Psyllid ID: psy18072

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170----
Protein Sequence
MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADDDEDEEDFDNERDGDEGEDEEEGENED
Secondary Structure (PSIPRED)
cccccccccccccccccEEEEEEEEEEccEEEEEEcccccEEEEEEcHHHHHHHHccHHHHcccccEEEEEEEEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHccccEEEEcccccccccHHHHHHHHHHHHHHccHHcccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEcccccccccEEEEEEEEHHHccEEEEEEEccccccEEEHHHHHHHHHHHHHHHHHccccEEEEEEEEcccccEEEcccccccHHHHHHHHHHHHHHHHHHHccccEEEEcccccccccHHHHHHHHHHHHHHHHHHcccccccHcccccccccccccccccccccc
Coil and Loop (DISEMBL)
mplscrfyaekypevEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLirvgktepVVVIRVDkekvmttvtpeKADGLKALQEAIDTIKAKIEQLggvfqvqmapkvvtasDEAELARQMERAEAenaevaadddedeedfdnerdgdegedeeegened
Flexible Loop (DISEMBL)
mplscrfyaekypeveDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSInklirvgktepvvvirvdkekvmttvtpekadgLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEaenaevaadddedeedfdnerdgdegedeeegened
Low Complexity Region (SEG)
MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMillselsrrrirsiNKLIRVGKTEPVVVIRVDKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMeraeaenaevaadddedeedfdnerdgdegedeeegened
Disordered region (IsUnstruct)
****CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKV*****************************************************
Disordered Region (DISOPRED)
***SCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMT******************************FQVQMAPKVVTASDEAELARQM****************************************
Disordered Region (DISEMBL)
MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMER**************************************
Disordered Region (DISPRO)
*PLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVA*****************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKADGxxxxxxxxxxxxxxxxxxxxxFQVQMAPKVVTASDxxxxxxxxxxxxxxxxxxxxxxxxxxxxFDNERDGDEGEDEEEGENED
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	174	2.2.26 [Sep-21-2011]
P41374	341	Eukaryotic translation in	yes	N/A	0.454	0.231	0.898	2e-35
P05198	315	Eukaryotic translation in	yes	N/A	0.454	0.250	0.862	2e-32
Q5ZLX2	315	Eukaryotic translation in	yes	N/A	0.454	0.250	0.862	2e-32
P68101	315	Eukaryotic translation in	yes	N/A	0.454	0.250	0.862	2e-32
Q6ZWX6	315	Eukaryotic translation in	yes	N/A	0.454	0.250	0.862	2e-32
P68102	315	Eukaryotic translation in	yes	N/A	0.454	0.250	0.862	2e-32
Q5R493	315	Eukaryotic translation in	yes	N/A	0.511	0.282	0.768	2e-32
Q6GL89	315	Eukaryotic translation in	yes	N/A	0.551	0.304	0.711	1e-31
Q7ZTK4	315	Eukaryotic translation in	N/A	N/A	0.643	0.355	0.589	1e-31
P20459	304	Eukaryotic translation in	yes	N/A	0.431	0.246	0.786	6e-28

>sp|P41374|IF2A_DROME Eukaryotic translation initiation factor 2 subunit 1 OS=Drosophila melanogaster GN=eIF-2alpha PE=2 SV=1

 Score =  148 bits (374), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 71/79 (89%), Positives = 75/79 (94%)

Query: 1  MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60
          M L+ RFY E+YPE+EDVVMV V+SIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
Sbjct: 1  MALTSRFYNERYPEIEDVVMVNVLSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60

Query: 61 LIRVGKTEPVVVIRVDKEK 79
          LIRVGKTEPVVVIRVDKEK
Sbjct: 61 LIRVGKTEPVVVIRVDKEK 79

eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This preinitiation complex mediates ribosomal recognition of a start codon during the scanning process of the leader region.
Drosophila melanogaster (taxid: 7227)

>sp|P05198|IF2A_HUMAN Eukaryotic translation initiation factor 2 subunit 1 OS=Homo sapiens GN=EIF2S1 PE=1 SV=3

 Score =  138 bits (347), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 69/80 (86%), Positives = 72/80 (90%), Gaps = 1/80 (1%)

Query: 1  MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSIN 59
          MP LSCRFY  K+PEVEDVVMV V SIAEMGAYV LLEYNNIEGMILLSELSRRRIRSIN
Sbjct: 1  MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query: 60 KLIRVGKTEPVVVIRVDKEK 79
          KLIR+G+ E VVVIRVDKEK
Sbjct: 61 KLIRIGRNECVVVIRVDKEK 80

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Homo sapiens (taxid: 9606)

>sp|Q5ZLX2|IF2A_CHICK Eukaryotic translation initiation factor 2 subunit 1 OS=Gallus gallus GN=EIF2S1 PE=2 SV=2

 Score =  138 bits (347), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 69/80 (86%), Positives = 72/80 (90%), Gaps = 1/80 (1%)

Query: 1  MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSIN 59
          MP LSCRFY  K+PEVEDVVMV V SIAEMGAYV LLEYNNIEGMILLSELSRRRIRSIN
Sbjct: 1  MPALSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query: 60 KLIRVGKTEPVVVIRVDKEK 79
          KLIR+G+ E VVVIRVDKEK
Sbjct: 61 KLIRIGRNECVVVIRVDKEK 80

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Gallus gallus (taxid: 9031)

>sp|P68101|IF2A_RAT Eukaryotic translation initiation factor 2 subunit 1 OS=Rattus norvegicus GN=Eif2s1 PE=1 SV=2

 Score =  138 bits (347), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 69/80 (86%), Positives = 72/80 (90%), Gaps = 1/80 (1%)

Query: 1  MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSIN 59
          MP LSCRFY  K+PEVEDVVMV V SIAEMGAYV LLEYNNIEGMILLSELSRRRIRSIN
Sbjct: 1  MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query: 60 KLIRVGKTEPVVVIRVDKEK 79
          KLIR+G+ E VVVIRVDKEK
Sbjct: 61 KLIRIGRNECVVVIRVDKEK 80

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Rattus norvegicus (taxid: 10116)

>sp|Q6ZWX6|IF2A_MOUSE Eukaryotic translation initiation factor 2 subunit 1 OS=Mus musculus GN=Eif2s1 PE=1 SV=3

 Score =  138 bits (347), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 69/80 (86%), Positives = 72/80 (90%), Gaps = 1/80 (1%)

Query: 1  MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSIN 59
          MP LSCRFY  K+PEVEDVVMV V SIAEMGAYV LLEYNNIEGMILLSELSRRRIRSIN
Sbjct: 1  MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query: 60 KLIRVGKTEPVVVIRVDKEK 79
          KLIR+G+ E VVVIRVDKEK
Sbjct: 61 KLIRIGRNECVVVIRVDKEK 80

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Mus musculus (taxid: 10090)

>sp|P68102|IF2A_BOVIN Eukaryotic translation initiation factor 2 subunit 1 OS=Bos taurus GN=EIF2S1 PE=2 SV=2

 Score =  138 bits (347), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 69/80 (86%), Positives = 72/80 (90%), Gaps = 1/80 (1%)

Query: 1  MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSIN 59
          MP LSCRFY  K+PEVEDVVMV V SIAEMGAYV LLEYNNIEGMILLSELSRRRIRSIN
Sbjct: 1  MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query: 60 KLIRVGKTEPVVVIRVDKEK 79
          KLIR+G+ E VVVIRVDKEK
Sbjct: 61 KLIRIGRNECVVVIRVDKEK 80

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Bos taurus (taxid: 9913)

>sp|Q5R493|IF2A_PONAB Eukaryotic translation initiation factor 2 subunit 1 OS=Pongo abelii GN=EIF2S1 PE=2 SV=1

 Score =  138 bits (347), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 73/95 (76%), Positives = 78/95 (82%), Gaps = 6/95 (6%)

Query: 1  MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSIN 59
          MP LSCRFY  K+PEVEDVVMV V SIAEMGAYV LLEYNNIEGMILLSELSRRRIRSIN
Sbjct: 1  MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query: 60 KLIRVGKTEPVVVIRVDKEKVMT-----TVTPEKA 89
          KLIR+G+ E VVVIRVDKEK         V+PE+A
Sbjct: 61 KLIRIGRNERVVVIRVDKEKGYIDLSKRRVSPEEA 95

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Pongo abelii (taxid: 9601)

>sp|Q6GL89|IF2A_XENTR Eukaryotic translation initiation factor 2 subunit 1 OS=Xenopus tropicalis GN=eif2s1 PE=2 SV=1

 Score =  135 bits (340), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 69/97 (71%), Positives = 79/97 (81%), Gaps = 1/97 (1%)

Query: 1  MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSIN 59
          MP LSCRFY  K+PEV+DVVMV V SIAEMGAYV LLEYNNIEGMILLSELSRRRIRSIN
Sbjct: 1  MPALSCRFYQHKFPEVDDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query: 60 KLIRVGKTEPVVVIRVDKEKVMTTVTPEKADGLKALQ 96
          KLIR+G+ E VVVIRVDK+K    ++  +    +AL+
Sbjct: 61 KLIRIGRNECVVVIRVDKDKGYIDLSKRRVSPEEALK 97

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Xenopus tropicalis (taxid: 8364)

>sp|Q7ZTK4|IF2A_XENLA Eukaryotic translation initiation factor 2 subunit 1 OS=Xenopus laevis GN=eif2s1 PE=2 SV=1

 Score =  135 bits (340), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 79/134 (58%), Positives = 91/134 (67%), Gaps = 22/134 (16%)

Query: 1   MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSIN 59
           MP L+CRFY  K+PEV+DVVMV V SIAEMGAYV LLEYNNIEGMILLSELSRRRIRSIN
Sbjct: 1   MPGLNCRFYQHKFPEVDDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query: 60  KLIRVGKTEPVVVIRVDKEKVMT-----TVTPEKA--------------DGLKALQEAID 100
           KLIR+G+ E VVVIRVDK+K         V+PE+A                L+ + E +D
Sbjct: 61  KLIRIGRNECVVVIRVDKDKGYIDLSKRRVSPEEALKCEDKFTKSKTVYSILRHVAEVLD 120

Query: 101 TIKAKIEQLGGVFQ 114
             K   EQL  +FQ
Sbjct: 121 YTKD--EQLDSLFQ 132

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Xenopus laevis (taxid: 8355)

>sp|P20459|IF2A_YEAST Eukaryotic translation initiation factor 2 subunit alpha OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SUI2 PE=1 SV=1

 Score =  123 bits (309), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 59/75 (78%), Positives = 65/75 (86%)

Query: 5  CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRV 64
          CRFY  KYPE++D+VMV V  IAEMGAYV LLEY+NIEGMILLSELSRRRIRSI KLIRV
Sbjct: 6  CRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRV 65

Query: 65 GKTEPVVVIRVDKEK 79
          GK +  VV+RVDKEK
Sbjct: 66 GKNDVAVVLRVDKEK 80

eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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	174
389609899	331	eukaryotic translation Initiation Factor	0.436	0.229	0.974	1e-37
357616974	332	eIF2 alpha subunit [Danaus plexippus]	0.436	0.228	0.962	5e-37
112984362	332	eukaryotic translation initiation factor	0.419	0.219	0.962	7e-37
27462592	331	eIF2 alpha subunit [Spodoptera frugiperd	0.436	0.229	0.962	7e-37
242022826	343	eukaryotic translation initiation factor	0.385	0.195	0.936	7e-36
307214990	300	Eukaryotic translation initiation factor	0.431	0.25	0.949	1e-35
156553998	334	PREDICTED: eukaryotic translation initia	0.442	0.230	0.949	1e-35
307167216	347	Eukaryotic translation initiation factor	0.448	0.224	0.949	1e-35
383864031	334	PREDICTED: eukaryotic translation initia	0.448	0.233	0.949	1e-35
340717144	334	PREDICTED: eukaryotic translation initia	0.448	0.233	0.949	1e-35

>gi|389609899|dbj|BAM18561.1| eukaryotic translation Initiation Factor 2alpha [Papilio xuthus]

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 77/79 (97%), Positives = 77/79 (97%)

Query: 1  MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60
          MPLSCRFY EKYPEVEDVVMVTV SIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
Sbjct: 1  MPLSCRFYQEKYPEVEDVVMVTVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60

Query: 61 LIRVGKTEPVVVIRVDKEK 79
          LIRVGKTEPVVVIRVDKEK
Sbjct: 61 LIRVGKTEPVVVIRVDKEK 79

Source: Papilio xuthus

Species: Papilio xuthus

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357616974|gb|EHJ70512.1| eIF2 alpha subunit [Danaus plexippus]

 Score =  159 bits (401), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 76/79 (96%), Positives = 76/79 (96%)

Query: 1  MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60
          MPLSCRFY EKYPEVEDVVMV V SIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
Sbjct: 1  MPLSCRFYQEKYPEVEDVVMVNVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60

Query: 61 LIRVGKTEPVVVIRVDKEK 79
          LIRVGKTEPVVVIRVDKEK
Sbjct: 61 LIRVGKTEPVVVIRVDKEK 79

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|112984362|ref|NP_001037516.1| eukaryotic translation initiation factor 2 alpha subunit [Bombyx mori] gi|66736329|gb|AAY54260.1| eukaryotic translation initiation factor 2 alpha subunit [Bombyx mori]

 Score =  158 bits (400), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 76/79 (96%), Positives = 76/79 (96%)

Query: 1  MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60
          MPLSCRFY EKYPEVEDVVMV V SIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
Sbjct: 1  MPLSCRFYQEKYPEVEDVVMVNVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60

Query: 61 LIRVGKTEPVVVIRVDKEK 79
          LIRVGKTEPVVVIRVDKEK
Sbjct: 61 LIRVGKTEPVVVIRVDKEK 79

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|27462592|gb|AAO15491.1|AF447395_1 eIF2 alpha subunit [Spodoptera frugiperda]

 Score =  158 bits (400), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 76/79 (96%), Positives = 76/79 (96%)

Query: 1  MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60
          MPLSCRFY EKYPEVEDVVMV V SIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
Sbjct: 1  MPLSCRFYQEKYPEVEDVVMVNVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60

Query: 61 LIRVGKTEPVVVIRVDKEK 79
          LIRVGKTEPVVVIRVDKEK
Sbjct: 61 LIRVGKTEPVVVIRVDKEK 79

Source: Spodoptera frugiperda

Species: Spodoptera frugiperda

Genus: Spodoptera

Family: Noctuidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242022826|ref|XP_002431839.1| eukaryotic translation initiation factor 2 subunit alpha, putative [Pediculus humanus corporis] gi|212517171|gb|EEB19101.1| eukaryotic translation initiation factor 2 subunit alpha, putative [Pediculus humanus corporis]

 Score =  155 bits (391), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 74/79 (93%), Positives = 76/79 (96%)

Query: 1  MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60
          MPLSCRFY EKYPEV+DVVMV V SIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
Sbjct: 1  MPLSCRFYNEKYPEVDDVVMVNVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60

