcCCCEEEEe
Confidence            679999 99999999999999999999888763

>COG0250 NusG Transcription antiterminator [Transcription]

Probab=96.19  E-value=0.017  Score=44.13  Aligned_cols=55  Identities=22%  Similarity=0.308  Sum_probs=43.2

Q ss_pred             ecCCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833           63 VIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL  119 (120)
Q Consensus        63 ViP~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~  119 (120)
                      +-+.+|+.| |+.|+++|..|++.++|.++..++|.+..=. .-..+ .++|+++-++
T Consensus       122 ~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~ifg-r~tPV-el~~~qVek~  177 (178)
T COG0250         122 VDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFG-RPTPV-ELEFDQVEKL  177 (178)
T ss_pred             ccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEeC-CceEE-EEehhhEEEe
Confidence            344689999 9999999999999999999888888777511 22344 4888888664

>PRK09014 rfaH transcriptional activator RfaH; Provisional

Probab=95.32  E-value=0.055  Score=39.66  Aligned_cols=51  Identities=22%  Similarity=0.209  Sum_probs=36.7

Q ss_pred             CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833           65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK  118 (120)
Q Consensus        65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck  118 (120)
                      +..|++| |+.|++.|..|.+..+|. +..+.|.++-= +....+ .++++++-+
T Consensus       110 ~~~G~~V~I~~Gp~~g~eg~v~~~~~-~~r~~v~v~~~-gr~~~v-~v~~~~~~~  161 (162)
T PRK09014        110 PKPGDKVIITEGAFEGLQAIYTEPDG-EARSILLLNLL-NKQVKH-SVDNTQFRK  161 (162)
T ss_pred             CCCCCEEEEecCCCCCcEEEEEEeCC-CeEEEEeehhh-CCcEEE-EECHHHeec
Confidence            4689999 999999999999999984 44566766541 122334 377777654

>TIGR01955 RfaH transcriptional activator RfaH

Probab=95.23  E-value=0.062  Score=38.99  Aligned_cols=34  Identities=24%  Similarity=0.241  Sum_probs=29.0

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEcc
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEK  100 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~  100 (120)
                      ..|++| |+.|++.|..|.+..+|. +..+.|.|+-
T Consensus       110 ~~G~~V~V~~GPf~g~~g~v~~~~~-~~r~~v~l~~  144 (159)
T TIGR01955       110 YKGDKVRITDGAFAGFEAIFLEPDG-EKRSMLLLNM  144 (159)
T ss_pred             CCCCEEEEeccCCCCcEEEEEEECC-CceEEEEEhh
Confidence            589999 999999999999999984 4467777664

This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.

>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]

Probab=94.87  E-value=0.058  Score=38.17  Aligned_cols=29  Identities=21%  Similarity=0.320  Sum_probs=26.2

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      ..|+.| |+.|.++|..|.+++++...  +.|
T Consensus         6 rkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~V   35 (104)
T COG0198           6 KKGDTVKVIAGKDKGKEGKVLKVLPKK--VVV   35 (104)
T ss_pred             ecCCEEEEEecCCCCcceEEEEEecCe--EEE
Confidence            579999 99999999999999999998  544

>TIGR01956 NusG_myco NusG family protein

Probab=94.69  E-value=0.12  Score=41.83  Aligned_cols=50  Identities=18%  Similarity=0.379  Sum_probs=37.9

Q ss_pred             CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccc
Q 038833           65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDI  116 (120)
Q Consensus        65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddv  116 (120)
                      +.+|+.| |+.|++.|..|.+.++|.++..+.|.|.-- +....+ .++|++|
T Consensus       206 f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~If-GR~TpV-eL~~~qV  256 (258)
T TIGR01956       206 FRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEIL-GKSVDV-DLNFKHL  256 (258)
T ss_pred             CCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEEec-CCcEEE-EEchHHE
Confidence            4789999 999999999999999997777777766541 122334 4777766

This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.

>PF15591 Imm17: Immunity protein 17

Probab=91.84  E-value=0.27  Score=32.82  Aligned_cols=28  Identities=21%  Similarity=0.281  Sum_probs=23.9

Q ss_pred             EEEEEeccCCCccceeeeEEEEEecCCc
Q 038833           23 IVEVMSKAFADKGYCKQKGIVRKVIDKY   50 (120)
Q Consensus        23 ~Vkii~k~~~~gk~y~~KgvV~~V~~~~   50 (120)
                      +|+|++....+.++++++|+|...+...
T Consensus        10 ~V~v~~s~p~~~ei~Gk~GVVlG~SeeD   37 (74)
T PF15591_consen   10 EVEVVRSCPCDAEIWGKRGVVLGISEED   37 (74)
T ss_pred             EEEEeccCcchhhhcCceeEEEEEecCC
Confidence            6889886677779999999999998755

>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function

Probab=90.85  E-value=0.74  Score=28.88  Aligned_cols=41  Identities=29%  Similarity=0.404  Sum_probs=28.0

Q ss_pred             ccCCcEEEEEeccCCCccceeeeEEEEEecCCc-----------eEEEeecCcee
Q 038833           18 LFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY-----------HVLRADHDELE   61 (120)
Q Consensus        18 l~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~-----------~~~~v~q~~LE   61 (120)
                      +.|+-.|++++-+  + -||.=.|.|..|.++.           +++.++-+.||
T Consensus         2 ilPG~~V~V~n~~--~-~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eLe   53 (53)
T PF11623_consen    2 ILPGSTVRVKNPN--D-IYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSELE   53 (53)
T ss_dssp             --TT-EEEE--TT--S-TTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGEE
T ss_pred             ccCCCEEEEeCCC--C-ccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhCC
Confidence            4689999997653  4 7999999999999976           56667666665

Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.

>COG5164 SPT5 Transcription elongation factor [Transcription]

Probab=90.73  E-value=0.33  Score=42.69  Aligned_cols=42  Identities=33%  Similarity=0.504  Sum_probs=35.9

Q ss_pred             Cceeeec----CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccC
Q 038833           58 DELETVI----PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKG  101 (120)
Q Consensus        58 ~~LETVi----P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g  101 (120)
                      ..||--|    |++|..| |=+|+|+|+.|.+.+.|.+.  |+|+|.++
T Consensus       341 ~~l~r~i~gRd~aigktVrIr~g~yKG~lGVVKdv~~~~--arVeLhs~  387 (607)
T COG5164         341 NELERKIVGRDPAIGKTVRIRCGEYKGHLGVVKDVDRNI--ARVELHSN  387 (607)
T ss_pred             hhhhccccccccccCceEEEeecccccccceeeeccCce--EEEEEecC
Confidence            4556556    7899999 99999999999999999888  88888884

>PRK04313 30S ribosomal protein S4e; Validated

Probab=86.63  E-value=2.9  Score=33.48  Aligned_cols=46  Identities=17%  Similarity=0.272  Sum_probs=33.3

