Psyllid ID: psy2574

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-----
Protein Sequence
MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGDSMTVRGCALDSGTPTTDTELIRMSHCGGFYFDDSQ
Secondary Structure (PSIPRED)
cccccccccccHHHHHHHHHcccccccccccEEEEEccccccEEEEEEccccEEEccccccccccccccccccccccccccEEEEEEEccccccccccEEEEEEccccEEEcccc
Secondary Structure Prediction (SSPRO)
ccHHHHcccccHHHHHHHHHccccccccccEEEEEcccccEEEEEEEEccEEEEEEccccEEEEcccccEEEEEcccccccEEEEEEEccccccccccEEEEEcccccEEEcccc
Coil and Loop (DISEMBL)
mplakdllhpsqAEEKRKHKLKRLvqhpnsyfmdvkcpgcykitTVFSHAQSVVICAGcstilcqptggrarlteddtgdsmtvrgcaldsgtpttdtelirmshcggfyfddsq
Flexible Loop (DISEMBL)
mplakdllhpsqaeeKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRArlteddtgdsmtvrgcaldsgtpttdtelirMSHCGGFYFDDSQ
Low Complexity Region (SEG)
MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGDSMTVRGCALDSGTPTTDTELIRMSHCGGFYFDDSQ
Disordered region (IsUnstruct)
***********************LVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGR*************VRGCAL******TDTELIRMSHCGGFYF****
Disordered Region (DISOPRED)
*PLAKDLLHPS*************VQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGDSMTVRGCALDSGTPTTDTELIRMSHCGGFYF****
Disordered Region (DISEMBL)
MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGDSMTVRGCALDSGTPTTDTELIRMSHCGGFYFDDSQ
Disordered Region (DISPRO)
MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGDSMTVRGCALDSGTPTTDTELIRMSHCGGFYFDD**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGDSMTVRGCALDSGTPTTDTELIRMSHCGGFYFDDSQ
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	115	2.2.26 [Sep-21-2011]
P55833	84	40S ribosomal protein S27	N/A	N/A	0.652	0.892	0.826	2e-32
Q3T0B7	84	40S ribosomal protein S27	yes	N/A	0.652	0.892	0.853	2e-29
Q9TXP0	83	40S ribosomal protein S27	yes	N/A	0.652	0.903	0.746	3e-28
P24051	84	40S ribosomal protein S27	no	N/A	0.652	0.892	0.853	4e-28
Q6ZWY3	84	40S ribosomal protein S27	yes	N/A	0.652	0.892	0.853	4e-28
Q71UM5	84	40S ribosomal protein S27	yes	N/A	0.652	0.892	0.853	4e-28
Q7RVN2	82	40S ribosomal protein S27	N/A	N/A	0.652	0.914	0.76	6e-28
Q71TY3	84	40S ribosomal protein S27	no	N/A	0.652	0.892	0.88	1e-27
Q6ZWU9	84	40S ribosomal protein S27	yes	N/A	0.652	0.892	0.88	1e-27
P42677	84	40S ribosomal protein S27	yes	N/A	0.652	0.892	0.88	1e-27

>sp|P55833|RS27_HOMAM 40S ribosomal protein S27 OS=Homarus americanus GN=RPS27 PE=3 SV=2

 Score =  137 bits (345), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 62/75 (82%), Positives = 71/75 (94%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLAKDLLHPS +EEKRK KLKRLVQHPNSYFMDVKCPGC+KI+TVFSHAQ+VV C GC+
Sbjct: 1  MPLAKDLLHPSPSEEKRKCKLKRLVQHPNSYFMDVKCPGCFKISTVFSHAQTVVACVGCA 60

Query: 61 TILCQPTGGRARLTE 75
          T+LCQPTGG+A+LT+
Sbjct: 61 TVLCQPTGGKAKLTD 75

Homarus americanus (taxid: 6706)

>sp|Q3T0B7|RS27L_BOVIN 40S ribosomal protein S27-like OS=Bos taurus GN=RPS27L PE=3 SV=3

 Score =  127 bits (319), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 64/75 (85%), Positives = 70/75 (93%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLA+DLLHPS  EEK+KHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct: 1  MPLARDLLHPSLDEEKKKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query: 61 TILCQPTGGRARLTE 75
          T+LCQPTGG+ARLTE
Sbjct: 61 TVLCQPTGGKARLTE 75

Bos taurus (taxid: 9913)

>sp|Q9TXP0|RS27_CAEEL 40S ribosomal protein S27 OS=Caenorhabditis elegans GN=rps-27 PE=1 SV=3

 Score =  123 bits (309), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 56/75 (74%), Positives = 64/75 (85%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLA DLLHP    E R HKLKRLVQHPNSYFMDVKC GC+KI+TVFSHA +VV+C GC+
Sbjct: 1  MPLAVDLLHPEPQREIRCHKLKRLVQHPNSYFMDVKCSGCFKISTVFSHATTVVVCVGCN 60

Query: 61 TILCQPTGGRARLTE 75
          T+LCQPT G+A+LTE
Sbjct: 61 TVLCQPTRGKAKLTE 75

Caenorhabditis elegans (taxid: 6239)

>sp|P24051|RS27L_RAT 40S ribosomal protein S27-like OS=Rattus norvegicus GN=Rps27l PE=1 SV=3

 Score =  123 bits (308), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 64/75 (85%), Positives = 70/75 (93%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLA+DLLHPS  EEK+KHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct: 1  MPLARDLLHPSLEEEKKKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query: 61 TILCQPTGGRARLTE 75
          T+LCQPTGG+ARLTE
Sbjct: 61 TVLCQPTGGKARLTE 75

Rattus norvegicus (taxid: 10116)

>sp|Q6ZWY3|RS27L_MOUSE 40S ribosomal protein S27-like OS=Mus musculus GN=Rps27l PE=2 SV=3

 Score =  123 bits (308), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 64/75 (85%), Positives = 70/75 (93%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLA+DLLHPS  EEK+KHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct: 1  MPLARDLLHPSLEEEKKKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query: 61 TILCQPTGGRARLTE 75
          T+LCQPTGG+ARLTE
Sbjct: 61 TVLCQPTGGKARLTE 75

Mus musculus (taxid: 10090)

>sp|Q71UM5|RS27L_HUMAN 40S ribosomal protein S27-like OS=Homo sapiens GN=RPS27L PE=1 SV=3

 Score =  123 bits (308), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 64/75 (85%), Positives = 70/75 (93%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLA+DLLHPS  EEK+KHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct: 1  MPLARDLLHPSLEEEKKKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query: 61 TILCQPTGGRARLTE 75
          T+LCQPTGG+ARLTE
Sbjct: 61 TVLCQPTGGKARLTE 75

Homo sapiens (taxid: 9606)

>sp|Q7RVN2|RS27_NEUCR 40S ribosomal protein S27 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=rps-27 PE=3 SV=1

 Score =  122 bits (307), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 57/75 (76%), Positives = 64/75 (85%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          M LA DLL+PS A E RKHKLK LV  P S+FMDVKCPGC+ ITTVFSHAQ+VVIC GC+
Sbjct: 1  MVLAVDLLNPSPASEARKHKLKTLVPAPRSFFMDVKCPGCFTITTVFSHAQTVVICQGCT 60

Query: 61 TILCQPTGGRARLTE 75
          T+LCQPTGG+ARLTE
Sbjct: 61 TVLCQPTGGKARLTE 75

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

>sp|Q71TY3|RS27_RAT 40S ribosomal protein S27 OS=Rattus norvegicus GN=Rps27 PE=2 SV=3

 Score =  121 bits (304), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 66/75 (88%), Positives = 70/75 (93%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLAKDLLHPS  EEKRKHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct: 1  MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query: 61 TILCQPTGGRARLTE 75
          T+LCQPTGG+ARLTE
Sbjct: 61 TVLCQPTGGKARLTE 75

Rattus norvegicus (taxid: 10116)

>sp|Q6ZWU9|RS27_MOUSE 40S ribosomal protein S27 OS=Mus musculus GN=Rps27 PE=1 SV=3

 Score =  121 bits (304), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 66/75 (88%), Positives = 70/75 (93%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLAKDLLHPS  EEKRKHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct: 1  MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query: 61 TILCQPTGGRARLTE 75
          T+LCQPTGG+ARLTE
Sbjct: 61 TVLCQPTGGKARLTE 75

Mus musculus (taxid: 10090)

>sp|P42677|RS27_HUMAN 40S ribosomal protein S27 OS=Homo sapiens GN=RPS27 PE=1 SV=3

 Score =  121 bits (304), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 66/75 (88%), Positives = 70/75 (93%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLAKDLLHPS  EEKRKHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct: 1  MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query: 61 TILCQPTGGRARLTE 75
          T+LCQPTGG+ARLTE
Sbjct: 61 TVLCQPTGGKARLTE 75

Homo sapiens (taxid: 9606)

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	115
110671452	84	putative ribosomal protein S27 [Diaphori	0.652	0.892	1.0	3e-37
121512016	84	ribosomal protein S27 [Xenopsylla cheopi	0.652	0.892	0.946	2e-35
149898784	84	40S ribosomal protein S27 [Triatoma infe	0.652	0.892	0.946	8e-35
209693462	84	ribosomal protein S27-1 [Acyrthosiphon p	0.652	0.892	0.92	2e-34
198462092	91	GA10310 [Drosophila pseudoobscura pseudo	0.652	0.824	0.906	6e-34
170038730	152	40S ribosomal protein S27 [Culex quinque	0.652	0.493	0.893	7e-34
24649976	84	ribosomal protein S27, isoform A [Drosop	0.652	0.892	0.906	7e-34
31199327	84	AGAP007157-PA [Anopheles gambiae str. PE	0.652	0.892	0.92	8e-34
224924394	84	ribosomal protein S27 [Stomoxys calcitra	0.652	0.892	0.893	2e-33
321461534	84	hypothetical protein DAPPUDRAFT_308217 [	0.652	0.892	0.866	2e-33

>gi|110671452|gb|ABG81977.1| putative ribosomal protein S27 [Diaphorina citri]

 Score =  158 bits (400), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 75/75 (100%), Positives = 75/75 (100%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS
Sbjct: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60

Query: 61 TILCQPTGGRARLTE 75
          TILCQPTGGRARLTE
Sbjct: 61 TILCQPTGGRARLTE 75

Source: Diaphorina citri

Species: Diaphorina citri

Genus: Diaphorina

Family: Psyllidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|121512016|gb|ABM55459.1| ribosomal protein S27 [Xenopsylla cheopis] gi|389032525|gb|AFK82399.1| ribosomal protein S27 [Ctenocephalides felis]

 Score =  152 bits (385), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 71/75 (94%), Positives = 74/75 (98%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLAKDLLHP+ AEEKR+HKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVV+CAGCS
Sbjct: 1  MPLAKDLLHPTIAEEKRRHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVVCAGCS 60

Query: 61 TILCQPTGGRARLTE 75
          TILCQPTGGRARLTE
Sbjct: 61 TILCQPTGGRARLTE 75

Source: Xenopsylla cheopis

Species: Xenopsylla cheopis

Genus: Xenopsylla

Family: Pulicidae

Order: Siphonaptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|149898784|gb|ABR27855.1| 40S ribosomal protein S27 [Triatoma infestans]

 Score =  150 bits (380), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 71/75 (94%), Positives = 72/75 (96%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLAKDLLHPS  EEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVV+CAGCS
Sbjct: 1  MPLAKDLLHPSPLEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVVCAGCS 60