Query: 61 LIRVGKTEPVVVIRVDKEK 79
          LIRVGKTEPVVVIRVDK+K
Sbjct: 61 LIRVGKTEPVVVIRVDKDK 79

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307214990|gb|EFN89835.1| Eukaryotic translation initiation factor 2 subunit 1 [Harpegnathos saltator]

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 75/79 (94%), Positives = 75/79 (94%)

Query: 1  MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60
          M LSCRFY EKYPEVEDVVMV V SIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
Sbjct: 1  MVLSCRFYKEKYPEVEDVVMVNVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60

Query: 61 LIRVGKTEPVVVIRVDKEK 79
          LIRVGKTEPVVVIRVDKEK
Sbjct: 61 LIRVGKTEPVVVIRVDKEK 79

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156553998|ref|XP_001603365.1| PREDICTED: eukaryotic translation initiation factor 2 subunit 1-like [Nasonia vitripennis]

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 75/79 (94%), Positives = 75/79 (94%)

Query: 1  MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60
          M LSCRFY EKYPEVEDVVMV V SIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
Sbjct: 1  MVLSCRFYKEKYPEVEDVVMVNVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60

Query: 61 LIRVGKTEPVVVIRVDKEK 79
          LIRVGKTEPVVVIRVDKEK
Sbjct: 61 LIRVGKTEPVVVIRVDKEK 79

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307167216|gb|EFN60920.1| Eukaryotic translation initiation factor 2 subunit 1 [Camponotus floridanus]

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 75/79 (94%), Positives = 75/79 (94%)

Query: 1  MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60
          M LSCRFY EKYPEVEDVVMV V SIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
Sbjct: 1  MVLSCRFYKEKYPEVEDVVMVNVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60

Query: 61 LIRVGKTEPVVVIRVDKEK 79
          LIRVGKTEPVVVIRVDKEK
Sbjct: 61 LIRVGKTEPVVVIRVDKEK 79

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383864031|ref|XP_003707483.1| PREDICTED: eukaryotic translation initiation factor 2 subunit 1-like [Megachile rotundata]

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 75/79 (94%), Positives = 75/79 (94%)

Query: 1  MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60
          M LSCRFY EKYPEVEDVVMV V SIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
Sbjct: 1  MVLSCRFYKEKYPEVEDVVMVNVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60

Query: 61 LIRVGKTEPVVVIRVDKEK 79
          LIRVGKTEPVVVIRVDKEK
Sbjct: 61 LIRVGKTEPVVVIRVDKEK 79

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340717144|ref|XP_003397047.1| PREDICTED: eukaryotic translation initiation factor 2 subunit 1-like [Bombus terrestris]

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 75/79 (94%), Positives = 75/79 (94%)

Query: 1  MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60
          M LSCRFY EKYPEVEDVVMV V SIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
Sbjct: 1  MVLSCRFYKEKYPEVEDVVMVNVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60

Query: 61 LIRVGKTEPVVVIRVDKEK 79
          LIRVGKTEPVVVIRVDKEK
Sbjct: 61 LIRVGKTEPVVVIRVDKEK 79

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

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	174
FB|FBgn0261609	341	eIF-2alpha "eukaryotic transla	0.454	0.231	0.721	1.9e-39
UNIPROTKB|Q5R493	315	EIF2S1 "Eukaryotic translation	0.454	0.250	0.687	1.9e-37
UNIPROTKB|P05198	315	EIF2S1 "Eukaryotic translation	0.454	0.250	0.687	2.4e-37
UNIPROTKB|Q5ZLX2	315	EIF2S1 "Eukaryotic translation	0.454	0.250	0.687	5.1e-37
ZFIN|ZDB-GENE-030131-283	315	eif2s1b "eukaryotic translatio	0.454	0.250	0.675	7.2e-36
ZFIN|ZDB-GENE-030131-526	315	eif2s1a "eukaryotic translatio	0.454	0.250	0.662	1.5e-35
UNIPROTKB|G3V4T5	273	EIF2S1 "Eukaryotic translation	0.454	0.289	0.687	7.7e-31
CGD|CAL0000442	300	SUI2 [Candida albicans (taxid:	0.436	0.253	0.618	2.5e-28
SGD|S000003767	304	SUI2 "Alpha subunit of the tra	0.431	0.246	0.6	3.2e-28
ASPGD|ASPL0000040948	308	AN3156 [Emericella nidulans (t	0.436	0.246	0.578	6.6e-28

FB|FBgn0261609 eIF-2alpha "eukaryotic translation Initiation Factor 2alpha" [Drosophila melanogaster (taxid:7227)]

 Score = 281 (104.0 bits), Expect = 1.9e-39, Sum P(2) = 1.9e-39
 Identities = 57/79 (72%), Positives = 61/79 (77%)

Query:     1 MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXNK 60
             M L+ RFY E+YPE+EDVVMV V+SIAEMGAYVHLLEYNNIEGM              NK
Sbjct:     1 MALTSRFYNERYPEIEDVVMVNVLSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60

Query:    61 LIRVGKTEPVVVIRVDKEK 79
             LIRVGKTEPVVVIRVDKEK
Sbjct:    61 LIRVGKTEPVVVIRVDKEK 79

GO:0003743 "translation initiation factor activity" evidence=IGI;ISS;NAS

GO:0005829 "cytosol" evidence=ISS

GO:0006413 "translational initiation" evidence=ISS

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=ISS;NAS

GO:0005525 "GTP binding" evidence=NAS

GO:0000049 "tRNA binding" evidence=NAS

GO:0001677 "formation of translation initiation ternary complex" evidence=NAS

GO:0005851 "eukaryotic translation initiation factor 2B complex" evidence=ISS

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0000022 "mitotic spindle elongation" evidence=IMP

GO:0005875 "microtubule associated complex" evidence=IDA

UNIPROTKB|Q5R493 EIF2S1 "Eukaryotic translation initiation factor 2 subunit 1" [Pongo abelii (taxid:9601)]

 Score = 257 (95.5 bits), Expect = 1.9e-37, Sum P(2) = 1.9e-37
 Identities = 55/80 (68%), Positives = 58/80 (72%)

Query:     1 MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXN 59
             MP LSCRFY  K+PEVEDVVMV V SIAEMGAYV LLEYNNIEGM              N
Sbjct:     1 MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query:    60 KLIRVGKTEPVVVIRVDKEK 79
             KLIR+G+ E VVVIRVDKEK
Sbjct:    61 KLIRIGRNERVVVIRVDKEK 80

GO:0010494 "cytoplasmic stress granule" evidence=ISS

UNIPROTKB|P05198 EIF2S1 "Eukaryotic translation initiation factor 2 subunit 1" [Homo sapiens (taxid:9606)]

 Score = 256 (95.2 bits), Expect = 2.4e-37, Sum P(2) = 2.4e-37
 Identities = 55/80 (68%), Positives = 58/80 (72%)

Query:     1 MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXN 59
             MP LSCRFY  K+PEVEDVVMV V SIAEMGAYV LLEYNNIEGM              N
Sbjct:     1 MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query:    60 KLIRVGKTEPVVVIRVDKEK 79
             KLIR+G+ E VVVIRVDKEK
Sbjct:    61 KLIRIGRNECVVVIRVDKEK 80

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0043558 "regulation of translational initiation in response to stress" evidence=IEA

GO:0046777 "protein autophosphorylation" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005851 "eukaryotic translation initiation factor 2B complex" evidence=IDA

GO:0003743 "translation initiation factor activity" evidence=IDA

GO:0043022 "ribosome binding" evidence=IDA

GO:0010494 "cytoplasmic stress granule" evidence=ISS

GO:0005844 "polysome" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0006987 "activation of signaling protein activity involved in unfolded protein response" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0030968 "endoplasmic reticulum unfolded protein response" evidence=TAS

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

UNIPROTKB|Q5ZLX2 EIF2S1 "Eukaryotic translation initiation factor 2 subunit 1" [Gallus gallus (taxid:9031)]

 Score = 256 (95.2 bits), Expect = 5.1e-37, Sum P(2) = 5.1e-37
 Identities = 55/80 (68%), Positives = 58/80 (72%)

Query:     1 MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXN 59
             MP LSCRFY  K+PEVEDVVMV V SIAEMGAYV LLEYNNIEGM              N
Sbjct:     1 MPALSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query:    60 KLIRVGKTEPVVVIRVDKEK 79
             KLIR+G+ E VVVIRVDKEK
Sbjct:    61 KLIRIGRNECVVVIRVDKEK 80

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005851 "eukaryotic translation initiation factor 2B complex" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0043022 "ribosome binding" evidence=IEA

GO:0043558 "regulation of translational initiation in response to stress" evidence=IEA

GO:0046777 "protein autophosphorylation" evidence=IEA

ZFIN|ZDB-GENE-030131-283 eif2s1b "eukaryotic translation initiation factor 2, subunit 1 alpha b" [Danio rerio (taxid:7955)]

 Score = 253 (94.1 bits), Expect = 7.2e-36, Sum P(2) = 7.2e-36
 Identities = 54/80 (67%), Positives = 58/80 (72%)

Query:     1 MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXN 59
             MP LSCRFY  ++PEVEDVVMV V SIAEMGAYV LLEYNNIEGM              N
Sbjct:     1 MPGLSCRFYQHRFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query:    60 KLIRVGKTEPVVVIRVDKEK 79
             KLIR+G+ E VVVIRVDKEK
Sbjct:    61 KLIRIGRNECVVVIRVDKEK 80

GO:0003723 "RNA binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA

GO:0006413 "translational initiation" evidence=IEA

ZFIN|ZDB-GENE-030131-526 eif2s1a "eukaryotic translation initiation factor 2, subunit 1 alpha a" [Danio rerio (taxid:7955)]

 Score = 243 (90.6 bits), Expect = 1.5e-35, Sum P(2) = 1.5e-35
 Identities = 53/80 (66%), Positives = 57/80 (71%)

Query:     1 MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXN 59
             MP LS RFY  ++PEVEDVVMV V SIAEMGAYV LLEYNNIEGM              N
Sbjct:     1 MPALSSRFYQHRFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query:    60 KLIRVGKTEPVVVIRVDKEK 79
             KLIR+G+ E VVVIRVDKEK
Sbjct:    61 KLIRIGRNECVVVIRVDKEK 80

GO:0003723 "RNA binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA

GO:0006413 "translational initiation" evidence=IEA

UNIPROTKB|G3V4T5 EIF2S1 "Eukaryotic translation initiation factor 2 subunit 1" [Homo sapiens (taxid:9606)]

 Score = 256 (95.2 bits), Expect = 7.7e-31, Sum P(2) = 7.7e-31
 Identities = 55/80 (68%), Positives = 58/80 (72%)

Query:     1 MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXN 59
             MP LSCRFY  K+PEVEDVVMV V SIAEMGAYV LLEYNNIEGM              N
Sbjct:     1 MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN 60

Query:    60 KLIRVGKTEPVVVIRVDKEK 79
             KLIR+G+ E VVVIRVDKEK
Sbjct:    61 KLIRIGRNECVVVIRVDKEK 80

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0043558 "regulation of translational initiation in response to stress" evidence=IEA

GO:0046777 "protein autophosphorylation" evidence=IEA

CGD|CAL0000442 SUI2 [Candida albicans (taxid:5476)]

 Score = 227 (85.0 bits), Expect = 2.5e-28, Sum P(2) = 2.5e-28
 Identities = 47/76 (61%), Positives = 52/76 (68%)

Query:     4 SCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXNKLIR 63
             +CRFY  KYPEV++VVMV V  IAEMGAYV LLEY+NIEGM               KLIR
Sbjct:     5 NCRFYENKYPEVDEVVMVNVQEIAEMGAYVKLLEYDNIEGMVLLSELSRRRIRSIQKLIR 64

Query:    64 VGKTEPVVVIRVDKEK 79
             VGK E  VV+RVDKEK
Sbjct:    65 VGKNEVAVVLRVDKEK 80

GO:0043614 "multi-eIF complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA

GO:0043561 "regulation of translational initiation in response to osmotic stress" evidence=IEA

GO:0007093 "mitotic cell cycle checkpoint" evidence=IEA

SGD|S000003767 SUI2 "Alpha subunit of the translation initiation factor eIF2" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 225 (84.3 bits), Expect = 3.2e-28, Sum P(2) = 3.2e-28
 Identities = 45/75 (60%), Positives = 51/75 (68%)

Query:     5 CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXNKLIRV 64
             CRFY  KYPE++D+VMV V  IAEMGAYV LLEY+NIEGM               KLIRV
Sbjct:     6 CRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRV 65

Query:    65 GKTEPVVVIRVDKEK 79
             GK +  VV+RVDKEK
Sbjct:    66 GKNDVAVVLRVDKEK 80

GO:0043614 "multi-eIF complex" evidence=IDA

GO:0005840 "ribosome" evidence=TAS

GO:0003723 "RNA binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA;TAS

GO:0006412 "translation" evidence=IEA

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA;ISS;IMP

GO:0006413 "translational initiation" evidence=IEA;TAS

GO:0005737 "cytoplasm" evidence=IDA

ASPGD|ASPL0000040948 AN3156 [Emericella nidulans (taxid:162425)]

 Score = 221 (82.9 bits), Expect = 6.6e-28, Sum P(2) = 6.6e-28
 Identities = 44/76 (57%), Positives = 52/76 (68%)

Query:     4 SCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXNKLIR 63
             +CRFY EKYPEV+  VMV V  IAEMGAYV LLEY+NI+GM               KLIR
Sbjct:     5 NCRFYEEKYPEVDSYVMVNVKQIAEMGAYVKLLEYDNIDGMILLSELSRRRIRSIQKLIR 64

Query:    64 VGKTEPVVVIRVDKEK 79
             +G+ E V+V+RVDKEK
Sbjct:    65 IGRNEVVIVLRVDKEK 80

GO:0007093 "mitotic cell cycle checkpoint" evidence=IEA

GO:0043561 "regulation of translational initiation in response to osmotic stress" evidence=IEA

GO:0043614 "multi-eIF complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0003743 "translation initiation factor activity" 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)
Q869N9	IF2A_DICDI	No assigned EC number	0.7466	0.4310	0.2199	yes	N/A
Q5ZLX2	IF2A_CHICK	No assigned EC number	0.8625	0.4540	0.2507	yes	N/A
P20459	IF2A_YEAST	No assigned EC number	0.7866	0.4310	0.2467	yes	N/A
P56286	IF2A_SCHPO	No assigned EC number	0.6973	0.4367	0.2483	yes	N/A
P41374	IF2A_DROME	No assigned EC number	0.8987	0.4540	0.2316	yes	N/A
Q6ZWX6	IF2A_MOUSE	No assigned EC number	0.8625	0.4540	0.2507	yes	N/A
Q5R493	IF2A_PONAB	No assigned EC number	0.7684	0.5114	0.2825	yes	N/A
P68101	IF2A_RAT	No assigned EC number	0.8625	0.4540	0.2507	yes	N/A
P68102	IF2A_BOVIN	No assigned EC number	0.8625	0.4540	0.2507	yes	N/A
P05198	IF2A_HUMAN	No assigned EC number	0.8625	0.4540	0.2507	yes	N/A
Q6GL89	IF2A_XENTR	No assigned EC number	0.7113	0.5517	0.3047	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	174
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	7e-36
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	1e-33
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	3e-23
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	7e-13
PRK03987	262	PRK03987, PRK03987, translation initiation factor	5e-12
pfam00575	74	pfam00575, S1, S1 RNA binding domain	8e-12
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	8e-11
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	4e-07
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	4e-06
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	6e-06
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	7e-06
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	3e-05
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	4e-05
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	6e-05
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	7e-05
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	8e-05
cd05698	70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	2e-04
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	3e-04
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	4e-04
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	8e-04
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	0.002
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	0.003
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	0.003
cd05708	77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	0.003
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	0.004