Q ss_pred             EEEeecCceeeecC-CCCCeE-EEecCCCCceEEEEEEeCCc----cEEEEE
Q 038833           52 VLRADHDELETVIP-QIEGLV-IVNGAYQGSNARLLGVDNDK----FCAKTK   97 (120)
Q Consensus        52 ~~~v~q~~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d~~~----~~~~V~   97 (120)
                      +++++...+.-.+| ..|.-+ |..|.+.|.+|++.++....    ..+.++
T Consensus       158 ~i~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~  209 (237)
T PRK04313        158 LISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLE  209 (237)
T ss_pred             EEECCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEE
Confidence            44554444555666 899999 99999999999999997333    445544

>PLN00036 40S ribosomal protein S4; Provisional

Probab=86.32  E-value=3.4  Score=33.62  Aligned_cols=37  Identities=14%  Similarity=0.316  Sum_probs=30.0

Q ss_pred             EEEeecCceeeecC-CCCCeE-EEecCCCCceEEEEEEe
Q 038833           52 VLRADHDELETVIP-QIEGLV-IVNGAYQGSNARLLGVD   88 (120)
Q Consensus        52 ~~~v~q~~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d   88 (120)
                      +++++...+.-.+| ..|.-+ |..|.+.|.+|++.++.
T Consensus       161 ~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~  199 (261)
T PLN00036        161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNRE  199 (261)
T ss_pred             EEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEE
Confidence            44555555666666 899999 99999999999999998

>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]

Probab=85.72  E-value=3  Score=33.58  Aligned_cols=49  Identities=12%  Similarity=0.189  Sum_probs=35.8

Q ss_pred             EEEeecCceeeecC-CCCCeE-EEecCCCCceEEEEEEeCCc--cEEEEEEcc
Q 038833           52 VLRADHDELETVIP-QIEGLV-IVNGAYQGSNARLLGVDNDK--FCAKTKIEK  100 (120)
Q Consensus        52 ~~~v~q~~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d~~~--~~~~V~l~~  100 (120)
                      +++++...+.-.|| ..|..+ |+.|.|.|.+|++.+|....  ..=+|.+++
T Consensus       160 ~i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~  212 (241)
T COG1471         160 KISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED  212 (241)
T ss_pred             EEeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec
Confidence            55676666666666 889999 99999999999999997553  222345555

>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]

Probab=82.67  E-value=4.6  Score=38.31  Aligned_cols=69  Identities=22%  Similarity=0.296  Sum_probs=51.0

Q ss_pred             ccCCcEEEEEeccCCCccceeeeEEEEEecCCceEEEeecCceeee----------cCCCCCeE-EEecCCCCceEEEEE
Q 038833           18 LFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHVLRADHDELETV----------IPQIEGLV-IVNGAYQGSNARLLG   86 (120)
Q Consensus        18 l~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~~~~~v~q~~LETV----------iP~~G~~V-Vv~G~~rG~~g~L~~   86 (120)
                      ++|+=.|.|+     .|.+-|-||+|..|.+...++.-.+++|-.=          .-.+|+.| |+.|.|.|.+|-++.
T Consensus       408 F~~GD~VeV~-----~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvr  482 (1024)
T KOG1999|consen  408 FSPGDAVEVI-----VGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVR  482 (1024)
T ss_pred             cCCCCeEEEe-----eeeeccceeEEEeccCceEEEeeccccCCCccccchHhhhhhccCCCeEEEEeccccCCcceEEE
Confidence            5677777776     5678889999999988663333333333221          12489999 999999999999999


Q ss_pred             EeCCc
Q 038833           87 VDNDK   91 (120)
Q Consensus        87 ~d~~~   91 (120)
                      ++...
T Consensus       483 Ve~~~  487 (1024)
T KOG1999|consen  483 VEQGD  487 (1024)
T ss_pred             EeCCe
Confidence            99876

>PTZ00118 40S ribosomal protein S4; Provisional

Probab=82.20  E-value=6.6  Score=31.94  Aligned_cols=38  Identities=16%  Similarity=0.316  Sum_probs=30.1

Q ss_pred             EEEeecCceeeecC-CCCCeE-EEecCCCCceEEEEEEeC
Q 038833           52 VLRADHDELETVIP-QIEGLV-IVNGAYQGSNARLLGVDN   89 (120)
Q Consensus        52 ~~~v~q~~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d~   89 (120)
                      +++++...+.-.+| ..|.-+ |..|.+.|.+|++.++..
T Consensus       161 ~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~  200 (262)
T PTZ00118        161 RLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEK  200 (262)
T ss_pred             EEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEe
Confidence            44555555666666 899999 999999999999998763

>PRK04333 50S ribosomal protein L14e; Validated

Probab=81.68  E-value=5.6  Score=26.91  Aligned_cols=26  Identities=8%  Similarity=0.242  Sum_probs=21.7

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCc
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDK   91 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~   91 (120)
                      .+|.-| +..|.++|..+.++++-.++
T Consensus         5 ~~GrvV~~~~Grd~gk~~vIv~i~d~~   31 (84)
T PRK04333          5 EVGRVCVKTAGREAGRKCVIVDIIDKN   31 (84)
T ss_pred             cccEEEEEeccCCCCCEEEEEEEecCC
Confidence            357667 88999999999999996665

>PTZ00065 60S ribosomal protein L14; Provisional

Probab=81.40  E-value=4.9  Score=29.51  Aligned_cols=46  Identities=15%  Similarity=0.127  Sum_probs=29.1

Q ss_pred             CCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCC-CCCceEeeeccccc
Q 038833           67 IEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGV-NDGRVLNAIDYEDI  116 (120)
Q Consensus        67 ~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~-~~~~~v~~~~yddv  116 (120)
                      +|.-| |-.|++.|.++.+.+|-..+. |.   -+|| .+|-.=..++|.++
T Consensus        10 iGRVvli~~Gp~~GKL~vIVDIID~nR-vL---VDGP~~tgV~Rq~i~~k~l   57 (130)
T PTZ00065         10 PGRLCLIQYGPDAGKLCFIVDIVTPTR-VL---VDGAFITGVKRQSIPLKRL   57 (130)
T ss_pred             eceEEEEecCCCCCCEEEEEEEEcCCe-EE---EeCCCcCCcceeEEeccce
Confidence            46555 779999999999999966662 43   3466 43322223555544

>PTZ00223 40S ribosomal protein S4; Provisional

Probab=81.08  E-value=5.2  Score=32.74  Aligned_cols=38  Identities=16%  Similarity=0.367  Sum_probs=29.9

Q ss_pred             EEEeecCceeeecC-CCCCeE-EEecCCCCceEEEEEEeC
Q 038833           52 VLRADHDELETVIP-QIEGLV-IVNGAYQGSNARLLGVDN   89 (120)
Q Consensus        52 ~~~v~q~~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d~   89 (120)
                      +++++...+.-.+| ..|.-+ |..|.+.|.+|++.++..
T Consensus       158 ~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~  197 (273)
T PTZ00223        158 VYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIER  197 (273)
T ss_pred             EEECCCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEe
Confidence            44555555665666 899999 999999999999999953