Query: 61 TILCQPTGGRARLTE 75
          TILCQPTGG ARLTE
Sbjct: 61 TILCQPTGGWARLTE 75

Source: Triatoma infestans

Species: Triatoma infestans

Genus: Triatoma

Family: Reduviidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|209693462|ref|NP_001129418.1| ribosomal protein S27-1 [Acyrthosiphon pisum]

 Score =  149 bits (376), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 69/75 (92%), Positives = 72/75 (96%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLAKDLLHP+  EE+RKHKLKRLVQHPNS+FMDVKCPGCYKITTVFSHAQSVVIC GCS
Sbjct: 1  MPLAKDLLHPTAIEERRKHKLKRLVQHPNSFFMDVKCPGCYKITTVFSHAQSVVICTGCS 60

Query: 61 TILCQPTGGRARLTE 75
          TILCQPTGGRARLTE
Sbjct: 61 TILCQPTGGRARLTE 75

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198462092|ref|XP_001352335.2| GA10310 [Drosophila pseudoobscura pseudoobscura] gi|198142795|gb|EAL29373.2| GA10310 [Drosophila pseudoobscura pseudoobscura]

 Score =  147 bits (372), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 68/75 (90%), Positives = 72/75 (96%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLAKDLLHP  AEEKRKHKLKRLVQHPNSYFMDVKCPGCY+ITTVFSHAQ VV+CAGC+
Sbjct: 1  MPLAKDLLHPLPAEEKRKHKLKRLVQHPNSYFMDVKCPGCYRITTVFSHAQGVVVCAGCA 60

Query: 61 TILCQPTGGRARLTE 75
          TILCQPTGGRA+LTE
Sbjct: 61 TILCQPTGGRAKLTE 75

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170038730|ref|XP_001847201.1| 40S ribosomal protein S27 [Culex quinquefasciatus] gi|167882447|gb|EDS45830.1| 40S ribosomal protein S27 [Culex quinquefasciatus]

 Score =  147 bits (371), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 67/75 (89%), Positives = 70/75 (93%)

Query: 1   MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
           MPLAKD LHP  AEEKR+HKLKRLV HPNSYFMDVKCPGCYKITTVFSHAQSVV+C GCS
Sbjct: 69  MPLAKDFLHPLPAEEKRRHKLKRLVPHPNSYFMDVKCPGCYKITTVFSHAQSVVVCTGCS 128

Query: 61  TILCQPTGGRARLTE 75
           TILCQPTGG+ARLTE
Sbjct: 129 TILCQPTGGKARLTE 143

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24649976|ref|NP_651359.1| ribosomal protein S27, isoform A [Drosophila melanogaster] gi|386766493|ref|NP_001247301.1| ribosomal protein S27, isoform B [Drosophila melanogaster] gi|194741052|ref|XP_001953003.1| GF17433 [Drosophila ananassae] gi|194908783|ref|XP_001981839.1| GG12272 [Drosophila erecta] gi|195038523|ref|XP_001990706.1| GH19510 [Drosophila grimshawi] gi|195110057|ref|XP_001999598.1| GI22987 [Drosophila mojavensis] gi|195157922|ref|XP_002019843.1| GL12615 [Drosophila persimilis] gi|195354834|ref|XP_002043901.1| GM17738 [Drosophila sechellia] gi|195392453|ref|XP_002054872.1| GJ24684 [Drosophila virilis] gi|195453461|ref|XP_002073798.1| GK14300 [Drosophila willistoni] gi|195504441|ref|XP_002099080.1| GE10722 [Drosophila yakuba] gi|195573795|ref|XP_002104877.1| GD18221 [Drosophila simulans] gi|198455434|ref|XP_002138072.1| GA27572 [Drosophila pseudoobscura pseudoobscura] gi|7301299|gb|AAF56428.1| ribosomal protein S27, isoform A [Drosophila melanogaster] gi|21430282|gb|AAM50819.1| LD37859p [Drosophila melanogaster] gi|38047869|gb|AAR09837.1| similar to Drosophila melanogaster CG10423, partial [Drosophila yakuba] gi|38048241|gb|AAR10023.1| similar to Drosophila melanogaster CG10423, partial [Drosophila yakuba] gi|190626062|gb|EDV41586.1| GF17433 [Drosophila ananassae] gi|190656477|gb|EDV53709.1| GG12272 [Drosophila erecta] gi|193894902|gb|EDV93768.1| GH19510 [Drosophila grimshawi] gi|193916192|gb|EDW15059.1| GI22987 [Drosophila mojavensis] gi|194116434|gb|EDW38477.1| GL12615 [Drosophila persimilis] gi|194129139|gb|EDW51182.1| GM17738 [Drosophila sechellia] gi|194152958|gb|EDW68392.1| GJ24684 [Drosophila virilis] gi|194169883|gb|EDW84784.1| GK14300 [Drosophila willistoni] gi|194185181|gb|EDW98792.1| GE10722 [Drosophila yakuba] gi|194200804|gb|EDX14380.1| GD18221 [Drosophila simulans] gi|198133243|gb|EDY68630.1| GA27572 [Drosophila pseudoobscura pseudoobscura] gi|220959350|gb|ACL92218.1| RpS27-PA [synthetic construct] gi|383292947|gb|AFH06618.1| ribosomal protein S27, isoform B [Drosophila melanogaster]

 Score =  147 bits (371), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 68/75 (90%), Positives = 72/75 (96%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLAKDLLHP  AEEKRKHKLKRLVQHPNSYFMDVKCPGCY+ITTVFSHAQ VV+CAGC+
Sbjct: 1  MPLAKDLLHPLPAEEKRKHKLKRLVQHPNSYFMDVKCPGCYRITTVFSHAQGVVVCAGCA 60

Query: 61 TILCQPTGGRARLTE 75
          TILCQPTGGRA+LTE
Sbjct: 61 TILCQPTGGRAKLTE 75

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|31199327|ref|XP_308611.1| AGAP007157-PA [Anopheles gambiae str. PEST] gi|30178745|gb|EAA04241.2| AGAP007157-PA [Anopheles gambiae str. PEST] gi|208657517|gb|ACI30055.1| 40S ribosomal protein S27 [Anopheles darlingi] gi|312378371|gb|EFR24968.1| hypothetical protein AND_27275 [Anopheles darlingi]

 Score =  147 bits (371), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 69/75 (92%), Positives = 71/75 (94%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLAKD LHP  AEEKRKHKLKRLV HPNSYFMDVKCPGCYKITTVFSHAQSVV+CAGCS
Sbjct: 1  MPLAKDFLHPLPAEEKRKHKLKRLVPHPNSYFMDVKCPGCYKITTVFSHAQSVVVCAGCS 60

Query: 61 TILCQPTGGRARLTE 75
          TILCQPTGG+ARLTE
Sbjct: 61 TILCQPTGGKARLTE 75

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|224924394|gb|ACN69147.1| ribosomal protein S27 [Stomoxys calcitrans]

 Score =  146 bits (368), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 67/75 (89%), Positives = 72/75 (96%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLAKDLLHP  A+EKRKHKLKRLVQHPNSYFMDVKCPGCY+ITTVFSHAQ VV+CAGC+
Sbjct: 1  MPLAKDLLHPLPAQEKRKHKLKRLVQHPNSYFMDVKCPGCYRITTVFSHAQGVVVCAGCA 60

Query: 61 TILCQPTGGRARLTE 75
          TILCQPTGGRA+LTE
Sbjct: 61 TILCQPTGGRAKLTE 75

Source: Stomoxys calcitrans

Species: Stomoxys calcitrans

Genus: Stomoxys

Family: Muscidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321461534|gb|EFX72565.1| hypothetical protein DAPPUDRAFT_308217 [Daphnia pulex]

 Score =  146 bits (368), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 65/75 (86%), Positives = 72/75 (96%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          MPLA+DLLHP+  EE+R+HKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQ+VV+CAGCS
Sbjct: 1  MPLARDLLHPTPEEERRRHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQTVVVCAGCS 60

Query: 61 TILCQPTGGRARLTE 75
           +LCQPTGGRARLTE
Sbjct: 61 AVLCQPTGGRARLTE 75

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	115
FB|FBgn0039300	84	RpS27 "Ribosomal protein S27"	0.652	0.892	0.906	5.1e-35
UNIPROTKB|Q2KHT7	84	RPS27 "40S ribosomal protein S	0.652	0.892	0.88	1.2e-33
UNIPROTKB|E2RLE2	84	RPS27L "40S ribosomal protein	0.652	0.892	0.88	1.2e-33
UNIPROTKB|P42677	84	RPS27 "40S ribosomal protein S	0.652	0.892	0.88	1.2e-33
RGD|621045	84	Rps27 "ribosomal protein S27"	0.652	0.892	0.88	1.2e-33
ZFIN|ZDB-GENE-040426-1735	84	rps27.2 "ribosomal protein S27	0.652	0.892	0.853	5.2e-33
UNIPROTKB|C9JLI6	97	RPS27L "40S ribosomal protein	0.652	0.773	0.853	6.7e-33
UNIPROTKB|Q71UM5	84	RPS27L "40S ribosomal protein	0.652	0.892	0.853	6.7e-33
UNIPROTKB|F2Z5B7	84	RPS27L "Uncharacterized protei	0.652	0.892	0.853	6.7e-33
MGI|MGI:1915191	84	Rps27l "ribosomal protein S27-	0.652	0.892	0.853	6.7e-33

FB|FBgn0039300 RpS27 "Ribosomal protein S27" [Drosophila melanogaster (taxid:7227)]

 Score = 379 (138.5 bits), Expect = 5.1e-35, P = 5.1e-35
 Identities = 68/75 (90%), Positives = 72/75 (96%)

Query:     1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
             MPLAKDLLHP  AEEKRKHKLKRLVQHPNSYFMDVKCPGCY+ITTVFSHAQ VV+CAGC+
Sbjct:     1 MPLAKDLLHPLPAEEKRKHKLKRLVQHPNSYFMDVKCPGCYRITTVFSHAQGVVVCAGCA 60

Query:    61 TILCQPTGGRARLTE 75
             TILCQPTGGRA+LTE
Sbjct:    61 TILCQPTGGRAKLTE 75

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISS

GO:0003735 "structural constituent of ribosome" evidence=ISS;IDA

GO:0006412 "translation" evidence=IEA

GO:0005811 "lipid particle" evidence=IDA

GO:0005840 "ribosome" evidence=IDA

UNIPROTKB|Q2KHT7 RPS27 "40S ribosomal protein S27" [Bos taurus (taxid:9913)]

 Score = 366 (133.9 bits), Expect = 1.2e-33, P = 1.2e-33
 Identities = 66/75 (88%), Positives = 70/75 (93%)

Query:     1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
             MPLAKDLLHPS  EEKRKHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct:     1 MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query:    61 TILCQPTGGRARLTE 75
             T+LCQPTGG+ARLTE
Sbjct:    61 TVLCQPTGGKARLTE 75

GO:0005634 "nucleus" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|E2RLE2 RPS27L "40S ribosomal protein S27" [Canis lupus familiaris (taxid:9615)]

 Score = 366 (133.9 bits), Expect = 1.2e-33, P = 1.2e-33
 Identities = 66/75 (88%), Positives = 70/75 (93%)

Query:     1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
             MPLAKDLLHPS  EEKRKHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct:     1 MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query:    61 TILCQPTGGRARLTE 75
             T+LCQPTGG+ARLTE
Sbjct:    61 TVLCQPTGGKARLTE 75

GO:0046872 "metal ion binding" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|P42677 RPS27 "40S ribosomal protein S27" [Homo sapiens (taxid:9606)]

 Score = 366 (133.9 bits), Expect = 1.2e-33, P = 1.2e-33
 Identities = 66/75 (88%), Positives = 70/75 (93%)