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score =  126 bits (318), Expect = 7e-36
 Identities = 57/77 (74%), Positives = 68/77 (88%)

Query: 3  LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLI 62
          L CRFY +K+PE +D+VMV V+ I EMGAYV LLEY++IEGMIL+SELS+RRIRSINKLI
Sbjct: 5  LDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLI 64

Query: 63 RVGKTEPVVVIRVDKEK 79
          RVG+ E VVV+RVDKEK
Sbjct: 65 RVGRHEVVVVLRVDKEK 81

Length = 319

>gnl|CDD|239899 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

 Score =  113 bits (286), Expect = 1e-33
 Identities = 51/67 (76%), Positives = 58/67 (86%)

Query: 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
          PE  ++V+VTV SIA+MGAYV LLEY NIEGMILLSELSRRRIRSI KL++VG+ E V V
Sbjct: 1  PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKV 60

Query: 73 IRVDKEK 79
          IRVDKEK
Sbjct: 61 IRVDKEK 67

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein. Length = 76

>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

 Score = 92.4 bits (230), Expect = 3e-23
 Identities = 26/75 (34%), Positives = 44/75 (58%)

Query: 5  CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRV 64
           R    +YPE  ++V+ TV  +A+ GAYV L EY   EG I +SE++   +++I   ++ 
Sbjct: 1  MRMKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKE 60

Query: 65 GKTEPVVVIRVDKEK 79
          G+     V+RVD ++
Sbjct: 61 GQKVVAKVLRVDPKR 75

Length = 269

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 64.7 bits (158), Expect = 7e-13
 Identities = 33/91 (36%), Positives = 54/91 (59%), Gaps = 5/91 (5%)

Query: 80  VMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEA 139
           V+ T   +K  G++ +  A++ IK  I++ GG F+V+  P+VV   DE +L   +E+AE 
Sbjct: 230 VIVTTCSDKDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGG-DEEDLEELLEKAEE 288

Query: 140 ENAEV----AADDDEDEEDFDNERDGDEGED 166
           E  E     + D+DE++ED + E D DEG+ 
Sbjct: 289 EEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319

Length = 319

>gnl|CDD|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha; Validated

 Score = 61.8 bits (151), Expect = 5e-12
 Identities = 24/70 (34%), Positives = 42/70 (60%)

Query: 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEP 69
          +++PE  ++V+ TV  + + GA+V L EY   EG I +SE++   +++I   ++ G+   
Sbjct: 3  KEWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVV 62

Query: 70 VVVIRVDKEK 79
            VIRVD  K
Sbjct: 63 CKVIRVDPRK 72

Length = 262

>gnl|CDD|216000 pfam00575, S1, S1 RNA binding domain

 Score = 57.7 bits (140), Expect = 8e-12
 Identities = 27/68 (39%), Positives = 42/68 (61%), Gaps = 2/68 (2%)

Query: 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71
           PE  DVV  TV  + + GA+V L   N +EG I +SE+S  R+   +++++VG    V 
Sbjct: 1  KPEEGDVVKGTVTRVTKGGAFVDLG--NGVEGFIPISEISDDRVEDPDEVLKVGDEVEVK 58

Query: 72 VIRVDKEK 79
          V++VDKE+
Sbjct: 59 VLKVDKER 66

The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Length = 74

>gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain

 Score = 54.9 bits (133), Expect = 8e-11
 Identities = 29/66 (43%), Positives = 42/66 (63%), Gaps = 2/66 (3%)

Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
          EV DVV  TV  I   GA+V L   N +EG+I +SELS +R++   ++++VG    V V+
Sbjct: 1  EVGDVVEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVL 58

Query: 74 RVDKEK 79
           VD+EK
Sbjct: 59 SVDEEK 64

Length = 72

>gnl|CDD|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain

 Score = 45.1 bits (107), Expect = 4e-07
 Identities = 21/61 (34%), Positives = 37/61 (60%), Gaps = 2/61 (3%)

Query: 19 VMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE 78
          V   V+SI + G +V L +   +EG++ +SELS + ++  +++ +VG    V V+ VD E
Sbjct: 1  VTGKVVSITKFGVFVELED--GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPE 58

Query: 79 K 79
          K
Sbjct: 59 K 59

Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold. Length = 65

>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 45.3 bits (108), Expect = 4e-06
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 3/71 (4%)

Query: 9   AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTE 68
            EKYP V  +V+  V+ IA  GA+V L     ++G++ +S++S +RI     ++  G+  
Sbjct: 557 EEKYP-VGSIVLGKVVRIAPFGAFVELEP--GVDGLVHISQISWKRIDKPEDVLSEGEEV 613

Query: 69  PVVVIRVDKEK 79
              ++ VD E+
Sbjct: 614 KAKILEVDPEE 624

Length = 647

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 44.8 bits (107), Expect = 6e-06
 Identities = 26/72 (36%), Positives = 45/72 (62%), Gaps = 4/72 (5%)

Query: 9   AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS-RRRIRSINKLIRVGKT 67
            +KYP V   V   V +I + GA+V L E   IEG++ +SE+S  ++ +  +K++ VG+ 
Sbjct: 281 EKKYP-VGSKVKGKVTNITDYGAFVELEE--GIEGLVHVSEMSWTKKNKHPSKVVSVGQE 337

Query: 68  EPVVVIRVDKEK 79
             V+V+ +D+EK
Sbjct: 338 VEVMVLEIDEEK 349

Length = 565

>gnl|CDD|240193 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

 Score = 41.5 bits (98), Expect = 7e-06
 Identities = 22/65 (33%), Positives = 41/65 (63%), Gaps = 3/65 (4%)

Query: 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74
            DVV  TV SI + GA+V L     ++G++ +S++S  R++  ++++ VG    V V++
Sbjct: 1  EGDVVEGTVKSITDFGAFVDL---GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLK 57

Query: 75 VDKEK 79
          +DKE+
Sbjct: 58 IDKER 62

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 68

>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 43.3 bits (103), Expect = 3e-05
 Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 13  PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
           PEV  +    V+ I + GA+V +L     +G++ +SE++  R+  +  +++ G    V V
Sbjct: 616 PEVGKIYEGKVVRIMDFGAFVEIL--PGKDGLVHISEIANERVEKVEDVLKEGDEVKVKV 673

Query: 73  IRVDK 77
           + +DK
Sbjct: 674 LEIDK 678

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family) [Transcription, Degradation of RNA]. Length = 684

>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 42.3 bits (101), Expect = 4e-05
 Identities = 18/65 (27%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 13  PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
           PEV ++    V+ I + GA+V +L     +G++ +SE++  R+  +  +++ G    V V
Sbjct: 619 PEVGEIYEGKVVRIVDFGAFVEIL--PGKDGLVHISEIADERVEKVEDVLKEGDEVKVKV 676

Query: 73  IRVDK 77
           + +DK
Sbjct: 677 LEIDK 681

Length = 693

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 41.9 bits (99), Expect = 6e-05
 Identities = 21/66 (31%), Positives = 42/66 (63%), Gaps = 3/66 (4%)

Query: 14  EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
           EV +VV   V +I + GA+V +     ++G++ +SE+S +R+   +++++VG    V VI
Sbjct: 191 EVGEVVEGVVKNITDYGAFVDI---GGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVI 247

Query: 74  RVDKEK 79
            +D+E+
Sbjct: 248 SLDEER 253

Length = 541

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 41.7 bits (99), Expect = 7e-05
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 3/72 (4%)

Query: 8   YAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKT 67
           +A+K+     +V  TV  + + GA+V L   + +EG+I  SELSR R+    ++++VG  
Sbjct: 454 FAKKHK-KGSIVTGTVTEVKDKGAFVEL--EDGVEGLIRASELSRDRVEDATEVLKVGDE 510

Query: 68  EPVVVIRVDKEK 79
               VI +D++ 
Sbjct: 511 VEAKVINIDRKN 522

Length = 565

>gnl|CDD|239918 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

 Score = 38.7 bits (91), Expect = 8e-05
 Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 2/56 (3%)

Query: 22 TVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK 77
           V+ I + GA+V +L     +G++ +SELS  R+  +  +++VG    V VI VD 
Sbjct: 7  KVVKIKDFGAFVEILP--GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD 60

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo. Length = 68

>gnl|CDD|240203 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 22 TVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVM 81
          T++ +   G  V    YNN++G +  SELS   I+   +  RVG+   V V+  D E+  
Sbjct: 7  TIVKVKPNGCIVSF--YNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQR 64

Query: 82 TTVT 85
            ++
Sbjct: 65 LLLS 68

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Length = 70

>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 28/101 (27%), Positives = 54/101 (53%), Gaps = 7/101 (6%)

Query: 14  EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
           EV DVV   V+ + +   +V++  Y  +EG+I +SELS   I  IN +++VG    V V+
Sbjct: 16  EVGDVVTGEVLKVEDKQVFVNIEGYK-VEGVIPISELSNDHIEDINDVVKVGDELEVYVL 74

Query: 74  RVDKEKVMTTVTPEKADGLKA---LQEAID---TIKAKIEQ 108
           +V+  +    ++  + +  KA   L+E  +    ++ K+ +
Sbjct: 75  KVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTE 115

Length = 390

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 39.4 bits (93), Expect = 4e-04
 Identities = 28/72 (38%), Positives = 42/72 (58%), Gaps = 4/72 (5%)

Query: 9   AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS-RRRIRSINKLIRVGKT 67
           AEKYP V DVV   V +I + GA+V L     I+G++ LS++S  ++     +L + G  
Sbjct: 368 AEKYP-VGDVVEGKVKNITDFGAFVGLEG--GIDGLVHLSDISWDKKGEEAVELYKKGDE 424

Query: 68  EPVVVIRVDKEK 79
              VV++VD EK
Sbjct: 425 VEAVVLKVDVEK 436

Length = 565

>gnl|CDD|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

 Score = 36.1 bits (84), Expect = 8e-04
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 17 DVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76
           VV  TV  +   GA+V L     I G++ +S+++ +R++ +  +++ G    V V+ +D
Sbjct: 2  SVVEGTVTRLKPFGAFVELG--GGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59

Query: 77 KEK 79
             
Sbjct: 60 ARG 62

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 69

>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 31/107 (28%), Positives = 55/107 (51%), Gaps = 16/107 (14%)

Query: 10  EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNI----EGMILLSELSRRRIRSINKLIRVG 65
           EK     D+V  TV+S+ E   +V      ++    EG+I L EL+   I S+ + ++VG
Sbjct: 297 EKQIRRGDIVKGTVVSVNENEVFV------DVGYKSEGVIPLRELTLDEISSLKESVKVG 350

Query: 66  KTEPVVVIRVDKEKVMTTVTPEKADGLKA---LQEAID---TIKAKI 106
               V V++++ E     ++ ++AD  KA   L+EA +    +K K+
Sbjct: 351 DEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKV 397

Length = 647

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 3/71 (4%)

Query: 9   AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTE 68
            +KYP V D V   V ++ + GA+V +     +EG++ +SE+S  +    +++++VG+  
Sbjct: 272 EKKYP-VGDKVEGKVTNLTDYGAFVEI--EEGVEGLVHVSEISWTKKNVPSEVVKVGQEV 328

Query: 69  PVVVIRVDKEK 79
            V V+ +D E+
Sbjct: 329 EVKVLDIDPER 339

Length = 541

>gnl|CDD|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 17  DVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76
           DVV  TV  +A  GA+V L     +EGM+ +SELS  R++  ++ + VG T  V V+ ++
Sbjct: 204 DVVEGTVTRLAPFGAFVELAP--GVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIE 261

Query: 77  KEK 79
           + K
Sbjct: 262 RAK 264

Length = 491

>gnl|CDD|240213 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
          +V   +  TV  + + G ++ + +  N+ G+   SE+S  R+   +KL RVG      V+
Sbjct: 1  KVGQKIDGTVRRVEDYGVFIDI-DGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVL 59

Query: 74 RVDKEK 79
          ++D EK
Sbjct: 60 KIDAEK 65

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Length = 77

>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 21/65 (32%), Positives = 38/65 (58%), Gaps = 2/65 (3%)

Query: 13  PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
            EV +V   TV+ I + GA+V LL     +G++ +S+L++ R+  +  +++ G    V V
Sbjct: 617 VEVGEVYEGTVVRIVDFGAFVELL--PGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKV 674

Query: 73  IRVDK 77
           I +DK
Sbjct: 675 IEIDK 679

Length = 692

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	174
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	100.0
KOG2916|consensus	304		99.96
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.85
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	99.85
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.77
PRK03987	262	translation initiation factor IF-2 subunit alpha;	99.69
PHA02945	88	interferon resistance protein; Provisional	99.63
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.62
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.61
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.6
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.58
PRK08582	139	hypothetical protein; Provisional	99.56
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.56
PRK08059	123	general stress protein 13; Validated	99.54
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.53
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.52
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.52
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.51
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.51
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.51
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.51
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.51
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.5
PRK05807	136	hypothetical protein; Provisional	99.5
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.49
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.47
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.47
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.46
PRK07252	120	hypothetical protein; Provisional	99.46
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	99.46
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.45
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.42
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.42
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	99.42
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.41
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.4
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	99.39
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.37
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	99.36
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	99.36
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.36
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.35
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.35
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	99.35
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.34
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	99.34
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.33
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.32
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.29
PRK07400	318	30S ribosomal protein S1; Reviewed	99.29
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	99.28
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	99.28
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.26
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.25
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	99.24
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	99.23
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.22
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	99.2
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	99.19
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	99.19
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.19
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	99.15
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	99.13
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.1
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	99.09
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.06
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.05
PRK07400	318	30S ribosomal protein S1; Reviewed	99.05
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.04
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.0
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.0
COG2183	780	Tex Transcriptional accessory protein [Transcripti	98.99
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	98.98
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.93
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.89
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	98.88
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	98.88
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.86
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	98.82
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	98.81
PRK11642	813	exoribonuclease R; Provisional	98.79
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.79
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.78
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	98.74
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.74
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	98.66
KOG1067|consensus	760		98.53
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.48
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	98.38
PRK05054	644	exoribonuclease II; Provisional	98.34
KOG1070|consensus	1710		98.3
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	98.25
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.19
TIGR01953	341	NusA transcription termination factor NusA. This m	98.19
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	98.08
COG0557	706	VacB Exoribonuclease R [Transcription]	98.05
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	98.01
KOG1070|consensus	1710		97.8
KOG3409|consensus	193		97.78
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.66
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.53
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.53
KOG1856|consensus	1299		97.52
PRK11712	489	ribonuclease G; Provisional	97.47
PRK12329	449	nusA transcription elongation factor NusA; Provisi	97.42
PRK10811	1068	rne ribonuclease E; Reviewed	97.23
KOG3013|consensus	301		96.56
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	96.42
KOG3298|consensus	170		95.66
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	94.02
KOG1004|consensus	230		92.86
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	92.33
PRK15464	70	cold shock-like protein CspH; Provisional	89.95
PRK15463	70	cold shock-like protein CspF; Provisional	89.06
TIGR00008	68	infA translation initiation factor IF-1. This fami	88.79
PRK12442	87	translation initiation factor IF-1; Reviewed	88.15
PRK09890	70	cold shock protein CspG; Provisional	87.35
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	87.3
cd04322	108	LysRS_N LysRS_N: N-terminal, anticodon recognition	86.61
PF04871	136	Uso1_p115_C: Uso1 / p115 like vesicle tethering pr	86.48
TIGR00638	69	Mop molybdenum-pterin binding domain. This model d	85.58
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	84.56
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	84.52
PRK10354	70	RNA chaperone/anti-terminator; Provisional	84.22
PRK09507	69	cspE cold shock protein CspE; Reviewed	82.33
PRK10943	69	cold shock-like protein CspC; Provisional	82.05
PRK09937	74	stationary phase/starvation inducible regulatory p	80.64