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	120
2ckk_A	127	High Resolution Crystal Structure Of The Human Kin1		2e-16

>pdb|2CKK|A Chain A, High Resolution Crystal Structure Of The Human Kin17 C- Terminal Domain Containing A Kow Motif Kin17 Length = 127

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 49/127 (38%), Positives = 71/127 (55%), Gaps = 12/127 (9%)
Query: 5   EKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHV----------LR 54
           E+ K++    DYWL   IIV++++K   +K Y K+K IV++VIDKY            L+
Sbjct: 2   EEEKKRTARTDYWLQPEIIVKIITKKLGEK-YHKKKAIVKEVIDKYTAVVKMIDSGDKLK 60
Query: 55  ADHDELETVIPQI-EGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDY 113
            D   LETVIP   + ++++NG Y+G+   L  ++   F A   IE G   GR +  I Y
Sbjct: 61  LDQTHLETVIPAPGKRILVLNGGYRGNEGTLESINEKTFSATIVIETGPLKGRRVEGIQY 120
Query: 114 EDICKLA 120
           EDI KLA
Sbjct: 121 EDISKLA 127

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	120
2ckk_A	127	KIN17; beta barrel, ribosomal protein, ribonucleop	1e-31
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>2ckk_A KIN17; beta barrel, ribosomal protein, ribonucleoprotein, nuclear protein; 1.45A {Homo sapiens} Length = 127

 Score =  107 bits (269), Expect = 1e-31
 Identities = 48/127 (37%), Positives = 69/127 (54%), Gaps = 12/127 (9%)

Query: 5   EKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY----------HVLR 54
           E+ K++    DYWL   IIV++++K   +K + K+K IV++VIDKY            L+
Sbjct: 2   EEEKKRTARTDYWLQPEIIVKIITKKLGEKYH-KKKAIVKEVIDKYTAVVKMIDSGDKLK 60

Query: 55  ADHDELETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDY 113
            D   LETVIP     + ++NG Y+G+   L  ++   F A   IE G   GR +  I Y
Sbjct: 61  LDQTHLETVIPAPGKRILVLNGGYRGNEGTLESINEKTFSATIVIETGPLKGRRVEGIQY 120

Query: 114 EDICKLA 120
           EDI KLA
Sbjct: 121 EDISKLA 127

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 5e-06
 Identities = 24/124 (19%), Positives = 52/124 (41%), Gaps = 25/124 (20%)

Query: 2   REEEKVKEKMNT---QDY-WLFKGIIVEVMSKAFADKGYCKQKGIVR---KVIDKYHVLR 54
           ++EE V++ +      +Y +L   I  E    +   + Y +Q+  +    +V  KY+V R
Sbjct: 74  KQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSR 133

Query: 55  AD-HDELETVIPQI--EGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGV-NDGRVLNA 110
              + +L   + ++     V+++G        +LG        KT +   V    +V   
Sbjct: 134 LQPYLKLRQALLELRPAKNVLIDG--------VLG------SGKTWVALDVCLSYKVQCK 179

Query: 111 IDYE 114
           +D++
Sbjct: 180 MDFK 183

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 37.9 bits (87), Expect = 3e-04
 Identities = 23/128 (17%), Positives = 44/128 (34%), Gaps = 44/128 (34%)

Query: 4   EEKVKEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKV-------IDKYHVLRAD 56
             KV+ KM+ + +WL              +   C     V ++       ID     R+D
Sbjct: 173 SYKVQCKMDFKIFWL--------------NLKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218

Query: 57  HD-----ELETVIPQIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAI 111
           H       + ++  ++  L + +  Y+     LL + N            V + +  NA 
Sbjct: 219 HSSNIKLRIHSIQAELRRL-LKSKPYENC---LLVLLN------------VQNAKAWNAF 262

Query: 112 DYEDICKL 119
           +    CK+
Sbjct: 263 NLS--CKI 268

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	120
2ckk_A	127	KIN17; beta barrel, ribosomal protein, ribonucleop	100.0
1nz9_A	58	Transcription antitermination protein NUSG; transc	97.57
2e6z_A	59	Transcription elongation factor SPT5; KOW motif, s	97.56
3p8b_B	152	Transcription antitermination protein NUSG; transc	97.22
2e70_A	71	Transcription elongation factor SPT5; KOW motif, s	96.94
2ftc_N	96	Mitochondrial ribosomal protein L24; mitochondrial	96.44
3j21_U	121	50S ribosomal protein L24P; archaea, archaeal, KIN	96.41
3u5e_Y	127	L33, YL33, 60S ribosomal protein L26-A; translatio	96.37
1vq8_T	120	50S ribosomal protein L24P; ribosome 50S, protein-	96.37
2jvv_A	181	Transcription antitermination protein NUSG; transc	96.27
2zjr_R	115	50S ribosomal protein L24; ribosome, large ribosom	96.17
2zkr_t	145	60S ribosomal protein L26; protein-RNA complex, 60	96.16
3iz5_Y	150	60S ribosomal protein L26 (L24P); eukaryotic ribos	96.11
4a17_S	135	RPL26, 60S ribosomal protein L21; eukaryotic ribos	96.1
3v2d_Y	110	50S ribosomal protein L24; ribosome associated inh	96.0
3r8s_U	102	50S ribosomal protein L24; protein biosynthesis, R	95.79
2do3_A	69	Transcription elongation factor SPT5; KOW motif, s	95.37
2xhc_A	352	Transcription antitermination protein NUSG; 2.45A	94.95
1m1h_A	248	Transcription antitermination protein NUSG; transc	92.77
3bbo_W	191	Ribosomal protein L24; large ribosomal subunit, sp	92.3
2jz2_A	66	SSL0352 protein; SH3-like, synechocystis SP. PCC 6	92.16
3izc_N	138	60S ribosomal protein RPL14 (L14E); eukaryotic rib	86.68
3h8z_A	128	FragIle X mental retardation syndrome-related Pro;	81.24

>2ckk_A KIN17; beta barrel, ribosomal protein, ribonucleoprotein, nuclear protein; 1.45A {Homo sapiens}

Probab=100.00  E-value=8.5e-41  Score=241.00  Aligned_cols=112  Identities=43%  Similarity=0.748  Sum_probs=102.9