Query:     1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
             MPLAKDLLHPS  EEKRKHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct:     1 MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query:    61 TILCQPTGGRARLTE 75
             T+LCQPTGG+ARLTE
Sbjct:    61 TVLCQPTGGKARLTE 75

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

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0008270 "zinc ion binding" evidence=NAS

GO:0008283 "cell proliferation" evidence=NAS

GO:0005634 "nucleus" evidence=IDA

GO:0003677 "DNA binding" evidence=NAS

GO:0005840 "ribosome" evidence=NAS

GO:0006412 "translation" evidence=IC;NAS;TAS

GO:0000087 "M phase of mitotic cell cycle" evidence=TAS

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=TAS

GO:0000236 "mitotic prometaphase" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0006414 "translational elongation" evidence=TAS

GO:0006415 "translational termination" evidence=TAS

GO:0006614 "SRP-dependent cotranslational protein targeting to membrane" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0019083 "viral transcription" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

RGD|621045 Rps27 "ribosomal protein S27" [Rattus norvegicus (taxid:10116)]

 Score = 366 (133.9 bits), Expect = 1.2e-33, P = 1.2e-33
 Identities = 66/75 (88%), Positives = 70/75 (93%)

Query:     1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
             MPLAKDLLHPS  EEKRKHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct:     1 MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query:    61 TILCQPTGGRARLTE 75
             T+LCQPTGG+ARLTE
Sbjct:    61 TVLCQPTGGKARLTE 75

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

GO:0005634 "nucleus" evidence=ISO

GO:0006412 "translation" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISO;IDA

GO:0046872 "metal ion binding" evidence=IEA

ZFIN|ZDB-GENE-040426-1735 rps27.2 "ribosomal protein S27, isoform 2" [Danio rerio (taxid:7955)]

 Score = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 64/75 (85%), Positives = 70/75 (93%)

Query:     1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
             MPLAKDLLHP+  EEKR+HK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct:     1 MPLAKDLLHPTPEEEKRRHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query:    61 TILCQPTGGRARLTE 75
             T+LCQPTGG+ARLTE
Sbjct:    61 TVLCQPTGGKARLTE 75

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

GO:0005622 "intracellular" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|C9JLI6 RPS27L "40S ribosomal protein S27" [Homo sapiens (taxid:9606)]

 Score = 359 (131.4 bits), Expect = 6.7e-33, P = 6.7e-33
 Identities = 64/75 (85%), Positives = 70/75 (93%)

Query:     1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
             MPLA+DLLHPS  EEK+KHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct:     1 MPLARDLLHPSLEEEKKKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query:    61 TILCQPTGGRARLTE 75
             T+LCQPTGG+ARLTE
Sbjct:    61 TVLCQPTGGKARLTE 75

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

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|Q71UM5 RPS27L "40S ribosomal protein S27-like" [Homo sapiens (taxid:9606)]

 Score = 359 (131.4 bits), Expect = 6.7e-33, P = 6.7e-33
 Identities = 64/75 (85%), Positives = 70/75 (93%)

Query:     1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
             MPLA+DLLHPS  EEK+KHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct:     1 MPLARDLLHPSLEEEKKKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query:    61 TILCQPTGGRARLTE 75
             T+LCQPTGG+ARLTE
Sbjct:    61 TVLCQPTGGKARLTE 75

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

GO:0005840 "ribosome" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0031571 "mitotic G1 DNA damage checkpoint" evidence=IMP

GO:0042771 "intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator" evidence=IDA

GO:0008656 "cysteine-type endopeptidase activator activity involved in apoptotic process" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

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

GO:0006412 "translation" evidence=IDA

GO:0008494 "translation activator activity" evidence=IDA

GO:0006281 "DNA repair" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IDA

GO:0045727 "positive regulation of translation" evidence=IDA

UNIPROTKB|F2Z5B7 RPS27L "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 359 (131.4 bits), Expect = 6.7e-33, P = 6.7e-33
 Identities = 64/75 (85%), Positives = 70/75 (93%)

Query:     1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
             MPLA+DLLHPS  EEK+KHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct:     1 MPLARDLLHPSLEEEKKKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query:    61 TILCQPTGGRARLTE 75
             T+LCQPTGG+ARLTE
Sbjct:    61 TVLCQPTGGKARLTE 75

GO:0042771 "intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator" evidence=IEA

GO:0031571 "mitotic G1 DNA damage checkpoint" evidence=IEA

GO:0008656 "cysteine-type endopeptidase activator activity involved in apoptotic process" evidence=IEA

GO:0008494 "translation activator activity" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

MGI|MGI:1915191 Rps27l "ribosomal protein S27-like" [Mus musculus (taxid:10090)]

 Score = 359 (131.4 bits), Expect = 6.7e-33, P = 6.7e-33
 Identities = 64/75 (85%), Positives = 70/75 (93%)

Query:     1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
             MPLA+DLLHPS  EEK+KHK KRLVQ PNSYFMDVKCPGCYKITTVFSHAQ+VV+C GCS
Sbjct:     1 MPLARDLLHPSLEEEKKKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS 60

Query:    61 TILCQPTGGRARLTE 75
             T+LCQPTGG+ARLTE
Sbjct:    61 TVLCQPTGGKARLTE 75

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

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005840 "ribosome" evidence=IEA

GO:0006281 "DNA repair" evidence=ISO

GO:0006412 "translation" evidence=ISO

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=ISO

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

GO:0008494 "translation activator activity" evidence=ISO

GO:0008656 "cysteine-type endopeptidase activator activity involved in apoptotic process" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0031571 "mitotic G1 DNA damage checkpoint" evidence=ISO

GO:0042771 "intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator" evidence=ISO

GO:0045727 "positive regulation of translation" evidence=ISO

GO:0046872 "metal ion binding" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9M2F1	RS272_ARATH	No assigned EC number	0.7428	0.6086	0.8139	no	N/A
P42677	RS27_HUMAN	No assigned EC number	0.88	0.6521	0.8928	yes	N/A
O64650	RS271_ARATH	No assigned EC number	0.7142	0.6086	0.8333	no	N/A
Q5RBK1	RS27_PONAB	No assigned EC number	0.8666	0.6521	0.8928	no	N/A
Q6ZWY3	RS27L_MOUSE	No assigned EC number	0.8533	0.6521	0.8928	yes	N/A
Q8L953	RS273_ARATH	No assigned EC number	0.7428	0.6086	0.8333	yes	N/A
O74330	RS27_SCHPO	No assigned EC number	0.72	0.6521	0.9036	yes	N/A
P38711	RS27B_YEAST	No assigned EC number	0.6933	0.6521	0.9146	yes	N/A
P55833	RS27_HOMAM	No assigned EC number	0.8266	0.6521	0.8928	N/A	N/A
P35997	RS27_YEAST	No assigned EC number	0.7066	0.6521	0.9146	yes	N/A
P47904	RS27_XENLA	No assigned EC number	0.8666	0.6521	0.8928	N/A	N/A
Q96564	RS27_HORVU	No assigned EC number	0.7285	0.6086	0.8139	N/A	N/A
Q3T0B7	RS27L_BOVIN	No assigned EC number	0.8533	0.6521	0.8928	yes	N/A
Q7RVN2	RS27_NEUCR	No assigned EC number	0.76	0.6521	0.9146	N/A	N/A
Q2KHT7	RS27_BOVIN	No assigned EC number	0.88	0.6521	0.8928	yes	N/A
P24051	RS27L_RAT	No assigned EC number	0.8533	0.6521	0.8928	no	N/A
Q71TY3	RS27_RAT	No assigned EC number	0.88	0.6521	0.8928	no	N/A
Q8T1V4	RS27_DICDI	No assigned EC number	0.7391	0.6	0.8117	yes	N/A
Q9TXP0	RS27_CAEEL	No assigned EC number	0.7466	0.6521	0.9036	yes	N/A
Q71UM5	RS27L_HUMAN	No assigned EC number	0.8533	0.6521	0.8928	yes	N/A
Q6ZWU9	RS27_MOUSE	No assigned EC number	0.88	0.6521	0.8928	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	115
PTZ00083	85	PTZ00083, PTZ00083, 40S ribosomal protein S27; Pro	1e-43
PLN00209	86	PLN00209, PLN00209, ribosomal protein S27; Provisi	2e-42
pfam01667	55	pfam01667, Ribosomal_S27e, Ribosomal protein S27	6e-23
COG2051	67	COG2051, RPS27A, Ribosomal protein S27E [Translati	2e-21
PRK00415	59	PRK00415, rps27e, 30S ribosomal protein S27e; Revi	8e-13

>gnl|CDD|185434 PTZ00083, PTZ00083, 40S ribosomal protein S27; Provisional

 Score =  137 bits (346), Expect = 1e-43
 Identities = 54/70 (77%), Positives = 61/70 (87%)

Query: 6  DLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQ 65
          DLL+P    E RKHKLKRLVQ PNSYFMDVKCPGC +ITTVFSHAQ+VV+C GCS+ LCQ
Sbjct: 7  DLLYPDPESEARKHKLKRLVQGPNSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQ 66

Query: 66 PTGGRARLTE 75
          PTGG+A+LTE
Sbjct: 67 PTGGKAKLTE 76

Length = 85

>gnl|CDD|165774 PLN00209, PLN00209, ribosomal protein S27; Provisional

 Score =  133 bits (337), Expect = 2e-42
 Identities = 52/70 (74%), Positives = 60/70 (85%)

Query: 6  DLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQ 65
          DLL+P    EKRKHKLKRLVQ PNS+FMDVKC GC+ ITTVFSH+Q+VV+C  C T+LCQ
Sbjct: 8  DLLNPPAELEKRKHKLKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQ 67

Query: 66 PTGGRARLTE 75
          PTGG+ARLTE
Sbjct: 68 PTGGKARLTE 77

Length = 86

>gnl|CDD|110652 pfam01667, Ribosomal_S27e, Ribosomal protein S27

 Score = 83.7 bits (207), Expect = 6e-23
 Identities = 32/48 (66%), Positives = 38/48 (79%)

Query: 28 PNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTE 75
          PNSYF+DVKCPGC  ITTVFSHAQ+VV C  C  +LC+PTGG+ +L  
Sbjct: 1  PNSYFLDVKCPGCGNITTVFSHAQTVVKCIICGKVLCEPTGGKGKLKA 48

Length = 55

>gnl|CDD|224962 COG2051, RPS27A, Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]

 Score = 80.1 bits (198), Expect = 2e-21
 Identities = 27/61 (44%), Positives = 36/61 (59%), Gaps = 3/61 (4%)

Query: 15 EKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLT 74
            RK K+ +    P S F+ VKCP C     VFSHA +VV C  C T L +PTGG+A+++
Sbjct: 3  RGRKVKIPK---EPRSRFLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEPTGGKAKIS 59

Query: 75 E 75
           
Sbjct: 60 G 60

Length = 67

>gnl|CDD|179013 PRK00415, rps27e, 30S ribosomal protein S27e; Reviewed

 Score = 58.0 bits (141), Expect = 8e-13
 Identities = 24/50 (48%), Positives = 31/50 (62%)

Query: 24 LVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARL 73
          L+  P S F+ VKCP C     VFSHA +VV C  C   L +PTGG+A++
Sbjct: 1  LIPQPRSRFLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAKI 50

Length = 59

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	115
PTZ00083	85	40S ribosomal protein S27; Provisional	100.0
PLN00209	86	ribosomal protein S27; Provisional	100.0
KOG1779|consensus	84		100.0
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	100.0
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	99.97
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	99.96
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	97.18
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	95.67
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	95.24
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	94.97
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	93.11
PF13248	26	zf-ribbon_3: zinc-ribbon domain	92.47
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	91.54
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	89.13
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	88.95
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	87.91
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	87.52
PRK14892	99	putative transcription elongation factor Elf1; Pro	87.37
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	87.06
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	84.35
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	83.47
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	83.42
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	83.25
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	82.74
PF05907	161	DUF866: Eukaryotic protein of unknown function (DU	82.72
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	82.46
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	81.98
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	81.68
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	81.24
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	81.16
PRK02935	110	hypothetical protein; Provisional	80.5