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=100.00  E-value=2.9e-32  Score=233.22  Aligned_cols=153  Identities=53%  Similarity=0.853  Sum_probs=143.0

Q ss_pred             CCcccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-
Q psy18072          1 MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-   79 (174)
Q Consensus         1 ~~~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-   79 (174)
                      |.+.||||.++||++|++|.|+|++|.+|||||.|.+|++++||||+|++||++++++++.+++||.|.|+|++||+.+ 
T Consensus         3 ~~~~cr~~~~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg   82 (319)
T PTZ00248          3 DLLDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKG   82 (319)
T ss_pred             CcccccchhhhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCC
Confidence            3589999999999999999999999999999999998878999999999999999999999999999999999999877 


Q ss_pred             --------------------------------------------------------------------------------
Q psy18072         80 --------------------------------------------------------------------------------   79 (174)
Q Consensus        80 --------------------------------------------------------------------------------   79 (174)
                                                                                                      
T Consensus        83 ~IdLS~K~v~~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af~~~v~~~~evl~~l~i  162 (319)
T PTZ00248         83 YIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDNVFEGLDI  162 (319)
T ss_pred             EEEEEeeecccchHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHhcCchhhhccCCC
Confidence                                                                                            


Q ss_pred             -------------------------------------------------------------------ceeeecccccchH
Q psy18072         80 -------------------------------------------------------------------VMTTVTPEKADGL   92 (174)
Q Consensus        80 -------------------------------------------------------------------~l~ls~~~k~~g~   92 (174)
                                                                                         .+++++.++..|.
T Consensus       163 ~~ev~~~l~~~i~~~l~~~~vkI~a~iel~c~~~dGIe~IK~aL~~~~~~~~~~~~i~i~~igaP~Y~i~~~~~d~k~g~  242 (319)
T PTZ00248        163 PEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCSDKDKGM  242 (319)
T ss_pred             CHHHHHHHHHHHHHhCCCCcEEEEEEEEEEeCCCchHHHHHHHHHHHHhcCCCcCcEEEEEEcCCeEEEEEEeCCHHHHH
Confidence                                                                               5788999999999


Q ss_pred             HHHHHHHHHHHHHHhhhCCeeEEeeCceeEeccCHHHHHHHHHHHHHhcccccCCCCccccc
Q psy18072         93 KALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADDDEDEED  154 (174)
Q Consensus        93 ~~i~~~~~~i~~~l~~~~g~l~~k~~P~~i~~~~~~~~k~~~~~l~k~~~e~~gd~~~~~~~  154 (174)
                      ..|.++++.|.+.|+++||.+.|+..|++++..++.. .++|+++.++++++++++++++++
T Consensus       243 ~~l~~a~~~i~~~i~~~gG~~~~~~~p~~v~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  303 (319)
T PTZ00248        243 EIIGAALEAIKEVIKKKGGDFKVKGEPEVVGGDEEDL-EELLEKAEEEEEEDDYSESEDEDE  303 (319)
T ss_pred             HHHHHHHHHHHHHHHHcCCeEEEEECCEEecchhHHH-HHHHHHHhhhhccccccccccccc
Confidence            9999999999999999999999999999999998888 999999999999999876554444

>KOG2916|consensus

Probab=99.96  E-value=1.8e-28  Score=202.89  Aligned_cols=148  Identities=73%  Similarity=1.081  Sum_probs=143.3

Q ss_pred             CC-cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072          1 MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus         1 ~~-~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      |+ +.||||+.+||+++++|.+.|.+|...||||.|.+|++++|||..|+||++|++++++.+++|..-.|.|++||+++
T Consensus         1 m~~~~cR~ye~kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkek   80 (304)
T KOG2916|consen    1 MSTLECRFYENKYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEK   80 (304)
T ss_pred             CCcceeehhhccCCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCC
Confidence            44 89999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             --------------------------------------------------------------------------------
Q psy18072         80 --------------------------------------------------------------------------------   79 (174)
Q Consensus        80 --------------------------------------------------------------------------------   79 (174)
                                                                                                      
T Consensus        81 GYIDLSkrrVs~ed~~kC~Er~~ksK~v~sIlrhvAe~~g~~LeeLY~~igW~~~rk~g~aYdaFK~~vtd~tV~d~l~~  160 (304)
T KOG2916|consen   81 GYIDLSKRRVSPEDKEKCEERFAKSKLVYSILRHVAEKLGYELEELYQRIGWPLERKYGHAYDAFKIAVTDPTVLDELDL  160 (304)
T ss_pred             CceechhccCCHHHHHHHHHHHHHhHHHHHHHHHHHHHhCCcHHHHHHHhCCchhhhhchHHHHHHHhccCcccccccCC
Confidence                                                                                            


Q ss_pred             -------------------------------------------------------------------ceeeecccccchH
Q psy18072         80 -------------------------------------------------------------------VMTTVTPEKADGL   92 (174)
Q Consensus        80 -------------------------------------------------------------------~l~ls~~~k~~g~   92 (174)
                                                                                         ++++++++|..|+
T Consensus       161 ~~~vk~~Llk~Irrrltpq~vKIRADIEv~Cf~yeGI~aIK~alk~a~~~~te~~piki~LIApPlYVlTT~tldK~~g~  240 (304)
T KOG2916|consen  161 SEEVKEVLLKNIRRRLTPQTVKIRADIEVSCFGYEGIDAIKAALKAALNLSTEECPIKIKLIAPPLYVLTTQTLDKTKGL  240 (304)
T ss_pred             CHHHHHHHHHHHHHhcCCcceEEEeeeEEEeccccCHHHHHHHHHHHHhCCcccCceEEEEecCceEEEEEeeccccccH
Confidence                                                                               6799999999999


Q ss_pred             HHHHHHHHHHHHHHhhhCCeeEEeeCceeEeccCHHHHHHHHHHHHHhcccccCCC
Q psy18072         93 KALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADD  148 (174)
Q Consensus        93 ~~i~~~~~~i~~~l~~~~g~l~~k~~P~~i~~~~~~~~k~~~~~l~k~~~e~~gd~  148 (174)
                      .++..+|..|...|.+.+|.+.+++.|++++.+|+..+++.|++...+|+|++|||
T Consensus       241 e~l~~Ai~~i~~~I~~~~G~~~V~~~pk~vte~d~~~l~~~~e~~E~e~~e~~~dd  296 (304)
T KOG2916|consen  241 EVLEEAIEVIISKIEEYGGTFTVIMEPKLVTETDEAELARRMEREEEENAEVSGDD  296 (304)
T ss_pred             HHHHHHHHHHHHHHHhhCCEEEEEeCCeecccccHHHHHHHHHhhhhhcccccCcc
Confidence            99999999999999999999999999999999999999999999999999999985

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]

Probab=99.85  E-value=2.7e-21  Score=161.19  Aligned_cols=115  Identities=20%  Similarity=0.237  Sum_probs=110.3

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccccchHHH
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKADGLKA   94 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k~~g~~~   94 (174)
                      .++.|.|+||++...|.||-+.+  ++.||||.||..        ..+++|+.+++||+.++.+++|++|++.+  +.++
T Consensus       155 ~nq~v~~tVYr~~~~G~fv~~e~--~~~GfIh~sEr~--------~~prlG~~l~~rVi~~reDg~lnLSl~p~--~~E~  222 (287)
T COG2996         155 KNQEVDATVYRLLESGTFVITEN--GYLGFIHKSERF--------AEPRLGERLTARVIGVREDGKLNLSLRPR--AHEM  222 (287)
T ss_pred             hcCeeeeEEEEEeccceEEEEcC--CeEEEEcchhhc--------ccccCCceEEEEEEEEccCCeeecccccc--cHHh
Confidence            48999999999999999999988  899999999987        67999999999999999999999999888  9999


Q ss_pred             HHHHHHHHHHHHhhhCCeeEE--eeCceeEe---ccCHHHHHHHHHHHHHhc
Q psy18072         95 LQEAIDTIKAKIEQLGGVFQV--QMAPKVVT---ASDEAELARQMERAEAEN  141 (174)
Q Consensus        95 i~~~~~~i~~~l~~~~g~l~~--k~~P~~i~---~~~~~~~k~~~~~l~k~~  141 (174)
                      +..+++.|.++|+.+||+||+  ||+|+.|+   ++||.+||||+|+|+|++
T Consensus       223 l~~daq~Il~yL~~~gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g  274 (287)
T COG2996         223 LDEDAQMILTYLESNGGFMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAG  274 (287)
T ss_pred             hhhhHHHHHHHHHHcCCccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCC
Confidence            999999999999999999999  89999999   999999999999999986

>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=99.85  E-value=5.3e-21  Score=158.61  Aligned_cols=75  Identities=35%  Similarity=0.590  Sum_probs=73.8

Q ss_pred             cchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072          5 CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus         5 ~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      ||++...||+.|++|.|+|.+|.+|||||.|.+|++.+||||+|+++..|+++++++++.||.+.|+|++||+.+
T Consensus         1 m~~~~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~r   75 (269)
T COG1093           1 MRMKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKR   75 (269)
T ss_pred             CcccccCCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999999988

>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]

Probab=99.77  E-value=6e-19  Score=131.78  Aligned_cols=73  Identities=21%  Similarity=0.368  Sum_probs=69.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEK   88 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k   88 (174)
                      ++|++++|+|++|++|||||+|++  +-.||||||+++..|++++.+++++||.|.|+|+++|.+++++||.+.-
T Consensus         4 kvG~~l~GkItgI~~yGAFV~l~~--g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~   76 (129)
T COG1098           4 KVGSKLKGKITGITPYGAFVELEG--GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKL   76 (129)
T ss_pred             cccceEEEEEEeeEecceEEEecC--CCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHHh
Confidence            599999999999999999999988  8999999999999999999999999999999999999999998887543

>PRK03987 translation initiation factor IF-2 subunit alpha; Validated

Probab=99.69  E-value=2.8e-16  Score=132.07  Aligned_cols=71  Identities=34%  Similarity=0.563  Sum_probs=66.8

Q ss_pred             hccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072          9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus         9 ~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      .+++|++|++|.|+|++|.++|+||.|.+|++++||||+|++++++++++++.|++||.|.|+|++++..+
T Consensus         2 ~~~~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k   72 (262)
T PRK03987          2 RKEWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRK   72 (262)
T ss_pred             CCCCCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEeccc
Confidence            46789999999999999999999999998767999999999999999999999999999999999999865

>PHA02945 interferon resistance protein; Provisional

Probab=99.63  E-value=1.4e-15  Score=107.42  Aligned_cols=73  Identities=30%  Similarity=0.383  Sum_probs=65.9

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceec--chhhhhccccccCCCCEEEEEEEEEeCCC-ceeeec
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSEL--SRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVT   85 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSel--s~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~   85 (174)
                      -.+|++|++|.|+|+. .+|||||.|.+|++.+||||+|++  +..++++ ++++ .||.|.|+|++||+.+ -+.+|+
T Consensus         6 y~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSl   81 (88)
T PHA02945          6 YSLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNY   81 (88)
T ss_pred             ecCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEe
Confidence            3688999999999999 999999999999999999999955  9999999 9999 9999999999999976 345554

>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain

Probab=99.62  E-value=2.7e-15  Score=102.67  Aligned_cols=72  Identities=24%  Similarity=0.342  Sum_probs=64.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVT   85 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~   85 (174)
                      |+.|+++.|+|++|.+||+||+|.++ +.+||+|+|++++.++.++.+.|++||.|+|+|++++..+.+.+|+
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l~~~-~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~   72 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKIPGC-RKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL   72 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEECCC-CeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence            35899999999999999999999653 2799999999999999999999999999999999999877666654

pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.