Q ss_pred             hhccCCCCCcccCCcEEEEEeccCCCccceeeeEEEEEecCCc----------eEEEeecCceeeecCCCCCeE-EEecC
Q 038833            8 KEKMNTQDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY----------HVLRADHDELETVIPQIEGLV-IVNGA   76 (120)
Q Consensus         8 k~~~~~~~~Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~----------~~~~v~q~~LETViP~~G~~V-Vv~G~   76 (120)
                      |+++++.++||+|+|+|||+++++++| ||++||+|++|.+++          +.++|+|+|||||||+.|++| ||+|+
T Consensus         5 k~~~~~~~~Wl~~~I~Vrii~k~~~~g-~y~~KgvV~~V~~~~~c~V~l~~~g~~v~v~q~~LETViP~~g~~V~Iv~G~   83 (127)
T 2ckk_A            5 KKRTARTDYWLQPEIIVKIITKKLGEK-YHKKKAIVKEVIDKYTAVVKMIDSGDKLKLDQTHLETVIPAPGKRILVLNGG   83 (127)
T ss_dssp             ---CCCCSCCCCTTBEEEECCSTTCGG-GTTCEEEEEEEETTTEEEEEETTTCCEEEEEGGGEEECCCCTTCEEEECSST
T ss_pred             ccccCCCCCcccCCeEEEEEEccCCCc-ccCceEEEEEecCCCeEEEEECCCCCEEEEchHHcEEecCCCCCEEEEEecc
Confidence            447889999999999999999999998 999999999998765          567999999999999999999 99999


Q ss_pred             CCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccccC
Q 038833           77 YQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKLA  120 (120)
Q Consensus        77 ~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~~  120 (120)
                      |||++|+|+++|.++|+|.|+|++++.+++.++.++|||||||+
T Consensus        84 ~rG~~g~L~~id~~~~~~~V~l~~~~~~~~~v~~l~~ddi~k~~  127 (127)
T 2ckk_A           84 YRGNEGTLESINEKTFSATIVIETGPLKGRRVEGIQYEDISKLA  127 (127)
T ss_dssp             TTTCEEEEEEEEGGGTEEEEEECSSTTTTCEEEEEEGGGEEEBC
T ss_pred             cCCcEEEEEEEeCCCcEEEEEEccCCCCCCEEEeeCHHHhhccC
Confidence            99999999999999999999999988778778789999999986

>1nz9_A Transcription antitermination protein NUSG; transcription elongation, riken structural genomics/proteomics initiative, RSGI; NMR {Thermus thermophilus} SCOP: b.34.5.4

Probab=97.57  E-value=0.00029  Score=43.08  Aligned_cols=53  Identities=11%  Similarity=0.172  Sum_probs=40.7

Q ss_pred             cCCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833           64 IPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK  118 (120)
Q Consensus        64 iP~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck  118 (120)
                      -...|++| |+.|++.|..|++.++|.++..+.|.+.--. ....+ .++|+++-+
T Consensus         4 ~~~~Gd~V~V~~Gpf~g~~g~v~~v~~~k~~v~V~v~~~G-r~t~v-~l~~~~vek   57 (58)
T 1nz9_A            4 AFREGDQVRVVSGPFADFTGTVTEINPERGKVKVMVTIFG-RETPV-ELDFSQVVK   57 (58)
T ss_dssp             SCCTTCEEEECSGGGTTCEEEEEEEETTTTEEEEEEESSS-SEEEE-EECGGGEEE
T ss_pred             ccCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEeCC-CEEEE-EECHHHEEE
Confidence            34789999 9999999999999999999888877666411 22334 488888755

>2e6z_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.56  E-value=7.4e-05  Score=46.46  Aligned_cols=52  Identities=15%  Similarity=0.110  Sum_probs=40.5

Q ss_pred             cCCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833           64 IPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL  119 (120)
Q Consensus        64 iP~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~  119 (120)
                      -+.+|+.| |+.|+++|..|++.++|.+  .+.|.+.-.. ..+.+ .++|.++.|+
T Consensus         7 ~f~~GD~V~V~~Gpf~g~~G~V~evd~e--~v~V~v~~fg-~~tpv-el~~~qv~K~   59 (59)
T 2e6z_A            7 GFQPGDNVEVCEGELINLQGKILSVDGN--KITIMPKHED-LKDML-EFPAQELRKY   59 (59)
T ss_dssp             SCCTTSEEEECSSTTTTCEEEECCCBTT--EEEEEECCSS-CCSCE-EEETTTEEEC
T ss_pred             cCCCCCEEEEeecCCCCCEEEEEEEeCC--EEEEEEEecC-CCceE-EEcHHHEEEC
Confidence            35789999 9999999999999999986  5767665322 23456 4999998875

>3p8b_B Transcription antitermination protein NUSG; transcription elongation factor, RNA polymerase, transferase transcription complex; 1.80A {Pyrococcus furiosus} PDB: 3qqc_D

Probab=97.22  E-value=0.00098  Score=47.69  Aligned_cols=53  Identities=15%  Similarity=0.260  Sum_probs=43.6

Q ss_pred             CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833           65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL  119 (120)
Q Consensus        65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~  119 (120)
                      +.+|+.| |+.|+++|..|++.++|.++..+.|.+.--. ....+ .++|++|-++
T Consensus        92 ~~~Gd~VrI~~Gpf~g~~g~V~~vd~~k~~v~V~v~~~g-r~tpv-el~~~~v~~i  145 (152)
T 3p8b_B           92 LEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAI-VPIPV-TIKGDYVRLI  145 (152)
T ss_dssp             CCTTCEEEECSSTTTTCEEEEEEEETTTTEEEEEESSCS-SCCEE-EEEGGGEEEE
T ss_pred             CCCCCEEEEeeecCCCCEEEEEEEeCCCCEEEEEEEecc-eeEEE-EECHHHEEEe
Confidence            3689999 9999999999999999999999999887632 23345 4999988654

>2e70_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.94  E-value=0.0023  Score=41.52  Aligned_cols=47  Identities=17%  Similarity=0.331  Sum_probs=38.3

Q ss_pred             CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccc
Q 038833           65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDIC  117 (120)
Q Consensus        65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvc  117 (120)
                      |.+|..| |..|+|+|..|.+.+.....  |.|+|.+   ..++|. ++.+++.
T Consensus        18 ~liGktV~I~kGpyKG~~GiVkd~t~~~--~RVELhs---~~K~Vt-V~r~~l~   65 (71)
T 2e70_A           18 ELIGQTVRISQGPYKGYIGVVKDATEST--ARVELHS---TCQTIS-VDRQRLT   65 (71)
T ss_dssp             SSTTSEEEECSSTTTTCEEEEEEECSSC--EEEEESS---SCCEEE-ECTTTEE
T ss_pred             ccCCCEEEEeccCCCCeEEEEEECCCCe--EEEEecC---CceEEE-EEhhhcc
Confidence            4579999 99999999999999999887  8888887   346563 7777664

>2ftc_N Mitochondrial ribosomal protein L24; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_N

Probab=96.44  E-value=0.0048  Score=41.97  Aligned_cols=30  Identities=17%  Similarity=0.237  Sum_probs=27.6

Q ss_pred             CCeE-EEecCCCCceEEEEEEeCCccEEEEE
Q 038833           68 EGLV-IVNGAYQGSNARLLGVDNDKFCAKTK   97 (120)
Q Consensus        68 G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~   97 (120)
                      |+.| ||.|.++|..|++++++.+++.+.|+
T Consensus         1 GD~V~Vi~GkdKGk~GkV~~V~~~~~~ViVe   31 (96)
T 2ftc_N            1 GDTVEILEGKDAGKQGKVVQVIRQRNWVVVG   31 (96)
T ss_pred             CCEEEEeEcCCCCcEEEEEEEECCCCEEEEe
Confidence            7899 99999999999999999999888763