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=100.00  E-value=4.5e-48  Score=271.27  Aligned_cols=79  Identities=68%  Similarity=1.118  Sum_probs=76.6

Q ss_pred             CcccccCCCCHHHHHHhhcccccccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCCCc
Q psy2574           2 PLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGD   80 (115)
Q Consensus         2 ~l~~DLl~Ps~e~ek~k~K~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f~   80 (115)
                      .|+.|||||++|+|++|||+|||||+||||||+||||+|+|||||||||||+|.|.+||++||+||||||+|+|||+|.
T Consensus         3 ~~~~DLl~p~~~~e~~khK~k~Lv~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~gc~fr   81 (85)
T PTZ00083          3 FMDVDLLYPDPESEARKHKLKRLVQGPNSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGGKAKLTEGCSFR   81 (85)
T ss_pred             cchhhhcCCCHHHHHhhhhceeEecCCCCeEEEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecCCceEE
Confidence            3577999999999999999999999999999999999999999999999999999999999999999999999999983

>PLN00209 ribosomal protein S27; Provisional

Probab=100.00  E-value=1.4e-47  Score=269.32  Aligned_cols=78  Identities=67%  Similarity=1.121  Sum_probs=75.9

Q ss_pred             cccccCCCCHHHHHHhhcccccccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCCCc
Q psy2574           3 LAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGD   80 (115)
Q Consensus         3 l~~DLl~Ps~e~ek~k~K~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f~   80 (115)
                      ++.|||||++|+|++|||+|||||+||||||+||||+|+|||||||||||+|.|.+||++||+||||||+|+|||+|-
T Consensus         5 ~~~DLl~P~~~~e~~khK~k~Lv~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~gc~fr   82 (86)
T PLN00209          5 NDIDLLNPPAELEKRKHKLKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQPTGGKARLTEGCSFR   82 (86)
T ss_pred             cchhccCCCHHHHHhhhhceeeecCCCCEEEEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecCCceEE
Confidence            467999999999999999999999999999999999999999999999999999999999999999999999999983

>KOG1779|consensus

Probab=100.00  E-value=2.7e-44  Score=251.42  Aligned_cols=80  Identities=80%  Similarity=1.331  Sum_probs=79.0

Q ss_pred             CCcccccCCCCHHHHHHhhcccccccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCCCc
Q psy2574           1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGD   80 (115)
Q Consensus         1 m~l~~DLl~Ps~e~ek~k~K~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f~   80 (115)
                      |+|++|||||++|+|+|+||+|||||+||||||+|||++|.||++|||||||+|.|.+|+++|++||||||+++|||+|-
T Consensus         1 m~la~dllhPs~e~e~r~hK~krLvq~~nsyFm~VkC~gc~~iT~vfSHaqtvVvc~~c~~il~~~tggra~ls~~csfr   80 (84)
T KOG1779|consen    1 MPLAKDLLHPSPEKEKRKHKLKRLVQSPNSYFMDVKCPGCFKITTVFSHAQTVVVCEGCSTILCQPTGGKAKLSEGCSFR   80 (84)
T ss_pred             CccchhhcCCCHHHHhhhhhhhhheeCCCceEEEEEcCCceEEEEEeecCceEEEcCCCceEEEEecCCcEEecCCCcce
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999983

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

Probab=100.00  E-value=8e-34  Score=185.38  Aligned_cols=52  Identities=73%  Similarity=1.252  Sum_probs=42.3

Q ss_pred             CCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCCC
Q psy2574          28 PNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTG   79 (115)
Q Consensus        28 PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f   79 (115)
                      |||||||||||+|+|+|+||||||++|.|.+||++|++||||||+|.+||.|
T Consensus         1 P~S~Fm~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~PtGGKa~l~~~~~~   52 (55)
T PF01667_consen    1 PNSYFMDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPTGGKARLTEGCSF   52 (55)
T ss_dssp             -S--EEEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-SSSEEESSSEEE
T ss_pred             CCccEEEEECCCCCCeeEEEecCCeEEEcccCCCEecCCCCcCeEEeCCeEE
Confidence            8999999999999999999999999999999999999999999999999976

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=99.97  E-value=2.6e-32  Score=180.75  Aligned_cols=52  Identities=46%  Similarity=0.916  Sum_probs=50.4

Q ss_pred             cccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeecc
Q psy2574          24 LVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTE   75 (115)
Q Consensus        24 LV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~e   75 (115)
                      |||+|||+||+||||+|+|+|+||||||++|.|.+||++|++||||||+|..
T Consensus         1 li~~p~S~F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGKa~i~~   52 (59)
T PRK00415          1 LIPQPRSRFLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAKIKG   52 (59)
T ss_pred             CCCCCCCeEEEEECCCCCCeEEEEecCCcEEECcccCCCcccCCCcceeeeh
Confidence            7999999999999999999999999999999999999999999999999963

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

Probab=99.96  E-value=1.3e-29  Score=171.60  Aligned_cols=56  Identities=45%  Similarity=0.819  Sum_probs=52.2

Q ss_pred             ccccc-CCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCC
Q psy2574          22 KRLVQ-HPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDD   77 (115)
Q Consensus        22 krLV~-~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc   77 (115)
                      |-++| .|||+||+||||||+|+|+|||||||+|.|.+||++|++||||||+|.+..
T Consensus         6 k~~~p~~p~s~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l~~PTGGka~i~~~i   62 (67)
T COG2051           6 KVKIPKEPRSRFLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEPTGGKAKISGKI   62 (67)
T ss_pred             eeeecCCCCceEEEEECCCCCCEEEEeccCceEEEecccccEEEecCCCeEEeeeee
Confidence            44555 999999999999999999999999999999999999999999999998864

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

Probab=97.18  E-value=0.00037  Score=42.08  Aligned_cols=31  Identities=29%  Similarity=0.752  Sum_probs=27.2

Q ss_pred             eCCCCCceeEEeeecceeEEcCCCCeeeecc
Q psy2574          36 KCPGCYKITTVFSHAQSVVICAGCSTILCQP   66 (115)
Q Consensus        36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~P   66 (115)
                      +||.|+...++|.+++..+.|..||.+|-+-
T Consensus         2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~   32 (43)
T PF08271_consen    2 KCPNCGSKEIVFDPERGELVCPNCGLVLEEN   32 (43)
T ss_dssp             SBTTTSSSEEEEETTTTEEEETTT-BBEE-T
T ss_pred             CCcCCcCCceEEcCCCCeEECCCCCCEeecc
Confidence            7999999999999999999999999999653

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

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=95.67  E-value=0.014  Score=33.88  Aligned_cols=32  Identities=25%  Similarity=0.619  Sum_probs=23.9

Q ss_pred             eEEeCCCCCceeEEee----ecceeEEcCCCCeeee
Q psy2574          33 MDVKCPGCYKITTVFS----HAQSVVICAGCSTILC   64 (115)
Q Consensus        33 m~VKCp~C~n~q~VFS----HAqt~V~C~~Cg~vL~   64 (115)
                      |+++||.|+..--|=+    .+...|.|..||+++-
T Consensus         1 M~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         1 MRIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             CEEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence            7899999998644432    2345799999999873

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

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=95.24  E-value=0.012  Score=48.02  Aligned_cols=32  Identities=19%  Similarity=0.646  Sum_probs=29.5

Q ss_pred             EeCCCCCceeEEeeecceeEEcCCCCeeeecc
Q psy2574          35 VKCPGCYKITTVFSHAQSVVICAGCSTILCQP   66 (115)
Q Consensus        35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~P   66 (115)
                      .+||+|+...+|+++++..+.|..||.||.+-
T Consensus        12 ~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~e~   43 (310)
T PRK00423         12 LVCPECGSDKLIYDYERGEIVCADCGLVIEEN   43 (310)
T ss_pred             CcCcCCCCCCeeEECCCCeEeecccCCccccc
Confidence            47999999999999999999999999999663

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

Probab=94.97  E-value=0.033  Score=33.86  Aligned_cols=36  Identities=17%  Similarity=0.296  Sum_probs=26.5

Q ss_pred             eEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCC
Q psy2574          33 MDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGG   69 (115)
Q Consensus        33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGG   69 (115)
                      +..+|++|+.+..+ ....+.+.|..||..+..-..+
T Consensus         2 ~~y~C~~CG~~~~~-~~~~~~~~Cp~CG~~~~~~~~~   37 (46)
T PRK00398          2 AEYKCARCGREVEL-DEYGTGVRCPYCGYRILFKERP   37 (46)
T ss_pred             CEEECCCCCCEEEE-CCCCCceECCCCCCeEEEccCC
Confidence            56899999996554 4444589999999987654433

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=93.11  E-value=0.11  Score=30.80  Aligned_cols=31  Identities=26%  Similarity=0.577  Sum_probs=23.9

Q ss_pred             eEEeCCCCCceeEEee----ecceeEEcCCCCeee
Q psy2574          33 MDVKCPGCYKITTVFS----HAQSVVICAGCSTIL   63 (115)
Q Consensus        33 m~VKCp~C~n~q~VFS----HAqt~V~C~~Cg~vL   63 (115)
                      |.+.||.|...--|=.    -+...|+|..|+.+.
T Consensus         1 M~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    1 MIITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             CEEECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence            7899999987655433    356799999999875

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=92.47  E-value=0.039  Score=30.50  Aligned_cols=26  Identities=27%  Similarity=0.680  Sum_probs=20.8

Q ss_pred             eEEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574          33 MDVKCPGCYKITTVFSHAQSVVICAGCSTIL   63 (115)
Q Consensus        33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL   63 (115)
                      |.+.||.|+++     +......|..||+.|
T Consensus         1 m~~~Cp~Cg~~-----~~~~~~fC~~CG~~L   26 (26)
T PF13248_consen    1 MEMFCPNCGAE-----IDPDAKFCPNCGAKL   26 (26)
T ss_pred             CcCCCcccCCc-----CCcccccChhhCCCC
Confidence            56889999983     366778899999865

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=91.54  E-value=0.27  Score=28.27  Aligned_cols=31  Identities=13%  Similarity=0.443  Sum_probs=22.2

Q ss_pred             eEEeCCCCCcee-EEeeec-ceeEEcCCCCeee
Q psy2574          33 MDVKCPGCYKIT-TVFSHA-QSVVICAGCSTIL   63 (115)
Q Consensus        33 m~VKCp~C~n~q-~VFSHA-qt~V~C~~Cg~vL   63 (115)
                      ++-+|++|+++- +..+-+ ...+.|..||..+
T Consensus         4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~   36 (41)
T smart00834        4 YEYRCEDCGHTFEVLQKISDDPLATCPECGGDV   36 (41)
T ss_pred             EEEEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence            467999999944 444333 6688899999843

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

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=89.13  E-value=0.46  Score=28.13  Aligned_cols=31  Identities=23%  Similarity=0.564  Sum_probs=21.3

Q ss_pred             eEEeCCCCCceeEEee----ecceeEEcCCCCeee
Q psy2574          33 MDVKCPGCYKITTVFS----HAQSVVICAGCSTIL   63 (115)
Q Consensus        33 m~VKCp~C~n~q~VFS----HAqt~V~C~~Cg~vL   63 (115)
                      |+|.||.|...--|=+    -....|.|..||.+.
T Consensus         1 M~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    1 MIITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             CEEECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence            7788888877654433    234578888888764