>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.61  E-value=2.8e-15  Score=102.59  Aligned_cols=69  Identities=16%  Similarity=0.116  Sum_probs=63.8

Q ss_pred             CCCCEEEEEEEEEec-ceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072         14 EVEDVVMVTVISIAE-MGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVT   85 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~-~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~   85 (174)
                      ++|++|.|+|+++.+ +|+||+|.+  +..|++|+|+++++++.++.+.|++||.|+|+|++++. +++.+|+
T Consensus         2 ~~G~iv~G~V~~i~~~~g~~v~l~~--~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LSl   71 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSGLTVQLPF--GKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD-GKYQLSL   71 (72)
T ss_pred             CCCCEEEEEEEEeeCCcEEEEECCC--CCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC-CEEEEEe
Confidence            489999999999985 899999988  89999999999999999999999999999999999986 6777775

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.60  E-value=4.1e-15  Score=102.53  Aligned_cols=64  Identities=23%  Similarity=0.365  Sum_probs=58.9

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhc---cccccCCCCEEEEEEEEEeCCC
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRS---INKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~---~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      ++|++|.|+|.+++++|+||.|.+  +++|+||++++++.++.+   +.+.|++||.|+|+|+++|+++
T Consensus         2 k~G~~V~g~V~~i~~~G~fV~l~~--~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~   68 (74)
T cd05705           2 KEGQLLRGYVSSVTKQGVFFRLSS--SIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEK   68 (74)
T ss_pred             CCCCEEEEEEEEEeCCcEEEEeCC--CCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCC
Confidence            489999999999999999999988  899999999999998666   4589999999999999999854

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

Probab=99.58  E-value=1.4e-14  Score=98.86  Aligned_cols=73  Identities=68%  Similarity=0.961  Sum_probs=64.9

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeec
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVT   85 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~   85 (174)
                      |++|++|.|+|+++.++|+||.|.++++++||||+|+++++++.++.+.|++||.|+|+|++++.. +.+.+++
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~   74 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSK   74 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEE
Confidence            468999999999999999999998654699999999999999999999999999999999999975 3466654

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c

>PRK08582 hypothetical protein; Provisional

Probab=99.56  E-value=1.7e-14  Score=110.82  Aligned_cols=73  Identities=26%  Similarity=0.431  Sum_probs=67.4

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEK   88 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k   88 (174)
                      ++|++|.|+|++|++|||||.|.+  +++||||+|++++.++.++.+.|++||.|+|+|++++.++.+.+++...
T Consensus         4 kvG~iv~G~V~~I~~fG~fV~L~~--~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~   76 (139)
T PRK08582          4 EVGSKLQGKVTGITNFGAFVELPE--GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKA   76 (139)
T ss_pred             cCCCEEEEEEEEEECCeEEEEECC--CCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEec
Confidence            489999999999999999999988  8999999999999999999999999999999999999877788777544

>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain

Probab=99.56  E-value=2.2e-14  Score=100.62  Aligned_cols=78  Identities=22%  Similarity=0.207  Sum_probs=69.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch----hhhhccccccCCCCEEEEEEEEEeCCCceeeeccc
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR----RRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPE   87 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~----~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~   87 (174)
                      .|++|++|.|+|+++.++|+||.|..  +++|+||+|++++    .+..++.+.+++||.|.|+|+++++++.+.+|++.
T Consensus         3 ~p~~GdiV~g~V~~i~~~g~~v~i~~--~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~   80 (86)
T cd05789           3 IPEVGDVVIGRVTEVGFKRWKVDINS--PYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRS   80 (86)
T ss_pred             cCCCCCEEEEEEEEECCCEEEEECCC--CeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCc
Confidence            45799999999999999999999987  8999999999985    45677888999999999999999988889999877


Q ss_pred             ccch
Q psy18072         88 KADG   91 (174)
Q Consensus        88 k~~g   91 (174)
                      ..+|
T Consensus        81 ~~~g   84 (86)
T cd05789          81 LKYG   84 (86)
T ss_pred             cccc
Confidence            7554

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>PRK08059 general stress protein 13; Validated

Probab=99.54  E-value=7.8e-15  Score=110.32  Aligned_cols=99  Identities=23%  Similarity=0.331  Sum_probs=82.4

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC-CCceeeecccccchH
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK-EKVMTTVTPEKADGL   92 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~-~~~l~ls~~~k~~g~   92 (174)
                      ++|++|.|+|+++.++|+||.|.+  ++.||||++++++.++.++.+.|++||.|.|+|++++. .+.+.++.+......
T Consensus         6 k~G~iv~G~V~~i~~~G~fV~i~~--~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~~~   83 (123)
T PRK08059          6 EVGSVVTGKVTGIQPYGAFVALDE--ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEAP   83 (123)
T ss_pred             CCCCEEEEEEEEEecceEEEEECC--CCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEcccCc
Confidence            489999999999999999999987  79999999999999988888999999999999999986 456776765443221


Q ss_pred             HHHHHHHHHHHHHHhhhCCeeEE
Q psy18072         93 KALQEAIDTIKAKIEQLGGVFQV  115 (174)
Q Consensus        93 ~~i~~~~~~i~~~l~~~~g~l~~  115 (174)
                      . .......++..++..||++++
T Consensus        84 ~-~~~~~~~~l~~~~~~~g~~~l  105 (123)
T PRK08059         84 E-AKRKKGKILIPNPSEQGFNTL  105 (123)
T ss_pred             c-cccccccccccccccCCchhH
Confidence            0 334456778888889999987

>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.53  E-value=8.1e-14  Score=94.70  Aligned_cols=70  Identities=14%  Similarity=0.168  Sum_probs=63.2

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeec
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVT   85 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~   85 (174)
                      ++|++|.|+|+++.++|+||+|.+  +++|++|++++++++..++.+.|++||.|+|+|++++.. +.+.+|+
T Consensus         2 ~~G~iv~g~V~~v~~~gi~v~l~~--~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~   72 (73)
T cd05706           2 KVGDILPGRVTKVNDRYVLVQLGN--KVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSL   72 (73)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC--CcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence            489999999999999999999998  899999999999988888889999999999999999985 4566554

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.52  E-value=6.3e-14  Score=94.39  Aligned_cols=68  Identities=25%  Similarity=0.328  Sum_probs=61.6

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeec
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVT   85 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~   85 (174)
                      |++|.|+|+++.++|+||+|.+  +++||||+|++++.++.++.+.|++||.++|+|+++++. +.+.+|.
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~~--~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~   69 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFYN--NVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSC   69 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECC--CCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEe
Confidence            7899999999999999999987  799999999999988889999999999999999999984 4555553

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.52  E-value=6.2e-14  Score=94.24  Aligned_cols=62  Identities=27%  Similarity=0.389  Sum_probs=58.7

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      |++|.|+|+++.++|+||+|.+  +++||||++++++.++.++.+.|++||.|+|+|+++++.+
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~--~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~   62 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLGR--GVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDN   62 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCC--CCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCC
Confidence            7899999999999999999987  7999999999999999999999999999999999999843

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain

Probab=99.51  E-value=1e-13  Score=96.55  Aligned_cols=79  Identities=19%  Similarity=0.193  Sum_probs=72.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccccc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKAD   90 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k~~   90 (174)
                      ++|++|++|.|+|+++.+.+|+|.+..  .++|+||.++++..+..++...|++||.|.|+|++++..+.+.||+....+
T Consensus         2 y~p~~GdiV~G~V~~v~~~~~~V~i~~--~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~~~~   79 (82)
T cd04454           2 YLPDVGDIVIGIVTEVNSRFWKVDILS--RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTADNEL   79 (82)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEeCC--CceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECCCCC
Confidence            356799999999999999999999977  799999999999888888889999999999999999987789999888766


Q ss_pred             h
Q psy18072         91 G   91 (174)
Q Consensus        91 g   91 (174)
                      |
T Consensus        80 G   80 (82)
T cd04454          80 G   80 (82)
T ss_pred             c
Confidence            5

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.51  E-value=8e-14  Score=95.72  Aligned_cols=68  Identities=21%  Similarity=0.273  Sum_probs=61.7

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh--hhccccccCCCCEEEEEEEEEeCCC-ceeeec
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR--IRSINKLIRVGKTEPVVVIRVDKEK-VMTTVT   85 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~--v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~   85 (174)
                      |++|.|+|+++.++|+||+|.+  +++|+||.+++++.+  ..++.+.|++||.|+|+|+++|+++ .+.+|.
T Consensus         1 G~~V~g~V~~i~~~g~~V~l~~--~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~   71 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTISP--DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSA   71 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCC--CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEe
Confidence            7899999999999999999988  899999999999764  7889999999999999999999864 667665

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

Probab=99.51  E-value=8.6e-14  Score=92.19  Aligned_cols=68  Identities=24%  Similarity=0.465  Sum_probs=62.1

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVT   85 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~   85 (174)
                      |++|.|+|+++.++|+||.|.+  ++.||||.++++++++.++.+.|++||.|+|+|++++..+.+.+++
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~~--~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~   68 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELGG--GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSI   68 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECC--CCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEE
Confidence            7899999999999999999987  7999999999999888888899999999999999999855666664

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.51  E-value=8.8e-14  Score=93.73  Aligned_cols=67  Identities=24%  Similarity=0.353  Sum_probs=60.7

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeee
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTV   84 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls   84 (174)
                      |++|.|+|++|.++|+||+|.+  +++||||++++++.++.++.+.|++||.++|+|+++|.. +.+.++
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~--~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls   68 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKLSD--HIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT   68 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecC--CcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence            7899999999999999999988  899999999999998888889999999999999999985 344443

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.51  E-value=1.3e-13  Score=93.61  Aligned_cols=70  Identities=39%  Similarity=0.541  Sum_probs=64.3

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCc-eeeec
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKV-MTTVT   85 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~-l~ls~   85 (174)
                      ++|++|.|+|+++.++|+||.|.+  +++||||.+++++.+...+...+++||.|.|+|++++..+. +.+|.
T Consensus         3 ~~G~iv~g~V~~v~~~g~~V~l~~--~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~   73 (74)
T PF00575_consen    3 KEGDIVEGKVTSVEDFGVFVDLGN--GIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSL   73 (74)
T ss_dssp             STTSEEEEEEEEEETTEEEEEEST--SSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEES
T ss_pred             CCCCEEEEEEEEEECCEEEEEECC--cEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEE
Confidence            589999999999999999999986  79999999999999888999999999999999999999763 66654

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....

>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.50  E-value=1.2e-13  Score=94.29  Aligned_cols=67  Identities=22%  Similarity=0.344  Sum_probs=60.9

Q ss_pred             CCEEE-EEEEEE-ecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeee
Q psy18072         16 EDVVM-VTVISI-AEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTV   84 (174)
Q Consensus        16 GdiV~-G~V~~i-~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls   84 (174)
                      |++|. |+|+++ .++|+||+|.+  +++||||+|++++.++.++.+.|++||.+.|+|+++++.. .+.+|
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l~~--gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS   70 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFELKD--GLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLS   70 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCC--CCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence            78899 999999 79999999988  8999999999999999999999999999999999999754 56665

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK05807 hypothetical protein; Provisional

Probab=99.50  E-value=1.3e-13  Score=105.66  Aligned_cols=72  Identities=21%  Similarity=0.402  Sum_probs=66.2

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEK   88 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k   88 (174)
                      ++|++|.|+|++|+++||||.| +  +..||||+|++++.++.++...|++||.|+|+|++++.++.+.+|++..
T Consensus         4 ~vG~vv~G~Vt~i~~~GafV~L-~--~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~   75 (136)
T PRK05807          4 KAGSILEGTVVNITNFGAFVEV-E--GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQA   75 (136)
T ss_pred             cCCCEEEEEEEEEECCeEEEEE-C--CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEec
Confidence            3899999999999999999999 5  5899999999999999999999999999999999999877888887553

>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains

Probab=99.49  E-value=1.2e-13  Score=96.47  Aligned_cols=69  Identities=22%  Similarity=0.226  Sum_probs=63.0

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeee
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTV   84 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls   84 (174)
                      ++|++|.|+|.++.++|+||.|.+  +.+||+|+++++++++.++.+.|++||.|+|+|++++.. +.+.+|
T Consensus        13 ~~G~i~~g~V~~v~~~G~fv~l~~--~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~ls   82 (83)
T cd04461          13 KPGMVVHGYVRNITPYGVFVEFLG--GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS   82 (83)
T ss_pred             CCCCEEEEEEEEEeeceEEEEcCC--CCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEe
Confidence            489999999999999999999987  899999999999999999999999999999999999974 345544

Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain

Probab=99.47  E-value=2.4e-13  Score=91.81  Aligned_cols=69  Identities=25%  Similarity=0.407  Sum_probs=62.9

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecc
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTP   86 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~   86 (174)
                      |++|.|+|+++.++|+||+|.+  +++|+||++++++.++.++.+.|++||.++|+|++++.. +.+.++.+
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~~--~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k   70 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLGD--GVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK   70 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCC--CCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence            7899999999999999999987  799999999999999989999999999999999999986 45666654

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain

Probab=99.47  E-value=3.2e-13  Score=91.50  Aligned_cols=65  Identities=26%  Similarity=0.535  Sum_probs=57.9

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchh-hhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRR-RIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~-~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      || +|+++.|+|++|+++|+||+|.+  +.+||+|++++++. +..++.+.|++||.|+|+|++++..+
T Consensus         1 ~~-~g~~~~g~V~~i~~~G~fv~l~~--~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~   66 (72)
T cd05689           1 YP-EGTRLFGKVTNLTDYGCFVELEE--GVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEER   66 (72)
T ss_pred             Cc-CCCEEEEEEEEEEeeEEEEEcCC--CCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCc
Confidence            45 89999999999999999999988  79999999999864 44467788999999999999999754

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain

Probab=99.46  E-value=2.4e-13  Score=91.07  Aligned_cols=62  Identities=29%  Similarity=0.532  Sum_probs=57.0

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch-hhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR-RRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~-~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      |++|.|+|++++++|+||+|.+  +.+||+|++++++ .+..++.+.|++||.|+|+|+++|..+
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~--~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~   63 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDG--GIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVER   63 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCC--CCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCc
Confidence            7899999999999999999988  8999999999996 567788899999999999999999753

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>PRK07252 hypothetical protein; Provisional

Probab=99.46  E-value=3.1e-13  Score=101.52  Aligned_cols=71  Identities=27%  Similarity=0.384  Sum_probs=63.5

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTP   86 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~   86 (174)
                      ++|++|.|+|++|.++|+||+|.+  ++.||||+|++++.++.++.+.|++||.|+|+|++++.. +.+.+++.
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~--~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk   73 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALEN--GTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLR   73 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECC--CCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence            479999999999999999999987  799999999999999999999999999999999999984 45555543

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

Probab=99.46  E-value=2e-13  Score=124.09  Aligned_cols=74  Identities=28%  Similarity=0.495  Sum_probs=66.0

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeeccc
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTPE   87 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~~   87 (174)
                      +.+. +|++|.|+|++|++|||||.|.+   +.||||+|++||.|+.+|.+.|++||.|+|+|+++|..+ .+++|++.
T Consensus       188 ~~l~-~G~vV~G~V~~It~~GafVdigG---vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~  262 (541)
T COG0539         188 NKLE-VGEVVEGVVKNITDYGAFVDIGG---VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQ  262 (541)
T ss_pred             hcCC-CCceEEEEEEEeecCcEEEEecC---eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehh
Confidence            4444 99999999999999999999964   999999999999999999999999999999999999765 56666543

>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.45  E-value=5.2e-13  Score=90.88  Aligned_cols=72  Identities=26%  Similarity=0.408  Sum_probs=63.2

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTP   86 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~   86 (174)
                      ++|++|.|+|+++.++|+||+|.+. +++|++|++++++.+..++.+.|++||.|+|+|++++.. +.+.++.+
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l~~~-~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k   73 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDIDGT-NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK   73 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECCC-CeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEE
Confidence            3699999999999999999999742 599999999999988888889999999999999999984 46666653

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide

Probab=99.42  E-value=9.1e-13  Score=91.08  Aligned_cols=70  Identities=21%  Similarity=0.327  Sum_probs=61.8

Q ss_pred             CCEEEEEEEEEecceEEEEECCC-CCeEEEEEceecchhhh-hccccccCCCCEEEEEEEEEeCCCceeeecc
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEY-NNIEGMILLSELSRRRI-RSINKLIRVGKTEPVVVIRVDKEKVMTTVTP   86 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~-~~~~GlI~iSels~~~v-~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~   86 (174)
                      |+++.|+|+++.+||+||+|.++ .+..||+|++++++.++ .++.+.|++||.|+|+|++++ .+.+.++.+
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k   72 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSMK   72 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe-CCEEEEEEE
Confidence            68999999999999999999853 25899999999999886 888999999999999999999 666666653

The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.