>3j21_U 50S ribosomal protein L24P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=96.41  E-value=0.0033  Score=44.51  Aligned_cols=31  Identities=23%  Similarity=0.520  Sum_probs=29.0

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      +.||.| ||.|.++|..|++++++.+++.+.|
T Consensus        47 kkGD~V~Vi~GkdKGk~GkV~~V~~k~~~V~V   78 (121)
T 3j21_U           47 RVGDKVRIMRGDYKGHEGKVVEVDLKRYRIYV   78 (121)
T ss_dssp             CSSSEEEECSSSCSSEEEEEEEEETTTTEEEE
T ss_pred             ccCCEEEEeecCCCCcEeEEEEEEecCCEEEE
Confidence            689999 9999999999999999999988876

>3u5e_Y L33, YL33, 60S ribosomal protein L26-A; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 2wwa_L 2ww9_L 2wwb_L 3o5h_X 3o58_X 3u5i_Y 4b6a_Y 1s1i_U 3izc_Y 3izs_Y 3jyw_U

Probab=96.37  E-value=0.0031  Score=45.02  Aligned_cols=32  Identities=22%  Similarity=0.398  Sum_probs=29.5

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTK   97 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~   97 (120)
                      ..|+.| ||.|.++|..|++++++.+++.+.|+
T Consensus        51 kkgD~V~Vi~GkdKGk~GkV~~V~~kk~~V~VE   83 (127)
T 3u5e_Y           51 RRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVD   83 (127)
T ss_dssp             CTTCEEEECSSTTTTCEEEEEEEEGGGTEEEEE
T ss_pred             cCCCEEEEeecCCCCccceEEEEECCCCEEEEe
Confidence            689999 99999999999999999999888763

>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: b.34.5.1 PDB: 1vq4_T* 1vq5_T* 1vq6_T* 1vq7_T* 1s72_T* 1vq9_T* 1vqk_T* 1vql_T* 1vqm_T* 1vqn_T* 1vqo_T* 1vqp_T* 1yhq_T* 1yi2_T* 1yij_T* 1yit_T* 1yj9_T* 1yjn_T* 1yjw_T* 2otj_T* ...

Probab=96.37  E-value=0.0043  Score=43.86  Aligned_cols=33  Identities=21%  Similarity=0.397  Sum_probs=30.2

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKI   98 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l   98 (120)
                      +.|+.| ||.|.++|..|++++++.+++.+.|+-
T Consensus        44 kkGD~V~Vi~G~dKGk~GkV~~V~~k~~~V~VEg   77 (120)
T 1vq8_T           44 NAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVED   77 (120)
T ss_dssp             CTTCEEEECSSTTTTCEEEEEEEETTTTEEEETT
T ss_pred             cCCCEEEEEecCCCCCEEEEEEEECCCCEEEEeC
Confidence            689999 999999999999999999999888743

>2jvv_A Transcription antitermination protein NUSG; transcription factor, transcription regulation, transcription termination; NMR {Escherichia coli} PDB: 2k06_A 2kvq_G

Probab=96.27  E-value=0.0064  Score=44.42  Aligned_cols=51  Identities=18%  Similarity=0.294  Sum_probs=37.8

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK  118 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck  118 (120)
                      ..|++| |+.|++.|..|++.++|.++..+.|.+.- -+....+ .++|++|-+
T Consensus       129 ~~Gd~V~V~~GPf~g~~G~v~~v~~~k~r~~V~v~i-fgr~t~v-el~~~qvek  180 (181)
T 2jvv_A          129 EPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSI-FGRATPV-ELDFSQVEK  180 (181)
T ss_dssp             CTTEEEEECSSTTTTEEEEEEEEETTTTEEEEEEEE-TTEEEEE-EECTTTEEE
T ss_pred             CCCCEEEEeccCCCCcEEEEEEEeCCCCEEEEEEEE-CCCCEEE-EECHHHEEE
Confidence            589999 99999999999999999877666554442 1122344 488888765

>2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.34.5.1 PDB: 1nwx_S* 1nwy_S* 1sm1_S* 1xbp_S* 2d3o_S 2zjp_R* 2zjq_R 1nkw_S 3cf5_R* 3dll_R* 3pio_R* 3pip_R* 1pnu_S 1pny_S 1vor_V 1vou_V 1vow_V 1voy_V 1vp0_V

Probab=96.17  E-value=0.0052  Score=43.03  Aligned_cols=33  Identities=12%  Similarity=0.094  Sum_probs=30.2

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKI   98 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l   98 (120)
                      +.|+.| ||.|.++|..|++++++.++..+.|+-
T Consensus        17 kkGD~V~Vi~GkdKGk~GkV~~V~~~~~~V~VEG   50 (115)
T 2zjr_R           17 KKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEG   50 (115)
T ss_dssp             CTTSEEECCSSSSTTCEEEEEEEETTTTEEEESS
T ss_pred             cCCCEEEEeEcCCCCcEEEEEEEECCCCEEEEeC
Confidence            689999 999999999999999999998888743

>2zkr_t 60S ribosomal protein L26; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}

Probab=96.16  E-value=0.0059  Score=44.45  Aligned_cols=34  Identities=24%  Similarity=0.545  Sum_probs=30.7

Q ss_pred             cC-CCCCeE-EEecCCCCce-EEEEEEeCCccEEEEE
Q 038833           64 IP-QIEGLV-IVNGAYQGSN-ARLLGVDNDKFCAKTK   97 (120)
Q Consensus        64 iP-~~G~~V-Vv~G~~rG~~-g~L~~~d~~~~~~~V~   97 (120)
                      +| ..|+.| ||.|.++|.. |++++++.+++.+.|+
T Consensus        47 ~~IkkGD~V~Vi~GkdKGk~~GkV~~V~~k~~~V~VE   83 (145)
T 2zkr_t           47 MPIRKDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIE   83 (145)
T ss_dssp             CBCCTTCEEEECSSTTTTCCSEEEEEEETTTTEEEET
T ss_pred             cccCCCCEEEEeecCCCCcceeEEEEEECCCCEEEEe
Confidence            45 689999 9999999999 9999999999888774

>4a17_S RPL26, 60S ribosomal protein L21; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_S 4a1c_S 4a1e_S

Probab=96.10  E-value=0.0062  Score=43.89  Aligned_cols=31  Identities=23%  Similarity=0.461  Sum_probs=28.9

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      ..|+.| ||.|.++|..|.+++++.+++.+.|
T Consensus        50 kkgD~V~Vi~GkdKGk~GkV~~V~~kk~~V~V   81 (135)
T 4a17_S           50 RKDDEVLIVRGKFKGNKGKVTQVYRKKWAIHV   81 (135)
T ss_dssp             CTTCEEEECSSTTTTCEEEEEEEETTTTEEEE
T ss_pred             cCCCEEEEeecCCCCceeeEEEEEcCCCEEEE
Confidence            689999 9999999999999999999988876

>3v2d_Y 50S ribosomal protein L24; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_S 2hgj_X 2hgq_X 2hgu_X 1vsa_S 2j03_Y 2jl6_Y 2jl8_Y 2v47_Y 2v49_Y 2wdi_Y 2wdj_Y 2wdl_Y 2wdn_Y 2wh2_Y 2wh4_Y 2wrj_Y 2wrl_Y 2wro_Y 2wrr_Y ...