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

Probab=88.95  E-value=0.17  Score=37.75  Aligned_cols=34  Identities=26%  Similarity=0.583  Sum_probs=29.1

Q ss_pred             CceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecc
Q psy2574          30 SYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQP   66 (115)
Q Consensus        30 S~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~P   66 (115)
                      .+...|+||+|++.+-+.++.+   .|--|+++|.-.
T Consensus        65 tkav~V~CP~C~K~TKmLGr~D---~CM~C~~pLTLd   98 (114)
T PF11023_consen   65 TKAVQVECPNCGKQTKMLGRVD---ACMHCKEPLTLD   98 (114)
T ss_pred             ccceeeECCCCCChHhhhchhh---ccCcCCCcCccC
Confidence            3457899999999999999986   899999998643

; GO: 0005887 integral to plasma membrane

>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]

Probab=87.91  E-value=0.42  Score=39.58  Aligned_cols=30  Identities=23%  Similarity=0.670  Sum_probs=28.4

Q ss_pred             eCCCCCceeEEeeecceeEEcCCCCeeeec
Q psy2574          36 KCPGCYKITTVFSHAQSVVICAGCSTILCQ   65 (115)
Q Consensus        36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~   65 (115)
                      .||.|+...++.++....+.|..||.+|-.
T Consensus         3 ~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~   32 (285)
T COG1405           3 SCPECGSTNIITDYERGEIVCADCGLVLED   32 (285)
T ss_pred             CCCCCCCccceeeccCCeEEeccCCEEecc
Confidence            699999999999999999999999999965

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

Probab=87.52  E-value=0.64  Score=27.80  Aligned_cols=28  Identities=32%  Similarity=0.785  Sum_probs=19.4

Q ss_pred             EeCCCCCceeEEeeecce---------eEEcCCCCee
Q psy2574          35 VKCPGCYKITTVFSHAQS---------VVICAGCSTI   62 (115)
Q Consensus        35 VKCp~C~n~q~VFSHAqt---------~V~C~~Cg~v   62 (115)
                      ++||.|++..++|-..|+         ...|..||..
T Consensus         1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~   37 (39)
T PF01096_consen    1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR   37 (39)
T ss_dssp             S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred             CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence            589999999999986654         4678888764

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

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=87.37  E-value=0.72  Score=33.18  Aligned_cols=29  Identities=21%  Similarity=0.685  Sum_probs=21.4

Q ss_pred             EeCCCCCceeE--EeeecceeEEcCCCCeee
Q psy2574          35 VKCPGCYKITT--VFSHAQSVVICAGCSTIL   63 (115)
Q Consensus        35 VKCp~C~n~q~--VFSHAqt~V~C~~Cg~vL   63 (115)
                      +.||.|++..+  -+.+-...+.|..||.--
T Consensus        22 f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~   52 (99)
T PRK14892         22 FECPRCGKVSISVKIKKNIAIITCGNCGLYT   52 (99)
T ss_pred             eECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence            68999995322  256767789999999753

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=87.06  E-value=0.74  Score=27.99  Aligned_cols=29  Identities=14%  Similarity=0.494  Sum_probs=20.4

Q ss_pred             eEEeCCCCCcee-EEee-ecceeEEcCCCCe
Q psy2574          33 MDVKCPGCYKIT-TVFS-HAQSVVICAGCST   61 (115)
Q Consensus        33 m~VKCp~C~n~q-~VFS-HAqt~V~C~~Cg~   61 (115)
                      ++-+|++|+++- +..+ +....+.|..||.
T Consensus         4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~   34 (52)
T TIGR02605         4 YEYRCTACGHRFEVLQKMSDDPLATCPECGG   34 (52)
T ss_pred             EEEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence            467999999944 4433 2235678999997

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

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

Probab=84.35  E-value=1.4  Score=26.50  Aligned_cols=30  Identities=20%  Similarity=0.562  Sum_probs=21.8

Q ss_pred             eeEEeCCCCCceeEEeee-cc-eeEEcCCCCe
Q psy2574          32 FMDVKCPGCYKITTVFSH-AQ-SVVICAGCST   61 (115)
Q Consensus        32 Fm~VKCp~C~n~q~VFSH-Aq-t~V~C~~Cg~   61 (115)
                      ..+-+|++|++.--++-. +. ..+.|..||.
T Consensus         3 ~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~   34 (42)
T PF09723_consen    3 IYEYRCEECGHEFEVLQSISEDDPVPCPECGS   34 (42)
T ss_pred             CEEEEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence            357799999955444433 33 5899999998

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

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=83.47  E-value=0.93  Score=32.53  Aligned_cols=37  Identities=14%  Similarity=0.293  Sum_probs=27.1

Q ss_pred             eEEeCCCCCceeEEeeecce-eEEcCCCCeeeecccCCcee
Q psy2574          33 MDVKCPGCYKITTVFSHAQS-VVICAGCSTILCQPTGGRAR   72 (115)
Q Consensus        33 m~VKCp~C~n~q~VFSHAqt-~V~C~~Cg~vL~~PTGGKA~   72 (115)
                      ...+|++|++   .|..... ...|+.||..-.+-.+|+--
T Consensus        69 ~~~~C~~Cg~---~~~~~~~~~~~CP~Cgs~~~~i~~G~El  106 (114)
T PRK03681         69 AECWCETCQQ---YVTLLTQRVRRCPQCHGDMLRIVADDGL  106 (114)
T ss_pred             cEEEcccCCC---eeecCCccCCcCcCcCCCCcEEccCCeE
Confidence            3589999996   4555433 36799999887788888753

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=83.42  E-value=1.2  Score=28.99  Aligned_cols=32  Identities=28%  Similarity=0.597  Sum_probs=21.9

Q ss_pred             eEEeCCCCCceeEE-eeecceeEEcCCCCeeee
Q psy2574          33 MDVKCPGCYKITTV-FSHAQSVVICAGCSTILC   64 (115)
Q Consensus        33 m~VKCp~C~n~q~V-FSHAqt~V~C~~Cg~vL~   64 (115)
                      |..+||.|+..-.+ =+..-..|.|..||..|=
T Consensus         1 ~~~~CP~CG~~iev~~~~~GeiV~Cp~CGaele   33 (54)
T TIGR01206         1 MQFECPDCGAEIELENPELGELVICDECGAELE   33 (54)
T ss_pred             CccCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence            35689999985433 112346889999998773

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

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=83.25  E-value=1.2  Score=30.61  Aligned_cols=29  Identities=24%  Similarity=0.551  Sum_probs=22.3

Q ss_pred             eEEeCCCCCceeEEeeecce---------eEEcCCCCe
Q psy2574          33 MDVKCPGCYKITTVFSHAQS---------VVICAGCST   61 (115)
Q Consensus        33 m~VKCp~C~n~q~VFSHAqt---------~V~C~~Cg~   61 (115)
                      .+++||.|++...+|.-.|+         .-.|..||.
T Consensus        61 ~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~   98 (104)
T TIGR01384        61 TRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGY   98 (104)
T ss_pred             ccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCC
Confidence            36899999999999986654         456777764

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=82.74  E-value=1.8  Score=26.79  Aligned_cols=30  Identities=23%  Similarity=0.452  Sum_probs=23.2

Q ss_pred             eEEeCCCCCceeEEeeecceeEEcCCCCeeee
Q psy2574          33 MDVKCPGCYKITTVFSHAQSVVICAGCSTILC   64 (115)
Q Consensus        33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~   64 (115)
                      |.-+|.+|+.+..+-  ....|.|..||.-+.
T Consensus         1 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~rIl   30 (44)
T smart00659        1 MIYICGECGRENEIK--SKDVVRCRECGYRIL   30 (44)
T ss_pred             CEEECCCCCCEeecC--CCCceECCCCCceEE
Confidence            345899999987764  568899999997553

present in RNA polymerase I, II and III

>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues

Probab=82.72  E-value=1.8  Score=32.97  Aligned_cols=37  Identities=24%  Similarity=0.494  Sum_probs=21.9

Q ss_pred             CCCCceeEEeCCCCCcee---EEee------------ecceeEEcCCCCeee
Q psy2574          27 HPNSYFMDVKCPGCYKIT---TVFS------------HAQSVVICAGCSTIL   63 (115)
Q Consensus        27 ~PnS~Fm~VKCp~C~n~q---~VFS------------HAqt~V~C~~Cg~vL   63 (115)
                      .|-.||++|||..|+.+.   |.++            -|..+.+|..|++..
T Consensus        23 ~~~~~~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~   74 (161)
T PF05907_consen   23 PDFEWFFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRES   74 (161)
T ss_dssp             TT--EEEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--E
T ss_pred             CCCEEEEEEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCcc
Confidence            467899999999999754   3444            467788999998743

; PDB: 1ZSO_B.

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=82.46  E-value=0.48  Score=25.84  Aligned_cols=23  Identities=30%  Similarity=0.725  Sum_probs=15.5

Q ss_pred             eCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574          36 KCPGCYKITTVFSHAQSVVICAGCSTIL   63 (115)
Q Consensus        36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL   63 (115)
                      +||.|+++.     ......|..||+.|
T Consensus         1 ~Cp~CG~~~-----~~~~~fC~~CG~~l   23 (23)
T PF13240_consen    1 YCPNCGAEI-----EDDAKFCPNCGTPL   23 (23)
T ss_pred             CCcccCCCC-----CCcCcchhhhCCcC
Confidence            478888764     23455588888764

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=81.98  E-value=1  Score=32.33  Aligned_cols=36  Identities=19%  Similarity=0.309  Sum_probs=26.0

Q ss_pred             eEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCce
Q psy2574          33 MDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRA   71 (115)
Q Consensus        33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA   71 (115)
                      ..++|++|++   .|........|+.||..=.+-.+|+-
T Consensus        69 ~~~~C~~Cg~---~~~~~~~~~~CP~Cgs~~~~i~~G~E  104 (113)
T PRK12380         69 AQAWCWDCSQ---VVEIHQHDAQCPHCHGERLRVDTGDS  104 (113)
T ss_pred             cEEEcccCCC---EEecCCcCccCcCCCCCCcEEccCCe
Confidence            4589999994   45555555669999987666677764

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=81.68  E-value=2.2  Score=25.68  Aligned_cols=27  Identities=26%  Similarity=0.642  Sum_probs=20.8

Q ss_pred             eCCCCCceeEEeeecc---------eeEEcCCCCee
Q psy2574          36 KCPGCYKITTVFSHAQ---------SVVICAGCSTI   62 (115)
Q Consensus        36 KCp~C~n~q~VFSHAq---------t~V~C~~Cg~v   62 (115)
                      +||.|++..++|-..|         ....|..||..
T Consensus         2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~   37 (40)
T smart00440        2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHR   37 (40)
T ss_pred             cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence            7999999999997554         35677777753

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

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=81.24  E-value=1.1  Score=32.10  Aligned_cols=36  Identities=22%  Similarity=0.559  Sum_probs=25.5

Q ss_pred             eEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCce
Q psy2574          33 MDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRA   71 (115)
Q Consensus        33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA   71 (115)
                      ...+|++|++   .|+.......|+.||..-.+-.+|+-
T Consensus        69 ~~~~C~~Cg~---~~~~~~~~~~CP~Cgs~~~~i~~G~E  104 (115)
T TIGR00100        69 VECECEDCSE---EVSPEIDLYRCPKCHGIMLQVRAGKE  104 (115)
T ss_pred             cEEEcccCCC---EEecCCcCccCcCCcCCCcEEecCCe
Confidence            3589999994   45555556789999987655566653