>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain

Probab=99.42  E-value=1e-12  Score=88.52  Aligned_cols=67  Identities=30%  Similarity=0.377  Sum_probs=60.5

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeee
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTV   84 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls   84 (174)
                      |++|.|+|.++.++|+||.|..  +.+|+||.+++++.+..++.+.|++||.++|+|+++++. +.+.+|
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~--~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS   68 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGY--KSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLS   68 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCC--CceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEE
Confidence            7899999999999999999976  799999999999999999999999999999999999854 345554

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

Probab=99.42  E-value=3e-13  Score=122.96  Aligned_cols=79  Identities=28%  Similarity=0.463  Sum_probs=71.3

Q ss_pred             hhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeec
Q psy18072          7 FYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVT   85 (174)
Q Consensus         7 ~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~   85 (174)
                      ....+|| +|+.+.|+|+++++|||||++.+  +++||+|+|+++|.+...|++++++||.|.|+|+.||+++ ++++++
T Consensus       270 ~i~~~~~-~g~~v~G~Vt~i~~~GafVei~~--GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~i  346 (541)
T COG0539         270 GIEKKYP-VGDKVEGKVTNLTDYGAFVEIEE--GVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGL  346 (541)
T ss_pred             HHhhhcC-CCCEEEEEEEEeecCcEEEEecC--CccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeee
Confidence            3467787 99999999999999999999988  9999999999999998889999999999999999999965 677776


Q ss_pred             ccc
Q psy18072         86 PEK   88 (174)
Q Consensus        86 ~~k   88 (174)
                      +..
T Consensus       347 Kq~  349 (541)
T COG0539         347 KQL  349 (541)
T ss_pred             hhh
Confidence            543

>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa

Probab=99.41  E-value=1e-12  Score=86.92  Aligned_cols=61  Identities=26%  Similarity=0.448  Sum_probs=57.3

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      |++|.|+|++++++|+||.|.+  +..||+|.+++++.++.++...|++||.|+|+|++++..
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~--~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~   61 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGV--KQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEE   61 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCC--CCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECC
Confidence            6899999999999999999987  799999999999888888889999999999999999974

The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.

>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

Probab=99.40  E-value=1.6e-12  Score=86.34  Aligned_cols=67  Identities=28%  Similarity=0.532  Sum_probs=60.3

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeee
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTV   84 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls   84 (174)
                      |+++.|+|+++.++|+||.|..  +..||+|++++++.++.++.+.|++||.|+|+|+++++.+.+.+|
T Consensus         1 g~~~~g~V~~v~~~G~~v~l~~--~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~~~~i~ls   67 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEILP--GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLS   67 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCC--CCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECCCCcEEee
Confidence            6899999999999999999987  799999999999998888889999999999999999974455444

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=99.39  E-value=1.6e-13  Score=110.14  Aligned_cols=96  Identities=18%  Similarity=0.242  Sum_probs=83.6

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCC--------CeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCcee
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYN--------NIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMT   82 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~--------~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~   82 (174)
                      ..|++|++|.|+|+++.++||||.|..+.        ++.|+||.+++++.+..++.+.|++||.|.|+|++++  +.+.
T Consensus        60 ~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~--~~i~  137 (189)
T PRK09521         60 PLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT--DPLQ  137 (189)
T ss_pred             CCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC--CcEE
Confidence            45569999999999999999999995321        5899999999999888889999999999999999998  6799


Q ss_pred             eecccccchHHHHHHHHHHHHHHHhhhC
Q psy18072         83 TVTPEKADGLKALQEAIDTIKAKIEQLG  110 (174)
Q Consensus        83 ls~~~k~~g~~~i~~~~~~i~~~l~~~~  110 (174)
                      +|++...+|  ++.+.|..|+..|...+
T Consensus       138 LS~k~~~lG--vv~a~~~~~g~~~~~~~  163 (189)
T PRK09521        138 LSTKGKDLG--VIYAMCSRCRTPLVKKG  163 (189)
T ss_pred             EEEecCCce--EEEEEccccCCceEECC
Confidence            999877665  78889999998887655

>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.37  E-value=1.7e-12  Score=94.46  Aligned_cols=72  Identities=18%  Similarity=0.282  Sum_probs=63.2

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-------------------ccccccCCCCEEEEEEEE
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-------------------SINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-------------------~~~~~l~vGd~V~vrVi~   74 (174)
                      ++|++|.|+|++|.++|+||.|++  ++.|++|++++++.+..                   ++.+.|++||.|+|+|++
T Consensus         2 ~~G~vV~G~V~~v~~~gl~v~L~~--g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~   79 (100)
T cd05693           2 SEGMLVLGQVKEITKLDLVISLPN--GLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVS   79 (100)
T ss_pred             CCCCEEEEEEEEEcCCCEEEECCC--CcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEE
Confidence            489999999999999999999988  89999999999987632                   367899999999999999


Q ss_pred             EeCC----Cceeeeccc
Q psy18072         75 VDKE----KVMTTVTPE   87 (174)
Q Consensus        75 Vd~~----~~l~ls~~~   87 (174)
                      +++.    +.+.+|.+.
T Consensus        80 ~d~~~~~~~~i~LSlr~   96 (100)
T cd05693          80 LDKSKSGKKRIELSLEP   96 (100)
T ss_pred             ccCCcCCCcEEEEEecH
Confidence            9985    477777654

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.36  E-value=3.1e-12  Score=86.60  Aligned_cols=64  Identities=23%  Similarity=0.242  Sum_probs=58.9

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh--hhccccccCCCCEEEEEEEEEeCCCce
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR--IRSINKLIRVGKTEPVVVIRVDKEKVM   81 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~--v~~~~~~l~vGd~V~vrVi~Vd~~~~l   81 (174)
                      |++|.|+|+++.++|+||.|..  +++|+||++++++.+  ..++.+.|++||.|.|+|++++..+.+
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~--~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~~   66 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLAD--NVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTH   66 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCC--CcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcccc
Confidence            7899999999999999999987  899999999999885  778889999999999999999987644

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain

Probab=99.36  E-value=2.7e-12  Score=92.08  Aligned_cols=80  Identities=23%  Similarity=0.269  Sum_probs=70.1

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEE--------CCCCCeEEEEEceecchhhhh--ccccccCCCCEEEEEEEEEeCCCc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHL--------LEYNNIEGMILLSELSRRRIR--SINKLIRVGKTEPVVVIRVDKEKV   80 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L--------~~~~~~~GlI~iSels~~~v~--~~~~~l~vGd~V~vrVi~Vd~~~~   80 (174)
                      ..|++|++|.|+|++++...|+|.|        ..  .+.|+||++++...+..  .+.+.|++||.|+|||+++.....
T Consensus         2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~--~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~   79 (92)
T cd05791           2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKE--SFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS   79 (92)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCC--CcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCC
Confidence            3578999999999999999999999        55  68999999999876655  688999999999999999987677


Q ss_pred             eeeecccccchH
Q psy18072         81 MTTVTPEKADGL   92 (174)
Q Consensus        81 l~ls~~~k~~g~   92 (174)
                      +.+|+.++++|.
T Consensus        80 ~~Lst~~~~lGV   91 (92)
T cd05791          80 YYLSTAENELGV   91 (92)
T ss_pred             cEEEecCCCCcc
Confidence            999999887773

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain

Probab=99.36  E-value=3.3e-12  Score=90.92  Aligned_cols=64  Identities=22%  Similarity=0.306  Sum_probs=58.0

Q ss_pred             CCCCEEEEEEEEEecc--eEEEEECCCCCeEEEEEceecch---hhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         14 EVEDVVMVTVISIAEM--GAYVHLLEYNNIEGMILLSELSR---RRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~--GafV~L~~~~~~~GlI~iSels~---~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      ++|++|.|+|++|.++  ||||+|.+  +.+||||+|++++   .++.++.+.+++||.|.|+|++.....
T Consensus         6 ~~G~iy~g~V~~i~~~~~GaFV~l~~--g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~   74 (88)
T cd04453           6 IVGNIYLGRVKKIVPGLQAAFVDIGL--GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGT   74 (88)
T ss_pred             CCCCEEEEEEEEeccCCcEEEEEeCC--CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCC
Confidence            4899999999999996  99999988  7999999999998   567788899999999999999976554

RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th

>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.35  E-value=4e-12  Score=85.54  Aligned_cols=60  Identities=15%  Similarity=0.227  Sum_probs=53.9

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      |++|.|+|+++.++|+||.|.+  +++|++|.++++..+..  .+.|++|+.|+|+|+.+++.+
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~~--~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~   60 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFLS--SFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPST   60 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcC--CceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCC
Confidence            7899999999999999999987  79999999999765444  678999999999999999854

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.35  E-value=2e-12  Score=120.89  Aligned_cols=71  Identities=25%  Similarity=0.537  Sum_probs=64.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecc----hhhhhccccccCCCCEEEEEEEEEeCCCceeee
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS----RRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTV   84 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels----~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls   84 (174)
                      .|++|++|.|+|++|++||+||+|.+  +.+||||+|+++    +.++.++.+.|++||.|+|+|+++|..++++++
T Consensus       644 ~~~vG~i~~GkV~~I~dfGaFVel~~--G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gKI~L~  718 (719)
T TIGR02696       644 MPEVGERFLGTVVKTTAFGAFVSLLP--GKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSLV  718 (719)
T ss_pred             cCCCCCEEEEEEEEEECceEEEEecC--CceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCCeeec
Confidence            36699999999999999999999987  899999999996    468999999999999999999999987777765

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=99.35  E-value=3.1e-12  Score=106.00  Aligned_cols=80  Identities=21%  Similarity=0.270  Sum_probs=72.3

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh----hccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI----RSINKLIRVGKTEPVVVIRVDKEKVMTTVT   85 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v----~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~   85 (174)
                      .+.|++||+|.|+|+++.++||||.|..  .+.|+||++++++.++    .+++..|++||.|+|||++++.++.+.+|+
T Consensus        58 ~y~P~vGDiViG~V~~i~~~~~~vdI~~--~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~  135 (235)
T PRK04163         58 KYIPKVGDLVIGKVTDVTFSGWEVDINS--PYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTL  135 (235)
T ss_pred             cccCCCCCEEEEEEEEEeCceEEEEeCC--CceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEE
Confidence            3667899999999999999999999987  7899999999999887    788999999999999999999888888888


Q ss_pred             ccccch
Q psy18072         86 PEKADG   91 (174)
Q Consensus        86 ~~k~~g   91 (174)
                      +.+.+|
T Consensus       136 k~~~lG  141 (235)
T PRK04163        136 KGKGLG  141 (235)
T ss_pred             cCCCCC
Confidence            877554

>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.34  E-value=8.3e-12  Score=86.06  Aligned_cols=66  Identities=17%  Similarity=0.175  Sum_probs=56.7

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeecc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTP   86 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~   86 (174)
                      +.|++|.|+|.+|.++|+||.+. +.++.||||.+++++.      ..+++||.+.|+|+++++.+ .+.+|++
T Consensus         3 ~~G~~v~g~V~si~d~G~~v~~g-~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k   69 (74)
T cd05694           3 VEGMVLSGCVSSVEDHGYILDIG-IPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSAD   69 (74)
T ss_pred             CCCCEEEEEEEEEeCCEEEEEeC-CCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEe
Confidence            48999999999999999999995 2279999999999975      67999999999999999865 4566553

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=99.34  E-value=4.3e-12  Score=89.02  Aligned_cols=67  Identities=31%  Similarity=0.543  Sum_probs=62.6

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEE-ceecchhhhhccccccCCCCEEEEEEEEEeCCCc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMIL-LSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKV   80 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~-iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~   80 (174)
                      .||++|+++. .|..+++.|+||.|.+|+ ++|||. .++++.++++++++.+ +|..+.|+|+++|+.+.
T Consensus        12 ~~P~v~dvv~-~Vv~i~d~~~YV~LleY~-iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KG   79 (86)
T PHA02858         12 VFPNINEVTK-GIVFVKDNIFYVKLIDYG-LEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKG   79 (86)
T ss_pred             ecCCCCeEEE-EEEEEeccEEEEEEecCc-cceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCC
Confidence            5889999999 677899999999999996 999999 9999999999999999 99999999999999764

>smart00316 S1 Ribosomal protein S1-like RNA-binding domain

Probab=99.33  E-value=8.6e-12  Score=82.27  Aligned_cols=69  Identities=38%  Similarity=0.558  Sum_probs=61.7

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeec
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVT   85 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~   85 (174)
                      +|++|.|+|+++.++|+||.+.+  ++.|++|.++++..+..++...|++||.|.|+|++++.. +.+.+++
T Consensus         2 ~G~~v~g~V~~v~~~g~~v~i~~--~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~   71 (72)
T smart00316        2 VGDVVEGTVTEITPFGAFVDLGN--GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL   71 (72)
T ss_pred             CCCEEEEEEEEEEccEEEEEeCC--CCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEe
Confidence            79999999999999999999987  799999999999887777778899999999999999986 5565554

>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

Probab=99.32  E-value=9.2e-12  Score=82.49  Aligned_cols=61  Identities=36%  Similarity=0.605  Sum_probs=56.6

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      +|++|.|+|+++.++|+||.|.   +++|+||.+++++.++.++.+.|++||.|+|+|++++..
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~---~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~   61 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLG---GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKE   61 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC---CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECC
Confidence            4899999999999999999995   489999999999888888889999999999999999975

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.29  E-value=5.6e-12  Score=120.22  Aligned_cols=73  Identities=27%  Similarity=0.396  Sum_probs=66.9

Q ss_pred             CCCCCEEE-EEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeeccc
Q psy18072         13 PEVEDVVM-VTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPE   87 (174)
Q Consensus        13 p~~GdiV~-G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~   87 (174)
                      |++|++|. |+|++|.+||+||+|.+  +.+||||+|++++.++.++.+.|++||.|+|+|+++|..+.+.++.+.
T Consensus       751 ~~vG~iy~~g~V~~I~~FGaFVeL~~--g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~~grI~LSlK~  824 (891)
T PLN00207        751 PTVGDIYRNCEIKSIAPYGAFVEIAP--GREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRA  824 (891)
T ss_pred             cCCCcEEECcEEEEEeccEEEEEeCC--CCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECCCCcEEEEEec
Confidence            56999995 69999999999999987  899999999999999999999999999999999999987777777643

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.29  E-value=1.9e-11  Score=105.48  Aligned_cols=73  Identities=27%  Similarity=0.462  Sum_probs=64.0

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecc
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTP   86 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~   86 (174)
                      +.+ ++|++|.|+|++|++||+||.+.   ++.||||+|++++.++.++.+.|++||.|+|+|++++.. +.+.++++
T Consensus       192 ~~~-k~G~vv~G~V~~I~~~G~fV~i~---gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K  265 (318)
T PRK07400        192 NRL-EVGEVVVGTVRGIKPYGAFIDIG---GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTK  265 (318)
T ss_pred             ccC-CCCCEEEEEEEEEECCeEEEEEC---CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence            344 48999999999999999999984   599999999999999999999999999999999999974 45555553

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

Probab=99.28  E-value=1.8e-12  Score=103.38  Aligned_cols=113  Identities=15%  Similarity=0.194  Sum_probs=94.6