Probab=96.00  E-value=0.0068  Score=42.19  Aligned_cols=31  Identities=19%  Similarity=0.351  Sum_probs=28.9

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      +.|+.| ||.|.++|..|++++++.++..+.|
T Consensus         8 kkGD~V~Vi~GkdKGk~GkV~~V~~~~~~ViV   39 (110)
T 3v2d_Y            8 KKGDTVLVASGKYKGRVGKVKEVLPKKYAVIV   39 (110)
T ss_dssp             CTTSEEEECSSTTTTCEEEEEEEEGGGTEEEE
T ss_pred             CCCCEEEEeEcCCCCeEeEEEEEECCCCEEEE
Confidence            679999 9999999999999999999888876

>3r8s_U 50S ribosomal protein L24; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 2j28_U* 3fik_U 3j19_U 2wwq_U 3oat_U* 3oas_U* 3ofd_U 3ofc_U 3ofr_U* 3ofz_U* 3og0_U 3ofq_U 3r8t_U 3i1n_U 1vs8_U 1vs6_U 1vt2_U 3i1p_U 3i1r_U 3i1t_U ...

Probab=95.79  E-value=0.012  Score=40.37  Aligned_cols=30  Identities=13%  Similarity=0.156  Sum_probs=27.4

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      +.|+.| ||.|.++|..|++++++.+ ..+.|
T Consensus         5 kkGD~V~Vi~GkdKGk~GkV~~V~~~-~~ViV   35 (102)
T 3r8s_U            5 RRDDEVIVLTGKDKGKRGKVKNVLSS-GKVIV   35 (102)
T ss_dssp             CSSCEEEECSSSSTTCEEEEEEEETT-TEEEE
T ss_pred             cCCCEEEEeEcCCCCeeeEEEEEEeC-CEEEE
Confidence            579999 9999999999999999998 77766

>2do3_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: b.34.5.5

Probab=95.37  E-value=0.041  Score=35.37  Aligned_cols=26  Identities=15%  Similarity=0.500  Sum_probs=24.1

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCc
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDK   91 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~   91 (120)
                      ++|+.| |+.|.|.|.+|.++.++.+-
T Consensus        19 ~~GDHVkVi~G~~~getGlVV~v~~d~   45 (69)
T 2do3_A           19 KMGDHVKVIAGRFEGDTGLIVRVEENF   45 (69)
T ss_dssp             CTTCEEEESSSTTTTCEEEEEEECSSC
T ss_pred             cCCCeEEEeccEEcCceEEEEEEeCCE
Confidence            579999 99999999999999999775

>2xhc_A Transcription antitermination protein NUSG; 2.45A {Thermotoga maritima}

Probab=94.95  E-value=0.046  Score=44.53  Aligned_cols=51  Identities=12%  Similarity=0.262  Sum_probs=38.8

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK  118 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck  118 (120)
                      .+|+.| |+.|++.|..|++.++|.++..+.|.+.-= +....+ .++|++|-+
T Consensus       300 ~~Gd~VrV~~GPF~G~~G~V~evd~ek~rv~V~V~if-GR~tpV-eL~~~qVek  351 (352)
T 2xhc_A          300 KVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVTIF-GRETPV-VLHVSEVEK  351 (352)
T ss_dssp             CTTCEEEECSSTTTTCEEEEEEEETTTTEEEEEEEET-TEEEEE-EEEGGGEEC
T ss_pred             CCCCEEEEeccCCCCcEEEEEEEcCCCCEEEEEEEEC-CCcEEE-EEchHHEEE
Confidence            689999 999999999999999998886676655531 012334 488888765

>1m1h_A Transcription antitermination protein NUSG; transcription termination, RNP motif, immunoglobulin fold, nucleic acid interaction; 1.95A {Aquifex aeolicus} SCOP: b.114.1.1 d.58.42.1 PDB: 1m1g_A 1npp_A 1npr_A

Probab=92.77  E-value=0.02  Score=44.58  Aligned_cols=53  Identities=15%  Similarity=0.173  Sum_probs=0.0

Q ss_pred             eecCCCCCeE-EEecCCCCceEEEEEEeCCccEEEEE--EccCCCCCceEeeeccccccc
Q 038833           62 TVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTK--IEKGVNDGRVLNAIDYEDICK  118 (120)
Q Consensus        62 TViP~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~--l~~g~~~~~~v~~~~yddvck  118 (120)
                      .+-+..|+.| |+.|++.|..|++.++|.++..+.|.  +..   ....+ .++|+.|-|
T Consensus       192 ~~~~~~Gd~V~I~~Gpf~g~~G~v~ev~~~k~~~~V~v~ifg---r~tpv-~l~~~~vek  247 (248)
T 1m1h_A          192 KVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFG---RMTPV-ELDFDQVEK  247 (248)
T ss_dssp             ------------------------------------------------------------
T ss_pred             cccCCCCCEEEEeccCCCCcEEEEEEEeCCCCEEEEEEEeCC---CcEEE-EEcHHHEEe
Confidence            4455799999 99999999999999999877555554  443   22335 488887755

>3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=92.30  E-value=0.013  Score=44.39  Aligned_cols=31  Identities=10%  Similarity=0.249  Sum_probs=28.1

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      +.||.| ||.|.++|..|++++++.++..+.|
T Consensus        70 kKGD~V~VIaGkDKGK~GkVl~V~~k~~rViV  101 (191)
T 3bbo_W           70 KVGDTVKVISGGEKGKIGEISKIHKHNSTVII  101 (191)
T ss_dssp             CCSSCEEECSSSSTTCCCSCCCCCSSSCCCCC
T ss_pred             ecCCEEEEeecCCCCceEEEEEEECCCCEEEE
Confidence            479999 9999999999999999988877765

>2jz2_A SSL0352 protein; SH3-like, synechocystis SP. PCC 6803, targe PSI, protein structure initiative, northeast structural GEN consortium, NESG; NMR {Synechocystis SP} PDB: 3c4s_A

Probab=92.16  E-value=0.51  Score=29.90  Aligned_cols=46  Identities=33%  Similarity=0.515  Sum_probs=38.2