In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=81.16  E-value=1.8  Score=25.52  Aligned_cols=28  Identities=21%  Similarity=0.414  Sum_probs=20.7

Q ss_pred             eCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574          36 KCPGCYKITTVFSHAQSVVICAGCSTIL   63 (115)
Q Consensus        36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL   63 (115)
                      -||.|+|+=.+=......+.|..|+..-
T Consensus         3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~   30 (35)
T PF02150_consen    3 FCPECGNLLYPKEDKEKRVACRTCGYEE   30 (35)
T ss_dssp             BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred             eCCCCCccceEcCCCccCcCCCCCCCcc
Confidence            3888988888777776666888888653

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

>PRK02935 hypothetical protein; Provisional

Probab=80.50  E-value=1  Score=33.53  Aligned_cols=36  Identities=25%  Similarity=0.540  Sum_probs=29.4

Q ss_pred             CCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeeccc
Q psy2574          29 NSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPT   67 (115)
Q Consensus        29 nS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PT   67 (115)
                      ..+...|.||+|++.+-+-.+..   .|--|+++|.-+.
T Consensus        65 StkavqV~CP~C~K~TKmLGrvD---~CM~C~~PLTLd~  100 (110)
T PRK02935         65 STKAVQVICPSCEKPTKMLGRVD---ACMHCNQPLTLDR  100 (110)
T ss_pred             cccceeeECCCCCchhhhcccee---ecCcCCCcCCcCc
Confidence            45678899999999998887754   8999999986543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	115
3izb_X	82	Localization Of The Small Subunit Ribosomal Protein		3e-27
3iz6_X	86	Localization Of The Small Subunit Ribosomal Protein		1e-22
2xzm_6	81	Crystal Structure Of The Eukaryotic 40s Ribosomal S		1e-21
3zey_W	86	High-resolution Cryo-electron Microscopy Structure		4e-21
3j20_W	63	Promiscuous Behavior Of Proteins In Archaeal Riboso		2e-04
1qxf_A	66	Solution Structure Of 30s Ribosomal Protein S27e Fr		3e-04

>pdb|3IZB|X Chain X, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 82

Iteration: 1
 Score =  116 bits (290), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 53/75 (70%), Positives = 60/75 (80%)
Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          M L +DLLHP+ A E RKHKLK LVQ P SYF+DVKCPGC  ITTVFSHAQ+ V C  CS
Sbjct: 1  MVLVQDLLHPTAASEARKHKLKTLVQGPRSYFLDVKCPGCLNITTVFSHAQTAVTCESCS 60
Query: 61 TILCQPTGGRARLTE 75
          TILC PTGG+A+L+E
Sbjct: 61 TILCTPTGGKAKLSE 75

>pdb|3IZ6|X Chain X, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 86

Iteration: 1
 Score =  101 bits (251), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/70 (72%), Positives = 59/70 (84%)
Query: 6  DLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQ 65
          DLL+P    EK KHK KRLVQ PNS+FMDVKC GC+ ITTVFSH+Q+VV+C GC T+LCQ
Sbjct: 8  DLLNPPAELEKLKHKKKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCPGCQTVLCQ 67
Query: 66 PTGGRARLTE 75
          PTGG+ARLTE
Sbjct: 68 PTGGKARLTE 77

>pdb|2XZM|6 Chain 6, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit In Complex With Initiation Factor 1. This File Contains The 40s Subunit And Initiation Factor For Molecule 1 Length = 81

Iteration: 1
 Score = 97.8 bits (242), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 41/71 (57%), Positives = 54/71 (76%)
Query: 3  LAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTI 62
          + +DLL+P   EEK+K+K KRL+Q PNSYFMDVKC  C  I  +FS+AQS +IC  CS I
Sbjct: 1  MERDLLNPIYEEEKQKNKFKRLIQAPNSYFMDVKCAQCQNIQMIFSNAQSTIICEKCSAI 60
Query: 63 LCQPTGGRARL 73
          LC+PTGG+ ++
Sbjct: 61 LCKPTGGKVQI 71

>pdb|3ZEY|W Chain W, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 86

Iteration: 1
 Score = 96.3 bits (238), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 44/69 (63%), Positives = 53/69 (76%)
Query: 6  DLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQ 65
          DL +P+   E+ KHK +RLVQ PNSYFMDVKCPGC  IT V+SHA S V C GC+T+LC+
Sbjct: 7  DLSYPTVRTERMKHKRRRLVQGPNSYFMDVKCPGCKNITVVYSHATSEVKCNGCATLLCR 66
Query: 66 PTGGRARLT 74
          PTGG+A L 
Sbjct: 67 PTGGKAMLV 75

>pdb|3J20|W Chain W, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (30s Ribosomal Subunit) Length = 63

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 26/50 (52%)
Query: 22 KRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRA 71
          K ++  P S F+ VKC  C     VFSH  + V C  C   L +PTGG+ 
Sbjct: 3  KPIIPMPRSRFLRVKCIDCGNEQIVFSHPATKVRCLICGATLVEPTGGKG 52

>pdb|1QXF|A Chain A, Solution Structure Of 30s Ribosomal Protein S27e From Archaeoglobus Fulgidus: Gr2, A Nesg Target Protein Length = 66

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 29 NSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARL 73
          +S F+ VKCP C     +F H  ++V C  C   + +PTGG+  +
Sbjct: 2  HSRFVKVKCPDCEHEQVIFDHPSTIVKCIICGRTVAEPTGGKGNI 46

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	115
3u5c_B	255	RP10A, 40S ribosomal protein S1-A; translation, ri	2e-48
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	4e-45
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	3e-42
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	2e-29

>3u5c_B RP10A, 40S ribosomal protein S1-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_B Length = 255

 Score =  148 bits (375), Expect = 2e-48
 Identities = 6/75 (8%), Positives = 18/75 (24%)

Query: 1  MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
          M + K+       + ++K  +    +                +     +  + +  A  +
Sbjct: 1  MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA 60

Query: 61 TILCQPTGGRARLTE 75
                    A L  
Sbjct: 61 LKGRVVEVCLADLQG 75

>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6 Length = 81

 Score =  140 bits (354), Expect = 4e-45
 Identities = 41/73 (56%), Positives = 54/73 (73%)

Query: 3  LAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTI 62
          + +DLL+P   EEK+K+K KRL+Q PNSYFMDVKC  C  I  +FS+AQS +IC  CS I
Sbjct: 1  MERDLLNPIYEEEKQKNKFKRLIQAPNSYFMDVKCAQCQNIQMIFSNAQSTIICEKCSAI 60

Query: 63 LCQPTGGRARLTE 75
          LC+PTGG+ ++  
Sbjct: 61 LCKPTGGKVQIQA 73

>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 86

 Score =  133 bits (335), Expect = 3e-42
 Identities = 53/77 (68%), Positives = 62/77 (80%), Gaps = 2/77 (2%)

Query: 1  MPLAK--DLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAG 58
          M L+   DLL+P    EK KHK KRLVQ PNS+FMDVKC GC+ ITTVFSH+Q+VV+C G
Sbjct: 1  MVLSNDIDLLNPPAELEKLKHKKKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCPG 60

Query: 59 CSTILCQPTGGRARLTE 75
          C T+LCQPTGG+ARLTE
Sbjct: 61 CQTVLCQPTGGKARLTE 77

>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4 Length = 66

 Score =  100 bits (250), Expect = 2e-29
 Identities = 16/48 (33%), Positives = 26/48 (54%)

Query: 29 NSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTED 76
          +S F+ VKCP C     +F H  ++V C  C   + +PTGG+  +  +
Sbjct: 2  HSRFVKVKCPDCEHEQVIFDHPSTIVKCIICGRTVAEPTGGKGNIKAE 49

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	115
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	100.0
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	100.0
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	100.0
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	100.0
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	99.96
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	98.25
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	96.78
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	95.11
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	92.97
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	92.71
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	92.31
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	91.86
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	90.6
1tfi_A	50	Transcriptional elongation factor SII; transcripti	89.2
1dxg_A	36	Desulforedoxin; non-heme iron protein, rubredoxin	86.92
1k81_A	36	EIF-2-beta, probable translation initiation factor	84.72
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	84.3
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	82.99
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	80.65
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	80.13
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	80.04

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

Probab=100.00  E-value=1.4e-50  Score=281.42  Aligned_cols=79  Identities=67%  Similarity=1.149  Sum_probs=77.4

Q ss_pred             CCcccccCCCCHHHHHHhhcccccccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCCC
Q psy2574           1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTG   79 (115)
Q Consensus         1 m~l~~DLl~Ps~e~ek~k~K~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f   79 (115)
                      |+|++|||||++|+|++|||+|||||+|||||||||||||+|||+|||||||+|.|.+||++||+||||||+|+|||+|
T Consensus         1 m~l~~dLl~P~~~~e~~khK~k~Lv~~PnS~Fm~VkCp~C~~~q~VFSha~t~V~C~~Cg~~L~~PTGGKa~l~egc~f   79 (82)
T 3u5c_b            1 MVLVQDLLHPTAASEARKHKLKTLVQGPRSYFLDVKCPGCLNITTVFSHAQTAVTCESCSTILCTPTGGKAKLSEGTSF   79 (82)
T ss_dssp             -CCSCCSSSCCHHHHHSSCTTTSSSCCCCCCEEEEECTTSCSCEEEESBCSSCCCCSSSCCCCEECCSSBCEECSSCEE
T ss_pred             CccchhhcCCCHHHHhhhhhheeeccCCCCcEEEEECCCCCCeeEEEecCCeEEEccccCCEEeccCCCCeEecCCcee
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999999987

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

Probab=100.00  E-value=4.5e-49  Score=273.22  Aligned_cols=78  Identities=53%  Similarity=0.971  Sum_probs=75.6

Q ss_pred             cccccCCCCHHHHHHhhcccccccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCCCc
Q psy2574           3 LAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGD   80 (115)
Q Consensus         3 l~~DLl~Ps~e~ek~k~K~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f~   80 (115)
                      |+.|||||++|+|+||||+|||||+|||+|||||||||+|||||||||||+|.|.+||++||+||||||+|+|||+|-
T Consensus         1 ~~~dll~p~~~~e~~k~K~k~Lv~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKA~l~egc~fr   78 (81)
T 2xzm_6            1 MERDLLNPIYEEEKQKNKFKRLIQAPNSYFMDVKCAQCQNIQMIFSNAQSTIICEKCSAILCKPTGGKVQIQAGCAFK   78 (81)
T ss_dssp             -CCCSSSCCHHHHHHSCTTTSSSCCCSCCEEEEECSSSCCEEEEETTCSSCEECSSSCCEEEEECSSCEEECSSCEEE
T ss_pred             CchhhcCCCHHHHhhhhheeeeeeCCCCcEEEeECCCCCCeeEEEecCccEEEccCCCCEEeecCCCCeEecCCccee
Confidence            568999999999999999999999999999999999999999999999999999999999999999999999999983

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

Probab=100.00  E-value=8.9e-49  Score=274.28  Aligned_cols=80  Identities=66%  Similarity=1.103  Sum_probs=49.2