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCC--------CeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCce
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYN--------NIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVM   81 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~--------~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l   81 (174)
                      ..+|+.|++|.|+|+++....|.|++....        ...|-||+|+++..+++++++.|++||.|+|+|++.-  ..+
T Consensus        59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~~  136 (188)
T COG1096          59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DPI  136 (188)
T ss_pred             CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--CCe
Confidence            578889999999999999999999886421        2678999999999999999999999999999999985  469


Q ss_pred             eeecccccchHHHHHHHHHHHHHHHhhhCCeeEE-eeCceeEeccC
Q psy18072         82 TTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQV-QMAPKVVTASD  126 (174)
Q Consensus        82 ~ls~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~-k~~P~~i~~~~  126 (174)
                      .||+..+.+|  ++.+.|++|+..|...+..|.- +.+-+....++
T Consensus       137 ~Lst~~~dlG--VI~A~CsrC~~~L~~~~~~l~Cp~Cg~tEkRKia  180 (188)
T COG1096         137 QLSTKGNDLG--VIYARCSRCRAPLVKKGNMLKCPNCGNTEKRKIA  180 (188)
T ss_pred             EEEecCCcce--EEEEEccCCCcceEEcCcEEECCCCCCEEeeeec
Confidence            9999999888  7899999999999986666654 45554444333

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=99.28  E-value=1e-11  Score=112.56  Aligned_cols=74  Identities=23%  Similarity=0.351  Sum_probs=67.4

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeecc
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTP   86 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~   86 (174)
                      ..|+ +|++|.|+|+++++||+||.|.+  ++.||||+|++++.+..++.+.|++||.|+|+|+.+++++ .++++.+
T Consensus       375 ~~~~-vG~~v~G~V~~i~~~G~FV~l~~--gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~  449 (491)
T PRK13806        375 ERFA-PGTTVTGTVEKRAQFGLFVNLAP--GVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPA  449 (491)
T ss_pred             hhCC-CCCEEEEEEEEEecCceEEEcCC--CcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEEEee
Confidence            4666 89999999999999999999987  8999999999999999889999999999999999999854 6777765

>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain

Probab=99.26  E-value=3.8e-11  Score=80.42  Aligned_cols=65  Identities=18%  Similarity=0.327  Sum_probs=55.9

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC-CCceeeec
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK-EKVMTTVT   85 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~-~~~l~ls~   85 (174)
                      |++|.|+|+++.++|+||.+ +  +++||||.|++++.+..++..  .+||.+.|+|++++. .+.+.+|.
T Consensus         1 G~iv~g~V~~v~~~G~~v~l-~--g~~gfip~s~~~~~~~~~~~~--~vG~~i~~~i~~vd~~~~~i~lS~   66 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDI-E--GVRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSR   66 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-C--CEEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEc
Confidence            78999999999999999999 6  799999999999887766655  389999999999997 44566553

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=99.25  E-value=2.2e-11  Score=114.44  Aligned_cols=72  Identities=25%  Similarity=0.533  Sum_probs=66.9

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecc
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTP   86 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~   86 (174)
                      +++|++|.|+|++|.+||+||+|.+  +.+||||+|++++.+++++.+.|++||.|+|+|+++|..+.+.+|.+
T Consensus       619 ~~vG~v~~G~V~~I~~fGafVei~~--~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~grI~LS~k  690 (693)
T PRK11824        619 PEVGEIYEGKVVRIVDFGAFVEILP--GKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRK  690 (693)
T ss_pred             CcCCeEEEEEEEEEECCeEEEEECC--CCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCCCcEEEEEE
Confidence            4699999999999999999999987  89999999999999999999999999999999999998777877763

>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease

Probab=99.24  E-value=8e-11  Score=81.37  Aligned_cols=62  Identities=24%  Similarity=0.340  Sum_probs=54.6

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVT   85 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~   85 (174)
                      ++|+.+.|+|++++++|+||.+.+  ++.||+|.|++.        +.+++||.++|+|+++...+.+.++.
T Consensus        15 ~~G~~~~g~V~~i~~~G~fV~l~~--~~~Glv~~se~~--------~~~~iGd~v~v~I~~i~e~~~i~l~~   76 (77)
T cd04473          15 EVGKLYKGKVNGVAKYGVFVDLND--HVRGLIHRSNLL--------RDYEVGDEVIVQVTDIPENGNIDLIP   76 (77)
T ss_pred             CCCCEEEEEEEeEecceEEEEECC--CcEEEEEchhcc--------CcCCCCCEEEEEEEEECCCCcEEEEE
Confidence            489999999999999999999988  799999999975        67999999999999995555666553

The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.

>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain

Probab=99.23  E-value=8.1e-11  Score=81.20  Aligned_cols=69  Identities=23%  Similarity=0.390  Sum_probs=57.0

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-----------ccccccCCCCEEEEEEEEEeCC-Ccee
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-----------SINKLIRVGKTEPVVVIRVDKE-KVMT   82 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-----------~~~~~l~vGd~V~vrVi~Vd~~-~~l~   82 (174)
                      +|+++.|+|++|+++|+||+|.+| +.+|++|.+++++.++.           .....|++||.|+|+|++++.. +.+.
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~-~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~   79 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNL-TVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKID   79 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCC-CEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEE
Confidence            389999999999999999999876 49999999999865432           3457899999999999999974 3444


Q ss_pred             ee
Q psy18072         83 TV   84 (174)
Q Consensus        83 ls   84 (174)
                      ++
T Consensus        80 ~~   81 (83)
T cd04471          80 FE   81 (83)
T ss_pred             EE
Confidence            43

RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.22  E-value=3.6e-11  Score=108.90  Aligned_cols=73  Identities=27%  Similarity=0.430  Sum_probs=65.4

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecc
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTP   86 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~   86 (174)
                      ..+. +|++|.|+|+++++||+||.| .  ++.||||+|+++|.++.++.+.|++||.|+|+|+++++. +.+.+|.+
T Consensus       204 ~~lk-~G~iv~G~V~~i~~~G~FVdl-g--gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK  277 (486)
T PRK07899        204 NQLQ-KGQVRKGVVSSIVNFGAFVDL-G--GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLK  277 (486)
T ss_pred             Hhcc-CCCEEEEEEEEEECCeEEEEE-C--CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEe
Confidence            3454 999999999999999999999 3  599999999999999999999999999999999999985 56666665

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=99.20  E-value=3.6e-11  Score=112.85  Aligned_cols=68  Identities=26%  Similarity=0.561  Sum_probs=62.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCce
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVM   81 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l   81 (174)
                      .|++|++|.|+|++|.+||+||+|.+  +.+||||+|++++.++.++.+.|++||.|+|+|++++..+.+
T Consensus       615 ~~~~G~i~~G~V~~I~~~GafVei~~--g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~~gki  682 (684)
T TIGR03591       615 EPEVGKIYEGKVVRIMDFGAFVEILP--GKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQGRI  682 (684)
T ss_pred             ccccCcEEEEEEEEEeCCEEEEEECC--CcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECCCCCc
Confidence            35699999999999999999999987  899999999999999999999999999999999999974443

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=99.19  E-value=4.4e-11  Score=114.53  Aligned_cols=75  Identities=27%  Similarity=0.478  Sum_probs=66.4

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch-hhhhccccccCCCCEEEEEEEEEeCCC-ceeeeccc
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR-RRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTPE   87 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~-~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~~   87 (174)
                      ++|+ +|++|.|+|+++.+||+||.|.+  +++||||+|+++| .++.++.+.|++||.|+|+|+++|..+ .+++|.+.
T Consensus       574 ~~~~-vG~iV~G~V~~I~~fG~fVeL~~--gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~  650 (863)
T PRK12269        574 NKFG-VNDVVKGRVTKIADFGAFIELAE--GIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQ  650 (863)
T ss_pred             ccCC-CCCEEEEEEEEEeCCeEEEEecC--CceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehh
Confidence            4566 99999999999999999999987  8999999999999 578899999999999999999999754 56666643

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=99.19  E-value=6.7e-11  Score=107.27  Aligned_cols=75  Identities=25%  Similarity=0.472  Sum_probs=65.7

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch-hhhhccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR-RRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE   87 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~-~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~   87 (174)
                      ..++ +|++|.|+|+++++||+||.|.+  +++||||+|+++| .++.++.+.+++||.|+|+|+++|+. +.+.+|.+.
T Consensus       288 ~~~~-~G~~v~G~V~~v~~~G~fV~l~~--gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~  364 (491)
T PRK13806        288 DRLK-AGDKVTGKVVRLAPFGAFVEILP--GIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRD  364 (491)
T ss_pred             ccCC-CCCEEEEEEEEEeCceEEEEeCC--CcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEee
Confidence            3565 89999999999999999999987  8999999999998 56788889999999999999999985 466666543

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.19  E-value=6.1e-11  Score=107.46  Aligned_cols=81  Identities=27%  Similarity=0.473  Sum_probs=69.7

Q ss_pred             hccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072          9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE   87 (174)
Q Consensus         9 ~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~   87 (174)
                      ...++ +|++|.|+|+++.+||+||+|.+  ++.||||+|++++.++..+.+.|++||.|+|+|+++|.. +.+.++.+.
T Consensus       288 ~~~~~-vG~vv~G~V~~I~~fGvFVeL~~--gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~  364 (486)
T PRK07899        288 ARTHA-IGQIVPGKVTKLVPFGAFVRVEE--GIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQ  364 (486)
T ss_pred             HHhcC-CCCEEEEEEEEEeccEEEEEeCC--CcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEEE
Confidence            34454 89999999999999999999987  899999999999999988999999999999999999974 467777665


Q ss_pred             ccchH
Q psy18072         88 KADGL   92 (174)
Q Consensus        88 k~~g~   92 (174)
                      ...+.
T Consensus       365 ~~~~~  369 (486)
T PRK07899        365 ANEGV  369 (486)
T ss_pred             cccCC
Confidence            54443

>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain

Probab=99.15  E-value=1.4e-10  Score=75.12  Aligned_cols=58  Identities=34%  Similarity=0.607  Sum_probs=53.5

Q ss_pred             EEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072         19 VMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus        19 V~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      |.|+|+++.++|+||.+..  +..|++|.+++++.++.++...|++||.|+|+|++++..
T Consensus         1 v~g~V~~v~~~g~~v~l~~--~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~   58 (65)
T cd00164           1 VTGKVVSITKFGVFVELED--GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPE   58 (65)
T ss_pred             CEEEEEEEEeeeEEEEecC--CCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCC
Confidence            5799999999999999987  799999999999888778888999999999999999874

Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.

>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain

Probab=99.13  E-value=3.7e-10  Score=81.44  Aligned_cols=73  Identities=18%  Similarity=0.360  Sum_probs=62.0

Q ss_pred             CEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhcc-----------ccccCCCCEEEEEEEEEeCC------C
Q psy18072         17 DVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSI-----------NKLIRVGKTEPVVVIRVDKE------K   79 (174)
Q Consensus        17 diV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~-----------~~~l~vGd~V~vrVi~Vd~~------~   79 (174)
                      ++|.|+|++|.++|+||+|..   ++||+|+++++..++...           ...|++||.|+|+|++++..      +
T Consensus         1 ~vv~g~V~~i~~~GifV~l~~---v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~   77 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIGP---VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRES   77 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEcC---eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCc
Confidence            479999999999999999963   899999999987765432           47899999999999999975      4


Q ss_pred             ceeeecccccchH
Q psy18072         80 VMTTVTPEKADGL   92 (174)
Q Consensus        80 ~l~ls~~~k~~g~   92 (174)
                      .+.+|.....+|.
T Consensus        78 ~i~ls~k~~~~g~   90 (99)
T cd04460          78 KIGLTMRQPGLGK   90 (99)
T ss_pred             eEEEEEecCCCCc
Confidence            6888888887773

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.

>TIGR00717 rpsA ribosomal protein S1

Probab=99.10  E-value=2.7e-10  Score=103.24  Aligned_cols=73  Identities=34%  Similarity=0.479  Sum_probs=65.8

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeec
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVT   85 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~   85 (174)
                      +.++ +|+++.|+|++++++|+||.|.+  ++.||||.|++++.++.++.+.|++||.|+|+|++++.. +.+.++.
T Consensus       442 ~~~~-~G~~v~g~V~~v~~~G~fV~l~~--~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~  515 (516)
T TIGR00717       442 AKYK-VGSVVKGKVTEIKDFGAFVELPG--GVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSV  515 (516)
T ss_pred             hccC-cceEEEEEEEEEecceEEEEcCC--CeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence            3455 89999999999999999999988  899999999999999999999999999999999999874 5666664

This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=99.09  E-value=3.1e-10  Score=108.74  Aligned_cols=76  Identities=22%  Similarity=0.444  Sum_probs=65.6

Q ss_pred             hhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-hccccccCCCCEEEEEEEEEeCC-Cceeeec
Q psy18072          8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-RSINKLIRVGKTEPVVVIRVDKE-KVMTTVT   85 (174)
Q Consensus         8 ~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~   85 (174)
                      +...|+ +|++|.|+|+++++||+||.|.+  +++||||+|+++|.+. .++...|++||.|+|+|+.+|+. +.+.+|.
T Consensus       659 ~~~~~~-vG~~v~G~V~~i~~~G~fV~l~~--gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~  735 (863)
T PRK12269        659 IEARYP-VGARFTRRIVKVTNAGAFIEMEE--GIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGV  735 (863)
T ss_pred             HHHhCC-CCCEEEEEEEEEecceEEEEeCC--CcEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEe
Confidence            456676 99999999999999999999987  8999999999998654 44556899999999999999986 4677776


Q ss_pred             c
Q psy18072         86 P   86 (174)
Q Consensus        86 ~   86 (174)
                      +
T Consensus       736 K  736 (863)
T PRK12269        736 K  736 (863)
T ss_pred             c
Confidence            4

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=99.06  E-value=2.9e-10  Score=105.20  Aligned_cols=72  Identities=29%  Similarity=0.528  Sum_probs=67.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecc
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTP   86 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~   86 (174)
                      +++|.+|.|+|+++.+|||||.|.+  +.+||+|+|++++.|+....+.+++||.|+|||+.+|..+++.++..
T Consensus       617 ~evg~iy~G~V~ri~~fGaFv~l~~--gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~  688 (692)
T COG1185         617 VEVGEVYEGTVVRIVDFGAFVELLP--GKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIK  688 (692)
T ss_pred             cccccEEEEEEEEEeecceEEEecC--CcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccceeh
Confidence            3599999999999999999999988  88999999999999999999999999999999999999888877753

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.05  E-value=6.2e-10  Score=97.77  Aligned_cols=75  Identities=28%  Similarity=0.504  Sum_probs=66.2