Q ss_pred             ccCCcEEEEEeccCCCccceeeeEEEEEecCCc-----------eEEEeecCceeeecCC
Q 038833           18 LFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY-----------HVLRADHDELETVIPQ   66 (120)
Q Consensus        18 l~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~-----------~~~~v~q~~LETViP~   66 (120)
                      +.||..|+++|-  .+ -||.=.|.|..|.++.           +++.+.-+.||.+-+.
T Consensus         2 ilPG~~V~V~np--~~-~Yy~y~G~VQRvsdgkaaVLFEGGnWDKLVTf~L~eLe~~~~~   58 (66)
T 2jz2_A            2 IFPGATVRVTNV--DD-TYYRFEGLVQRVSDGKAAVLFENGNWDKLVTFRLSELEAVKPI   58 (66)
T ss_dssp             CCTTCEEEECCT--TS-TTBTCEEEEEEEETTEEEEEEESSSCEEEEEEESTTEEECCCC
T ss_pred             ccCCCEEEEeCC--CC-cccceeEEEEEecCCcEEEEecCCCceeEEEEEhhHceecccc
Confidence            568999999764  34 7999999999999977           6888999999987653

>3h8z_A FragIle X mental retardation syndrome-related Pro; tudor domains, FXR2, structura genomics, structural genomics consortium, SGC; 1.92A {Homo sapiens} PDB: 3o8v_A 3kuf_A 2bkd_N*

Probab=81.24  E-value=11  Score=26.37  Aligned_cols=74  Identities=18%  Similarity=0.157  Sum_probs=48.1

Q ss_pred             CCcEEEEEeccCCCccceeeeEEEEEecCCce----------EEEeecCceeeecC-------CCCCeE-EEe-cCC---
Q 038833           20 KGIIVEVMSKAFADKGYCKQKGIVRKVIDKYH----------VLRADHDELETVIP-------QIEGLV-IVN-GAY---   77 (120)
Q Consensus        20 ~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~~----------~~~v~q~~LETViP-------~~G~~V-Vv~-G~~---   77 (120)
                      .++.|.+.+   .+|.||+  |.|.++.+..-          .-.++-+++-+..|       ..|+.| |.. ...   
T Consensus         4 ~~~~VEV~~---~~G~~y~--a~V~~v~~d~~~V~f~n~w~~~~~vp~~~vRlpP~~~~~~~f~~gd~VEV~~~~~d~ep   78 (128)
T 3h8z_A            4 QGLPVEVRG---SNGAFYK--GFVKDVHEDSVTIFFENNWQSERQIPFGDVRLPPPADYNKEITEGDEVEVYSRANEQEP   78 (128)
T ss_dssp             TTCEEEEEC---TTSCEEE--EEEEEECSSEEEEEETTCTTCCEEEEGGGEECCCCC----CCCTTCEEEEEECC---CC
T ss_pred             cccEEEEec---CCCCEEE--EEEEEEeCCcEEEEEccccCcceEechhhEEcCCCcccccCCCCCCEEEEEecCCCCCc
Confidence            467777765   4589997  89999976551          22455556666655       489999 884 222   


Q ss_pred             -CCceEEEEEEeCCccEEEEEEcc
Q 038833           78 -QGSNARLLGVDNDKFCAKTKIEK  100 (120)
Q Consensus        78 -rG~~g~L~~~d~~~~~~~V~l~~  100 (120)
                       .--.|++.++..+-  ..|....
T Consensus        79 ~gWw~a~I~~~kg~f--~~V~y~~  100 (128)
T 3h8z_A           79 CGWWLARVRMMKGDF--YVIEYAA  100 (128)
T ss_dssp             CEEEEEEEEEEETTE--EEEEETT
T ss_pred             CccEEEEEEEeeCCE--EEEEEcC
Confidence             34578999888755  3455443

---

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	120
d1nz9a_	58	N-utilization substance G protein NusG, C-terminal	97.83
d1nppa2	58	N-utilization substance G protein NusG, C-terminal	97.62
d1vqot1	119	Ribosomal proteins L24 (L24p) {Archaeon Haloarcula	96.66
d2do3a1	62	Transcription elongation factor SPT5 {Human (Homo	96.09
d2zjrr1	110	Ribosomal proteins L24 (L24p) {Deinococcus radiodu	95.95
d2gycs1	99	Ribosomal proteins L24 (L24p) {Escherichia coli [T	93.66
d2j01y1	101	Ribosomal proteins L24 (L24p) {Thermus thermophilu	93.51
d1nxza1	72	Hypothetical protein HI0303 {Haemophilus influenza	82.53
d1vhka1	72	Hypothetical protein YqeU {Bacillus subtilis [TaxI	81.78

>d1nz9a_ b.34.5.4 (A:) N-utilization substance G protein NusG, C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: N-utilization substance G protein NusG, C-terminal domain
domain: N-utilization substance G protein NusG, C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=97.83  E-value=2.5e-05  Score=47.22  Aligned_cols=51  Identities=12%  Similarity=0.268  Sum_probs=40.5

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK  118 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck  118 (120)
                      ++|+.| |+.|++.|..|++.++|.++..+.|.|+= -+....+ .+++++|-|
T Consensus         6 ~~Gd~V~I~~GpF~g~~g~V~~i~~~k~rv~V~v~i-fGr~t~v-el~~~~ieK   57 (58)
T d1nz9a_           6 REGDQVRVVSGPFADFTGTVTEINPERGKVKVMVTI-FGRETPV-ELDFSQVVK   57 (58)
T ss_dssp             CTTCEEEECSGGGTTCEEEEEEEETTTTEEEEEEES-SSSEEEE-EECGGGEEE
T ss_pred             cCCCEEEEeccCCCCCEEEEEEEcCCCCEEEEEEEe-cCCCceE-eeCHHHEEc
Confidence            789999 99999999999999999998888887654 1122334 489988765

>d1nppa2 b.34.5.4 (A:191-248) N-utilization substance G protein NusG, C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: N-utilization substance G protein NusG, C-terminal domain
domain: N-utilization substance G protein NusG, C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.62  E-value=7e-05  Score=45.08  Aligned_cols=52  Identities=13%  Similarity=0.202  Sum_probs=39.9

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL  119 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~  119 (120)
                      ++|+.| |+.|++.|..|++.++|.++..+.|.++== +....+ .++|++|-|+
T Consensus         6 ~~Gd~V~I~~GpF~g~~g~V~~i~~~~~rv~V~v~~f-Gr~t~v-el~~~~veki   58 (58)
T d1nppa2           6 EKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIF-GRMTPV-ELDFDQVEKI   58 (58)
T ss_dssp             CTTCEEEECSSTTTTCEEEEEEEEGGGTEEEEEEEET-TEEEEE-EEEGGGEEEC
T ss_pred             cCCCEEEEcccCCCCCEEEEEEEcCCCCEEEEEEeec-CCCceE-eeCHHHEEeC
Confidence            689999 999999999999999998887777766530 012234 4888888664

>d1vqot1 b.34.5.1 (T:1-119) Ribosomal proteins L24 (L24p) {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=96.66  E-value=0.0009  Score=45.62  Aligned_cols=31  Identities=23%  Similarity=0.451  Sum_probs=29.3