Q ss_pred             CCc--ccccCCCCHHHHHHhhcccccccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCC
Q psy2574           1 MPL--AKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDT   78 (115)
Q Consensus         1 m~l--~~DLl~Ps~e~ek~k~K~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~   78 (115)
                      |+|  +.|||||++|+||+|||+|||||+|||||||||||+|+|+|+|||||||+|.|.+||++||+||||||+|+|||+
T Consensus         1 m~~~~~~DLl~P~~e~e~~khK~k~Lv~~PnS~Fm~VkCp~C~~~~~VFShA~t~V~C~~CgtvL~~PTGGKa~l~egc~   80 (86)
T 3iz6_X            1 MVLSNDIDLLNPPAELEKLKHKKKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCPGCQTVLCQPTGGKARLTEGCS   80 (86)
T ss_dssp             --------------------------------CEEEEECTTTCCEEEEETTCSSCCCCSSSCCCCSCCCSSSCCCSCBCC
T ss_pred             CccccchhccCCCHHHHhhhhhheeeccCCCCcEeEEECCCCCCeeEEEecCCcEEEccCCCCEeecCCCCCEEecCCce
Confidence            555  458999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Cc
Q psy2574          79 GD   80 (115)
Q Consensus        79 f~   80 (115)
                      |.
T Consensus        81 fr   82 (86)
T 3iz6_X           81 FR   82 (86)
T ss_dssp             CC
T ss_pred             eE
Confidence            84

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

Probab=100.00  E-value=4.8e-35  Score=194.96  Aligned_cols=54  Identities=37%  Similarity=0.696  Sum_probs=52.5

Q ss_pred             ccccccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeec
Q psy2574          21 LKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLT   74 (115)
Q Consensus        21 ~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~   74 (115)
                      -|||||+|||||||||||+|+|+|+||||||++|.|.+||++||+||||||+|.
T Consensus         2 ~krLv~~PnS~Fm~VkCp~C~~~q~VFSha~t~V~C~~Cgt~L~~PTGGKa~l~   55 (63)
T 3j20_W            2 AKPIIPMPRSRFLRVKCIDCGNEQIVFSHPATKVRCLICGATLVEPTGGKGIVK   55 (63)
T ss_dssp             CGGGCCCCSCCEEEEECSSSCCEEEEESSCSSCEECSSSCCEEEECCSSSCEEC
T ss_pred             ccccccCCCCcEEEEECCCCCCeeEEEecCCeEEEccCcCCEEecCCCCcEEEE
Confidence            378999999999999999999999999999999999999999999999999995

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

Probab=99.96  E-value=6.7e-30  Score=171.58  Aligned_cols=48  Identities=33%  Similarity=0.797  Sum_probs=46.4

Q ss_pred             CCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeecc
Q psy2574          28 PNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTE   75 (115)
Q Consensus        28 PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~e   75 (115)
                      .||||||||||||+|+|+|||||||+|.|.+||++||+||||||+|+.
T Consensus         1 mnS~Fm~VKCp~C~niq~VFShA~tvV~C~~Cg~~L~~PTGGKA~l~~   48 (66)
T 1qxf_A            1 MHSRFVKVKCPDCEHEQVIFDHPSTIVKCIICGRTVAEPTGGKGNIKA   48 (66)
T ss_dssp             CCCCEEEEECTTTCCEEEEESSCSSCEECSSSCCEEEECCSSSCEECS
T ss_pred             CCceeEEEECCCCCCceEEEecCceEEEcccCCCEEeecCCcceeeeh
Confidence            489999999999999999999999999999999999999999999983

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

Probab=98.25  E-value=2.8e-07  Score=58.77  Aligned_cols=38  Identities=16%  Similarity=0.283  Sum_probs=35.3

Q ss_pred             CCCceeEE-eCCCCCceeEEeeecceeEEcCCCCeeeec
Q psy2574          28 PNSYFMDV-KCPGCYKITTVFSHAQSVVICAGCSTILCQ   65 (115)
Q Consensus        28 PnS~Fm~V-KCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~   65 (115)
                      .+|+|+.+ +||+|++.++||.+++..+.|..||.+|.+
T Consensus         4 ~~~~ll~~~~Cp~C~~~~lv~D~~~ge~vC~~CGlVl~e   42 (58)
T 1dl6_A            4 SRLDALPRVTCPNHPDAILVEDYRAGDMICPECGLVVGD   42 (58)
T ss_dssp             CSCCCCSCCSBTTBSSSCCEECSSSCCEECTTTCCEECC
T ss_pred             chhhccccccCcCCCCCceeEeCCCCeEEeCCCCCEEec
Confidence            37889999 999999999999999999999999999965

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

Probab=96.78  E-value=0.00069  Score=40.82  Aligned_cols=31  Identities=19%  Similarity=0.689  Sum_probs=28.4

Q ss_pred             EeCCCCCceeEEeeecceeEEcCCCCeeeec
Q psy2574          35 VKCPGCYKITTVFSHAQSVVICAGCSTILCQ   65 (115)
Q Consensus        35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~   65 (115)
                      ++||.|+..+++|..++....|..||.++.+
T Consensus         6 ~~CP~C~~~~l~~d~~~gelvC~~CG~v~~e   36 (50)
T 1pft_A            6 KVCPACESAELIYDPERGEIVCAKCGYVIEE   36 (50)
T ss_dssp             CSCTTTSCCCEEEETTTTEEEESSSCCBCCC
T ss_pred             EeCcCCCCcceEEcCCCCeEECcccCCcccc
Confidence            4799999999999999999999999999854

>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M

Probab=95.11  E-value=0.012  Score=47.53  Aligned_cols=32  Identities=28%  Similarity=0.585  Sum_probs=28.8

Q ss_pred             EEeCCCCCc--eeEEeeecceeEEcCCCCeeeec
Q psy2574          34 DVKCPGCYK--ITTVFSHAQSVVICAGCSTILCQ   65 (115)
Q Consensus        34 ~VKCp~C~n--~q~VFSHAqt~V~C~~Cg~vL~~   65 (115)
                      ..+||+|+.  ..+|+.+++....|..||.||-+
T Consensus        21 ~~~Cp~C~~~~~~lv~D~~~G~~vC~~CGlVl~e   54 (345)
T 4bbr_M           21 VLTCPECKVYPPKIVERFSEGDVVCALCGLVLSD   54 (345)
T ss_dssp             -CCCSSCCCSSCCEEEEGGGTEEEETTTCBEEES
T ss_pred             CCcCCCCCCCCCceeEECCCCcEEeCCCCCCccC
Confidence            568999996  78999999999999999999975

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}

Probab=92.97  E-value=0.018  Score=46.03  Aligned_cols=31  Identities=29%  Similarity=0.655  Sum_probs=28.3

Q ss_pred             EeCCCCCce--eEEeeecceeEEcCCCCeeeec
Q psy2574          35 VKCPGCYKI--TTVFSHAQSVVICAGCSTILCQ   65 (115)
Q Consensus        35 VKCp~C~n~--q~VFSHAqt~V~C~~Cg~vL~~   65 (115)
                      .+||.|+..  .+|+.+++-.+.|..||.||-+
T Consensus        22 ~~Cp~Cg~~~~~iv~D~~~G~~vC~~CG~Vl~e   54 (345)
T 3k7a_M           22 LTCPECKVYPPKIVERFSEGDVVCALCGLVLSD   54 (345)
T ss_dssp             CCCSTTCCSCCCCCCCSSSCSCCCSSSCCCCCC
T ss_pred             CcCcCCCCCCCceEEECCCCCEecCCCCeEccc
Confidence            579999997  6999999999999999999954

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

Probab=92.71  E-value=0.054  Score=42.45  Aligned_cols=33  Identities=27%  Similarity=0.592  Sum_probs=29.1

Q ss_pred             eEEeCCCCCc--eeEEeeecceeEEcCCCCeeeec
Q psy2574          33 MDVKCPGCYK--ITTVFSHAQSVVICAGCSTILCQ   65 (115)
Q Consensus        33 m~VKCp~C~n--~q~VFSHAqt~V~C~~Cg~vL~~   65 (115)
                      ...+||.|+.  ..+|++++.-...|..||.||-+
T Consensus        20 ~~~~CPECGs~~t~IV~D~erGE~VCsdCGLVLEE   54 (197)
T 3k1f_M           20 IVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSD   54 (197)
T ss_dssp             CCCCCTTTCCSSCCEEEEGGGTEEEETTTCBBCCC
T ss_pred             cCeECcCCCCcCCeEEEeCCCCEEEEcCCCCCcCC
Confidence            3458999998  57999999999999999999954

>1vq8_Z 50S ribosomal protein L37AE; 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: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=92.31  E-value=0.066  Score=36.26  Aligned_cols=43  Identities=19%  Similarity=0.376  Sum_probs=32.2

Q ss_pred             HhhcccccccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeee
Q psy2574          17 RKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILC   64 (115)
Q Consensus        17 ~k~K~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~   64 (115)
                      ||.-+|+.+....    +-+||.|+. ..+|..++-...|..||.+.+
T Consensus        14 Rk~vk~ie~~q~~----~y~Cp~CG~-~~v~r~atGiW~C~~Cg~~~a   56 (83)
T 1vq8_Z           14 RRRVAEIESEMNE----DHACPNCGE-DRVDRQGTGIWQCSYCDYKFT   56 (83)
T ss_dssp             HHHHHHHHHHHHS----CEECSSSCC-EEEEEEETTEEEETTTCCEEE
T ss_pred             HHHHHHHHHhccc----cCcCCCCCC-cceeccCCCeEECCCCCCEec
Confidence            3333444444443    359999998 689999999999999999873

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

Probab=91.86  E-value=0.22  Score=30.51  Aligned_cols=30  Identities=23%  Similarity=0.541  Sum_probs=24.4

Q ss_pred             eEEeCCCCCceeEEeeeccee---------EEcCCCCee
Q psy2574          33 MDVKCPGCYKITTVFSHAQSV---------VICAGCSTI   62 (115)
Q Consensus        33 m~VKCp~C~n~q~VFSHAqt~---------V~C~~Cg~v   62 (115)
                      ..++||.|++...+|...|+.         ..|..||..
T Consensus        14 ~~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~   52 (57)
T 1qyp_A           14 TKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHT   52 (57)
T ss_dssp             EECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCE
T ss_pred             eEeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCE
Confidence            479999999999999988763         577777764

>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1

Probab=90.60  E-value=0.23  Score=32.85  Aligned_cols=30  Identities=13%  Similarity=0.430  Sum_probs=24.3

Q ss_pred             eeEEeCCCCCceeEEeeecceeEEcCCCCeeee
Q psy2574          32 FMDVKCPGCYKITTVFSHAQSVVICAGCSTILC   64 (115)
Q Consensus        32 Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~   64 (115)
                      |+-|.|| |++..++=. .+-...|. ||++|-
T Consensus         2 Y~vv~C~-C~~~~~~~~-~~kT~~C~-CG~~~~   31 (71)
T 1gh9_A            2 YIIFRCD-CGRALYSRE-GAKTRKCV-CGRTVN   31 (71)
T ss_dssp             EEEEEET-TSCCEEEET-TCSEEEET-TTEEEE
T ss_pred             eEEEECC-CCCEEEEcC-CCcEEECC-CCCeee
Confidence            6789999 999976655 56678998 999984

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=89.20  E-value=0.17  Score=31.14  Aligned_cols=29  Identities=24%  Similarity=0.604  Sum_probs=23.7

Q ss_pred             EEeCCCCCceeEEeeeccee---------EEcCCCCee
Q psy2574          34 DVKCPGCYKITTVFSHAQSV---------VICAGCSTI   62 (115)
Q Consensus        34 ~VKCp~C~n~q~VFSHAqt~---------V~C~~Cg~v   62 (115)
                      +++||.|++...+|-..|+.         ..|..||..
T Consensus         9 ~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~   46 (50)
T 1tfi_A            9 LFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNR   46 (50)
T ss_dssp             CSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCE
T ss_pred             ccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCe
Confidence            57999999999999987653         788888753

>1dxg_A Desulforedoxin; non-heme iron protein, rubredoxin type metal center, electron transport; 1.80A {Desulfovibrio gigas} SCOP: g.41.5.2 PDB: 1dcd_A 1dhg_A 1cfw_A 2lk5_A 2lk6_A

Probab=86.92  E-value=0.65  Score=26.50  Aligned_cols=27  Identities=22%  Similarity=0.667  Sum_probs=21.2

Q ss_pred             EeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574          35 VKCPGCYKITTVFSHAQSVVICAGCSTIL   63 (115)
Q Consensus        35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL   63 (115)
                      -+|+.|+|+-.+..-....+.|  ||..+
T Consensus         7 Y~C~~CGnivev~~~g~~~l~C--CG~~M   33 (36)
T 1dxg_A            7 YKCELCGQVVKVLEEGGGTLVC--CGEDM   33 (36)
T ss_dssp             EECTTTCCEEEEEECCSSCEEE--TTEEC
T ss_pred             EEcCCCCcEEEEEeCCCcCEEe--CCccc
Confidence            4799999998888777777777  66655

>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1

Probab=84.72  E-value=0.8  Score=26.39  Aligned_cols=28  Identities=29%  Similarity=0.558  Sum_probs=21.8

Q ss_pred             EeCCCCCceeEEeee--cceeEEcCCCCee
Q psy2574          35 VKCPGCYKITTVFSH--AQSVVICAGCSTI   62 (115)
Q Consensus        35 VKCp~C~n~q~VFSH--Aqt~V~C~~Cg~v   62 (115)
                      |.|+.|++..+.+..  -.....|..||..
T Consensus         1 VlC~~C~~peT~l~~~~~~~~l~C~aCG~~   30 (36)
T 1k81_A            1 VICRECGKPDTKIIKEGRVHLLKCMACGAI   30 (36)
T ss_dssp             CCCSSSCSCEEEEEEETTEEEEEEETTTEE
T ss_pred             CCCcCCCCCCcEEEEeCCcEEEEhhcCCCc
Confidence            679999998887775  4556779999875

>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...

Probab=84.30  E-value=0.28  Score=32.23  Aligned_cols=33  Identities=21%  Similarity=0.530  Sum_probs=26.7

Q ss_pred             eEEeCCCCCceeEEeeecceeEEcCCCCe-eeeccc
Q psy2574          33 MDVKCPGCYKITTVFSHAQSVVICAGCST-ILCQPT   67 (115)
Q Consensus        33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~-vL~~PT   67 (115)
                      |.-+|++|+.+.-+  |....|.|..||. +|-+..
T Consensus        27 v~Y~C~~CG~~~e~--~~~d~irCp~CG~RILyK~R   60 (70)
T 1twf_L           27 LKYICAECSSKLSL--SRTDAVRCKDCGHRILLKAR   60 (70)
T ss_dssp             CCEECSSSCCEECC--CTTSTTCCSSSCCCCCBCCC
T ss_pred             EEEECCCCCCccee--CCCCCccCCCCCceEeEecC
Confidence            55689999998655  5778899999999 887664

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=82.99  E-value=0.28  Score=33.78  Aligned_cols=36  Identities=17%  Similarity=0.429  Sum_probs=27.6

Q ss_pred             eEEeCCCCCceeEEeeecceeE-EcCCCCeeeecccCCce
Q psy2574          33 MDVKCPGCYKITTVFSHAQSVV-ICAGCSTILCQPTGGRA   71 (115)
Q Consensus        33 m~VKCp~C~n~q~VFSHAqt~V-~C~~Cg~vL~~PTGGKA   71 (115)
                      ...+|.+|+++-.+   ..... .|+.||....+..+|+-
T Consensus        72 ~~~~C~~CG~~~e~---~~~~~~~CP~Cgs~~~~i~~G~e  108 (119)
T 2kdx_A           72 VELECKDCSHVFKP---NALDYGVCEKCHSKNVIITQGNE  108 (119)
T ss_dssp             CEEECSSSSCEECS---CCSTTCCCSSSSSCCCEEEESSC
T ss_pred             ceEEcCCCCCEEeC---CCCCCCcCccccCCCcEEecCCe
Confidence            36899999987544   45567 89999999877777763

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4

Probab=80.65  E-value=0.98  Score=29.47  Aligned_cols=29  Identities=21%  Similarity=0.387  Sum_probs=22.0

Q ss_pred             eCCCCCceeEEeeecceeEEcCCCCeeeec
Q psy2574          36 KCPGCYKITTVFSHAQSVVICAGCSTILCQ   65 (115)
Q Consensus        36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~   65 (115)
                      -||+|.+..+.- -.+..|.|..|+...|-
T Consensus        27 wCP~C~~~~~~~-~~~~~v~C~~C~~~FC~   55 (86)
T 2ct7_A           27 WCAQCSFGFIYE-REQLEATCPQCHQTFCV   55 (86)
T ss_dssp             CCSSSCCCEECC-CSCSCEECTTTCCEECS
T ss_pred             ECcCCCchheec-CCCCceEeCCCCCcccc
Confidence            399999976543 34677999999988763

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...

Probab=80.13  E-value=0.9  Score=31.78  Aligned_cols=33  Identities=33%  Similarity=0.724  Sum_probs=26.9

Q ss_pred             eEEeCCCCCceeEEeeeccee---------EEcCCCCeeeec
Q psy2574          33 MDVKCPGCYKITTVFSHAQSV---------VICAGCSTILCQ   65 (115)
Q Consensus        33 m~VKCp~C~n~q~VFSHAqt~---------V~C~~Cg~vL~~   65 (115)
                      .+++||.|++...+|-..|+.         ..|..||..--+
T Consensus        71 t~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~~w~~  112 (122)
T 1twf_I           71 SDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTS  112 (122)
T ss_dssp             CCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEEC
T ss_pred             cCCCCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCCEecc
Confidence            478999999999999987653         689999876544

>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A

Probab=80.04  E-value=0.91  Score=36.23  Aligned_cols=35  Identities=17%  Similarity=0.391  Sum_probs=26.1

Q ss_pred             CCCceeEEeCCCCCceeEEeeecce---------eEEcCCCCee
Q psy2574          28 PNSYFMDVKCPGCYKITTVFSHAQS---------VVICAGCSTI   62 (115)
Q Consensus        28 PnS~Fm~VKCp~C~n~q~VFSHAqt---------~V~C~~Cg~v   62 (115)
                      |+..=-.++||.|++...+|...|+         .+.|..||..
T Consensus       262 ~~~~~~~~~C~~C~~~~~~~~q~Q~rsaDe~~t~f~~C~~Cg~~  305 (309)
T 1pqv_S          262 ERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNR  305 (309)
T ss_pred             cccCcccccCCCCCCCeeEEEEeecccCCCCCcEEEEeCCCCCc
Confidence            4443235799999999999987664         4788888863

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	115
d1qxfa_	58	g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Arc	2e-25

>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 58

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

 Score = 88.3 bits (219), Expect = 2e-25
 Identities = 16/48 (33%), Positives = 26/48 (54%)

Query: 29 NSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTED 76
          +S F+ VKCP C     +F H  ++V C  C   + +PTGG+  +  +
Sbjct: 2  HSRFVKVKCPDCEHEQVIFDHPSTIVKCIICGRTVAEPTGGKGNIKAE 49

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	115
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	99.95
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	97.2
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	96.51
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	89.8
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	80.62

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

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

Probab=99.95  E-value=1.7e-29  Score=164.29  Aligned_cols=48  Identities=33%  Similarity=0.797  Sum_probs=46.1

Q ss_pred             CCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeecc
Q psy2574          28 PNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTE   75 (115)
Q Consensus        28 PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~e   75 (115)
                      .|||||+||||+|+|+|+|||||+++|.|.+||++|++||||||+|..
T Consensus         1 mnS~F~~VkC~~C~n~~ivFsha~t~V~C~~Cg~~L~~PtGGKa~i~g   48 (58)
T d1qxfa_           1 MHSRFVKVKCPDCEHEQVIFDHPSTIVKCIICGRTVAEPTGGKGNIKA   48 (58)
T ss_dssp             CCCCEEEEECTTTCCEEEEESSCSSCEECSSSCCEEEECCSSSCEECS
T ss_pred             CCceeEEeECCCCCCeEEEEecCceEEEccccCCEEeccCCCeEEEee
Confidence            389999999999999999999999999999999999999999999864

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.20  E-value=5e-05  Score=47.30  Aligned_cols=33  Identities=21%  Similarity=0.412  Sum_probs=30.4

Q ss_pred             EEeCCCCCceeEEeeecceeEEcCCCCeeeecc
Q psy2574          34 DVKCPGCYKITTVFSHAQSVVICAGCSTILCQP   66 (115)
Q Consensus        34 ~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~P   66 (115)
                      ++|||.|+...+|+.+++-.+.|..||.||-+.
T Consensus        11 ~~~Cp~Cgs~~ii~D~~~Ge~vC~~CG~Vlee~   43 (58)
T d1dl6a_          11 RVTCPNHPDAILVEDYRAGDMICPECGLVVGDR   43 (58)
T ss_dssp             CCSBTTBSSSCCEECSSSCCEECTTTCCEECCS
T ss_pred             ccCCCCCCCCCEEEECCCCcEecccCCCEeccc
Confidence            589999999999999999999999999999653

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.51  E-value=0.00069  Score=40.71  Aligned_cols=32  Identities=19%  Similarity=0.659  Sum_probs=29.3

Q ss_pred             EeCCCCCceeEEeeecceeEEcCCCCeeeecc
Q psy2574          35 VKCPGCYKITTVFSHAQSVVICAGCSTILCQP   66 (115)
Q Consensus        35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~P   66 (115)
                      .+||.|+...+|+++++-.+.|..||.||-+.
T Consensus         6 ~~Cp~Cgs~~iv~D~~~Ge~vC~~CG~Viee~   37 (50)
T d1pfta_           6 KVCPACESAELIYDPERGEIVCAKCGYVIEEN   37 (50)
T ss_dssp             CSCTTTSCCCEEEETTTTEEEESSSCCBCCCC
T ss_pred             ccCcCCCCCcEEEECCCCeEecccCCcEeccc
Confidence            47999999999999999999999999998654

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

Probab=89.80  E-value=0.12  Score=31.41  Aligned_cols=30  Identities=23%  Similarity=0.564  Sum_probs=24.9

Q ss_pred             eEEeCCCCCceeEEeeecce---------eEEcCCCCee
Q psy2574          33 MDVKCPGCYKITTVFSHAQS---------VVICAGCSTI   62 (115)
Q Consensus        33 m~VKCp~C~n~q~VFSHAqt---------~V~C~~Cg~v   62 (115)
                      .+++||.|++..++|-..|+         ...|..||..
T Consensus        14 ~~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~Cg~~   52 (57)
T d1qypa_          14 TKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHT   52 (57)
T ss_dssp             EECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCE
T ss_pred             ccCCCCCCCCCceEEEEeecccccCCCeEEEEeCCCCCc
Confidence            35799999999999987776         5788888864

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.62  E-value=0.59  Score=29.37  Aligned_cols=30  Identities=37%  Similarity=0.838  Sum_probs=24.7

Q ss_pred             EEeCCCCCceeEEeeecce---------eEEcCCCCeee
Q psy2574          34 DVKCPGCYKITTVFSHAQS---------VVICAGCSTIL   63 (115)
Q Consensus        34 ~VKCp~C~n~q~VFSHAqt---------~V~C~~Cg~vL   63 (115)
                      +.+||.|++..++|-..|+         ...|..||..-
T Consensus        23 ~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~C~h~W   61 (72)
T d1twfi2          23 DRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF   61 (72)
T ss_dssp             CCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEE
T ss_pred             CCCCCCCCCCeEEEEEeecCccCCCceEEEEcCCCCCCc
Confidence            5799999999999987776         46788887654