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      ..|+.| |+.|.++|..|++++++.++..+.|
T Consensus        43 kkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~V~V   74 (119)
T d1vqot1          43 NAGDTVEVLRGDFAGEEGEVINVDLDKAVIHV   74 (119)
T ss_dssp             CTTCEEEECSSTTTTCEEEEEEEETTTTEEEE
T ss_pred             eCCCEEEEeecCCCCCcceEEEEECCCCEEEE
Confidence            689999 9999999999999999999988876

>d2do3a1 b.34.5.5 (A:462-523) Transcription elongation factor SPT5 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: SPT5 KOW domain-like
domain: Transcription elongation factor SPT5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.09  E-value=0.006  Score=37.06  Aligned_cols=46  Identities=13%  Similarity=0.257  Sum_probs=32.3

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccc
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDIC  117 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvc  117 (120)
                      ++|+.| |+.|.|.|.+|-++.++.+.  +++  .++. +.+.++ +.-.|+.
T Consensus        12 ~~GDhVkVi~G~~~g~tGlVV~v~~~~--v~~--~SD~-t~~Ei~-V~~~dL~   58 (62)
T d2do3a1          12 KMGDHVKVIAGRFEGDTGLIVRVEENF--VIL--FSDL-TMHELK-VLPRDLQ   58 (62)
T ss_dssp             CTTCEEEESSSTTTTCEEEEEEECSSC--EEE--EESS-SCSEEE-ECTTSEE
T ss_pred             CCCCeEEEeccEEcCccEEEEEEeCCE--EEE--EeCC-CCCEEE-EehHHhh
Confidence            579999 99999999999999997665  443  4433 334454 4444443

>d2zjrr1 b.34.5.1 (R:4-113) Ribosomal proteins L24 (L24p) {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Deinococcus radiodurans [TaxId: 1299]

Probab=95.95  E-value=0.0036  Score=41.90  Aligned_cols=32  Identities=13%  Similarity=0.144  Sum_probs=29.1

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTK   97 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~   97 (120)
                      +.|+.| ||.|.++|..|++++++.++..+.|+
T Consensus        14 kkGD~V~VisGkdKGk~G~Vl~V~~~~~~ViVe   46 (110)
T d2zjrr1          14 KKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVE   46 (110)
T ss_dssp             CTTSEEECCSSSSTTCEEEEEEEETTTTEEEES
T ss_pred             eCCCEEEEeecCCCCcceEEEEEECCCCEEEEe
Confidence            469999 99999999999999999999888773

>d2gycs1 b.34.5.1 (S:3-101) Ribosomal proteins L24 (L24p) {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Escherichia coli [TaxId: 562]

Probab=93.66  E-value=0.027  Score=36.75  Aligned_cols=30  Identities=13%  Similarity=0.156  Sum_probs=25.5

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      +.|+.| ||.|.++|..|+++++..+ ..+.|
T Consensus         3 kkGD~V~VisGkdKGK~G~V~~V~~~-~~viV   33 (99)
T d2gycs1           3 RRDDEVIVLTGKDKGKRGKVKNVLSS-GKVIV   33 (99)
T ss_dssp             CTTSEEECSSSTTTTCEEEEEEECTT-SEEEE
T ss_pred             cCCCEEEEeeCCCCCCceEEEEEECC-CeEEE
Confidence            469999 9999999999999999764 46655

>d2j01y1 b.34.5.1 (Y:2-102) Ribosomal proteins L24 (L24p) {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Thermus thermophilus [TaxId: 274]

Probab=93.51  E-value=0.0022  Score=42.36  Aligned_cols=31  Identities=19%  Similarity=0.351  Sum_probs=27.9

Q ss_pred             CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833           66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT   96 (120)
Q Consensus        66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V   96 (120)
                      ..|+.| |+.|.++|..|++++++.++..+.|
T Consensus         7 kkGD~V~VisGkdKGk~G~Vl~V~~~~~~ViV   38 (101)
T d2j01y1           7 KKGDTVLVASGKYKGRVGKVKEVLPKKYAVIV   38 (101)
T ss_dssp             CCSSCEECCSSTTSSCCBSCCCCCCTTCBCCT
T ss_pred             ECCCEEEEeeCCCCCCeEEEEEEECCCCEEEE
Confidence            469999 9999999999999999999877754

>d1nxza1 b.122.1.2 (A:2-73) Hypothetical protein HI0303 {Haemophilus influenzae [TaxId: 727]}

class: All beta proteins
fold: PUA domain-like
superfamily: PUA domain-like
family: YggJ N-terminal domain-like
domain: Hypothetical protein HI0303
species: Haemophilus influenzae [TaxId: 727]

Probab=82.53  E-value=0.63  Score=27.36  Aligned_cols=40  Identities=13%  Similarity=0.215  Sum_probs=33.5

Q ss_pred             ceeeecC-CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEcc
Q 038833           59 ELETVIP-QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEK  100 (120)
Q Consensus        59 ~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~  100 (120)
                      ||-.|+= ++|+.| +.+|.-.-..|++.+++.+.  +.+++.+
T Consensus        26 Hl~~VLR~k~Gd~v~l~dg~g~~~~~~I~~i~k~~--~~~~i~~   67 (72)
T d1nxza1          26 HVARVLRMTEGEQLELFDGSNHIYPAKIIESNKKS--VKVEILG   67 (72)
T ss_dssp             HHHTTSCCCTTCEEEEECSSSEEEEEEEEEEETTE--EEEEECC
T ss_pred             HHHheeCCCCCCEEEEEeCCCCEEEEEEEEEeCCE--EEEEEEE
Confidence            6777887 689999 99999999999999999887  5556554

>d1vhka1 b.122.1.2 (A:2-73) Hypothetical protein YqeU {Bacillus subtilis [TaxId: 1423]}

class: All beta proteins
fold: PUA domain-like
superfamily: PUA domain-like
family: YggJ N-terminal domain-like
domain: Hypothetical protein YqeU
species: Bacillus subtilis [TaxId: 1423]

Probab=81.78  E-value=0.59  Score=27.60  Aligned_cols=38  Identities=13%  Similarity=0.125  Sum_probs=32.0

Q ss_pred             cCceeeecC-CCCCeE-EEecCCCCceEEEEEEeCCccEE
Q 038833           57 HDELETVIP-QIEGLV-IVNGAYQGSNARLLGVDNDKFCA   94 (120)
Q Consensus        57 q~~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~   94 (120)
                      ..||-.|+= ++|+.+ +.+|...-..|++.+++.+...+
T Consensus        25 ~hHl~~VLR~k~Gd~i~l~dg~g~~~~~~I~~i~k~~v~~   64 (72)
T d1vhka1          25 VHHIVNVMRMNEGDQIICCSQDGFEAKCELQSVSKDKVSC   64 (72)
T ss_dssp             HHHHHTTTCCCTTCEEEEECTTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHheeccCCCCEEEEEECCCCEEEEEEEEEECCEEEE
Confidence            446777888 789999 99999999999999999888444