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecccc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPEK   88 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~k   88 (174)
                      .+. +|+++.|+|+++.++|+||+|.+  ++.||+|+|++++.++.++...|++||.|+|+|+++|.. +.+.++.+..
T Consensus       274 ~~~-~G~~v~g~V~~i~~~G~fV~l~~--gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~  349 (390)
T PRK06676        274 KLP-EGDVIEGTVKRLTDFGAFVEVLP--GVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKAL  349 (390)
T ss_pred             hhc-CCcEEEEEEEEEeCceEEEEECC--CCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEec
Confidence            354 89999999999999999999987  899999999999988888889999999999999999964 5677776543

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.05  E-value=9.1e-10  Score=95.03  Aligned_cols=73  Identities=18%  Similarity=0.271  Sum_probs=65.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE   87 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~   87 (174)
                      .++|++|.|+|.++.++|+||.|..  +..|+||.+++++.++.++...|++||.|.|+|++++.. +.+.+|.+.
T Consensus        29 ~~~G~iv~G~V~~i~~~g~~Vdig~--k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~  102 (318)
T PRK07400         29 FKPGDIVNGTVFSLEPRGALIDIGA--KTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRR  102 (318)
T ss_pred             cCCCCEEEEEEEEEECCEEEEEECC--CeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhh
Confidence            3599999999999999999999965  799999999999999999999999999999999999875 456777654

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.04  E-value=5.7e-10  Score=102.31  Aligned_cols=75  Identities=35%  Similarity=0.526  Sum_probs=65.6

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-hccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-RSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE   87 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~   87 (174)
                      ..++ +|++|.|+|++++++|+||+|.+  +++||||+|++++.+. .++...|++||.|+|+|+++|+. +.+.+|.+.
T Consensus       369 ~~~~-~G~~v~g~V~~v~~~G~fV~l~~--~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~  445 (565)
T PRK06299        369 EKYP-VGDVVEGKVKNITDFGAFVGLEG--GIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQ  445 (565)
T ss_pred             HhCC-CCCEEEEEEEEEecceEEEECCC--CCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEeh
Confidence            3454 89999999999999999999987  7999999999998876 78889999999999999999974 467666543

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.00  E-value=1.3e-09  Score=95.71  Aligned_cols=71  Identities=28%  Similarity=0.494  Sum_probs=63.7

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE   87 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~   87 (174)
                      ++|++|.|+|+++.++|+||.+.   +++|+||+|++++.++.++.+.|++||.|+|+|+++++. +.+.+|.+.
T Consensus       191 ~~G~~v~g~V~~v~~~G~fV~l~---~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~  262 (390)
T PRK06676        191 KEGDVVEGTVARLTDFGAFVDIG---GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKD  262 (390)
T ss_pred             CCCCEEEEEEEEEecceEEEEeC---CeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence            48999999999999999999994   599999999999999999999999999999999999874 566666653

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.00  E-value=1.2e-09  Score=100.14  Aligned_cols=73  Identities=29%  Similarity=0.496  Sum_probs=66.8

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPEK   88 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~k   88 (174)
                      ++|++|.|+|+++.++|+||.+.+  ++.||||.|+++..++.++.+.|++||.|+|+|++++.+ +.+++|....
T Consensus       459 ~~G~vV~G~V~~v~~~G~fV~l~~--gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS~k~~  532 (565)
T PRK06299        459 KKGSIVTGTVTEVKDKGAFVELED--GVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKAL  532 (565)
T ss_pred             CCCCEEEEEEEEEecCceEEecCC--CcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEccccCEEEEEeeeh
Confidence            389999999999999999999987  899999999999999999999999999999999999974 5788887544

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=98.99  E-value=7.4e-10  Score=103.90  Aligned_cols=76  Identities=22%  Similarity=0.353  Sum_probs=68.0

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeeccccc
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTPEKA   89 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~~k~   89 (174)
                      ..++|.++.|+|.++.+||+||.|.-  +..|+||+|+++.+++.+|.+++++||.|+|+|+.||..+ .+.+|.+..+
T Consensus       655 dLk~Gm~leg~Vrnv~~fgafVdIgv--~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~  731 (780)
T COG2183         655 DLKPGMILEGTVRNVVDFGAFVDIGV--HQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDE  731 (780)
T ss_pred             hccCCCEEEEEEEEeeeccceEEecc--ccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence            44599999999999999999999987  7899999999999999999999999999999999999865 5666665543

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

Probab=98.98  E-value=1.7e-09  Score=101.07  Aligned_cols=76  Identities=32%  Similarity=0.554  Sum_probs=67.2

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecccc
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPEK   88 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~k   88 (174)
                      ..++ +|++|.|+|++++++|+||.|.+  ++.||+|++++++.++.++...|++||.|+|+|++++.+ +.+.++.+..
T Consensus       558 ~~~~-~G~~v~g~V~~i~~~G~fV~l~~--~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~  634 (647)
T PRK00087        558 EKYP-VGSIVLGKVVRIAPFGAFVELEP--GVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEV  634 (647)
T ss_pred             hhcc-CCeEEEEEEEEEECCeEEEEECC--CCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence            3454 89999999999999999999987  899999999999999999999999999999999999974 5666666544

>TIGR02063 RNase_R ribonuclease R

Probab=98.93  E-value=3.1e-09  Score=100.18  Aligned_cols=78  Identities=21%  Similarity=0.364  Sum_probs=63.5

Q ss_pred             cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-----------hccccccCCCCEEEEE
Q psy18072          3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-----------RSINKLIRVGKTEPVV   71 (174)
Q Consensus         3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-----------~~~~~~l~vGd~V~vr   71 (174)
                      +.|+|+...   +|.++.|+|++|++||+||+|.++ +++||||+|++++.++           ++..+.|++||.|+|+
T Consensus       618 ~~~~yl~~~---iG~~~~g~V~~v~~fGifV~L~~~-~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vk  693 (709)
T TIGR02063       618 KKAEYMSEK---IGEEFEGVISGVTSFGLFVELENN-TIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVR  693 (709)
T ss_pred             HHHHhhhcc---CCcEEEEEEEEEEeCCEEEEecCC-ceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEE
Confidence            368876653   699999999999999999999875 4999999999986653           2345689999999999


Q ss_pred             EEEEeCC-Cceeee
Q psy18072         72 VIRVDKE-KVMTTV   84 (174)
Q Consensus        72 Vi~Vd~~-~~l~ls   84 (174)
                      |++||.. +.+.++
T Consensus       694 v~~vd~~~~~I~~~  707 (709)
T TIGR02063       694 VVKADLDTGKIDFE  707 (709)
T ss_pred             EEEEecccCeEEEE
Confidence            9999974 445443

This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.

>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional

Probab=98.89  E-value=1.5e-08  Score=80.97  Aligned_cols=87  Identities=20%  Similarity=0.423  Sum_probs=69.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-----------ccccccCCCCEEEEEEEEEeCCC--
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-----------SINKLIRVGKTEPVVVIRVDKEK--   79 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-----------~~~~~l~vGd~V~vrVi~Vd~~~--   79 (174)
                      |.+|+++.|+|+++.++|+||+|..   ++|++|.+++..+++.           +....+++||.|++||++++...  
T Consensus        79 P~~GEVv~g~V~~v~~~Gi~V~lg~---~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~  155 (187)
T PRK08563         79 PELQEVVEGEVVEVVEFGAFVRIGP---VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERR  155 (187)
T ss_pred             ccCCCEEEEEEEEEEccEEEEEEeC---ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCC
Confidence            4589999999999999999999964   8999999999866432           34568999999999999998752  


Q ss_pred             ----ceeeecccccchHHHHHHHHHHHHHHHhh
Q psy18072         80 ----VMTTVTPEKADGLKALQEAIDTIKAKIEQ  108 (174)
Q Consensus        80 ----~l~ls~~~k~~g~~~i~~~~~~i~~~l~~  108 (174)
                          .+.+|...+-+|      .++|+.+..++
T Consensus       156 ~~~~~I~ls~~~~~LG------~~~w~~~~~~~  182 (187)
T PRK08563        156 PRGSKIGLTMRQPGLG------KLEWIEEEKKK  182 (187)
T ss_pred             CCCCEEEEEecCCCCC------cHHHHHHHHhh
Confidence                577788777666      45777665554

>TIGR00717 rpsA ribosomal protein S1

Probab=98.88  E-value=4.9e-09  Score=95.00  Aligned_cols=73  Identities=26%  Similarity=0.495  Sum_probs=63.1

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchh-hhhccccccCCCCEEEEEEEEEeCC-Cceeeecc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRR-RIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTP   86 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~-~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~   86 (174)
                      .++ +|+++.|+|+++.++|+||.|.+  ++.||||+|++++. ...++.+.+++||.|+|+|+++|+. +.+.+|++
T Consensus       269 ~~~-~G~i~~g~V~~v~~~G~fV~l~~--~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k  343 (516)
T TIGR00717       269 KFP-VGDKITGRVTNLTDYGVFVEIEE--GIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK  343 (516)
T ss_pred             hcc-CCCEEEEEEEEeeCCcEEEEeCC--CCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEeh
Confidence            454 89999999999999999999987  89999999999975 3556677899999999999999985 46777654

This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

Probab=98.88  E-value=5.6e-09  Score=97.60  Aligned_cols=71  Identities=28%  Similarity=0.513  Sum_probs=64.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE   87 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~   87 (174)
                      ++|++|.|+|+++.++|+||.| +  +++||||+|++++.++.++.+.|++||.|+|+|+++++. +.+.+|++.
T Consensus       476 ~~G~iV~g~V~~v~~~G~fV~l-~--gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~  547 (647)
T PRK00087        476 EEGDVVEGEVKRLTDFGAFVDI-G--GVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKK  547 (647)
T ss_pred             CCCCEEEEEEEEEeCCcEEEEE-C--CEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeec
Confidence            4899999999999999999999 6  799999999999999999999999999999999999874 567777643

>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain

Probab=98.86  E-value=1.4e-08  Score=68.28  Aligned_cols=57  Identities=19%  Similarity=0.188  Sum_probs=50.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      +.|++|.|+|.++.++|+||.+.   +.+|+||.++++.      .+.+++||.|+|.|++++..+
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig---~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~   58 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLG---KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTS   58 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcC---CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCC
Confidence            37999999999999999999994   4899999999872      367899999999999998653

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=98.82  E-value=1.4e-08  Score=84.06  Aligned_cols=85  Identities=22%  Similarity=0.360  Sum_probs=73.2

Q ss_pred             cchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh----hccccccCCCCEEEEEEEEEeCCCc
Q psy18072          5 CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI----RSINKLIRVGKTEPVVVIRVDKEKV   80 (174)
Q Consensus         5 ~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v----~~~~~~l~vGd~V~vrVi~Vd~~~~   80 (174)
                      +++...+.|++||+|.|+|..+...+|.|.|..  .+.|++|+|++.++.+    ++++..|++||.|.|||.+++....
T Consensus        54 Ipl~g~YiP~~gD~VIG~I~~v~~~~W~VDI~s--p~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~  131 (239)
T COG1097          54 IPLEGRYIPEVGDVVIGKIIEVGPSGWKVDIGS--PYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGE  131 (239)
T ss_pred             EeCCCcccCCCCCEEEEEEEEEcccceEEEcCC--ccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCc
Confidence            455566778899999999999999999999988  7999999999966553    4678999999999999999999998


Q ss_pred             eeeecccccch
Q psy18072         81 MTTVTPEKADG   91 (174)
Q Consensus        81 l~ls~~~k~~g   91 (174)
                      ..+++++...|
T Consensus       132 ~~L~~k~~~~G  142 (239)
T COG1097         132 VELTLKDEGLG  142 (239)
T ss_pred             eEEEeecCCCc
Confidence            88888666433

>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]

Probab=98.81  E-value=1.2e-09  Score=99.75  Aligned_cols=110  Identities=25%  Similarity=0.259  Sum_probs=92.6

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-----------cee
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-----------VMT   82 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-----------~l~   82 (174)
                      +.|.+|.|+|+++..||+||+|+.  .+.||+|.+.++..      ..+.+|+.+.|+|..|.+.+           .+.
T Consensus       121 e~g~~Y~g~v~~v~~~GvFv~Ln~--~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~~Y~  192 (715)
T COG1107         121 EAGKYYKGIVSRVEKYGVFVELNS--HVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLDRYR  192 (715)
T ss_pred             ccceeeeccccchhhhcceeecCh--hhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCccch
Confidence            589999999999999999999998  89999999998852      46899999999999999884           233


Q ss_pred             eecccccchHHHHHHHHHHHHHHHhhhCCeeEEe--eCceeEeccCHHHHH
Q psy18072         83 TVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQ--MAPKVVTASDEAELA  131 (174)
Q Consensus        83 ls~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k--~~P~~i~~~~~~~~k  131 (174)
                      .....+++++..+.+.-+.+++.+...|...++|  ++|++|+-+|...+.
T Consensus       193 ~~~~~ke~~r~~i~~id~~ig~tV~I~GeV~qikqT~GPTVFtltDetg~i  243 (715)
T COG1107         193 EVQVEKELPRTLIDDLDEMIGKTVRIEGEVTQIKQTSGPTVFTLTDETGAI  243 (715)
T ss_pred             hhhhhhhcccccHHHHHhhcCceEEEEEEEEEEEEcCCCEEEEEecCCCce
Confidence            5556677887778888888899998899888884  999999977764443

>PRK11642 exoribonuclease R; Provisional

Probab=98.79  E-value=1.4e-08  Score=97.16  Aligned_cols=73  Identities=27%  Similarity=0.452  Sum_probs=61.2

Q ss_pred             cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-----------ccccccCCCCEEEEE
Q psy18072          3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-----------SINKLIRVGKTEPVV   71 (174)
Q Consensus         3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-----------~~~~~l~vGd~V~vr   71 (174)
                      +.|+|+..+   +|+++.|+|++|++||+||+|.++ +++||||++++.++++.           ...+.|++||.|+|+
T Consensus       634 ~~~~~m~~~---iGe~f~G~Is~V~~fGifVeL~~~-~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~Vk  709 (813)
T PRK11642        634 LKCDFMLDQ---VGNVFKGVISSVTGFGFFVRLDDL-FIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVR  709 (813)
T ss_pred             HHHhhhhcc---CCcEEEEEEEEeecCceEEEECCC-CeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEE
Confidence            468866662   799999999999999999999873 39999999999876432           234789999999999


Q ss_pred             EEEEeCCC
Q psy18072         72 VIRVDKEK   79 (174)
Q Consensus        72 Vi~Vd~~~   79 (174)
                      |++|+..+
T Consensus       710 V~~vD~~~  717 (813)
T PRK11642        710 VEAVNMDE  717 (813)
T ss_pred             EEEeecCC
Confidence            99999755

>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form

Probab=98.79  E-value=2.9e-08  Score=78.98  Aligned_cols=75  Identities=20%  Similarity=0.314  Sum_probs=60.7

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-----------ccccccCCCCEEEEEEEEEeC-----
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-----------SINKLIRVGKTEPVVVIRVDK-----   77 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-----------~~~~~l~vGd~V~vrVi~Vd~-----   77 (174)
                      .+|+++.|+|++++++|+||+|.   .++|++|.+++...++.           +....+++||.|++||++++.     
T Consensus        80 ~~gEvv~G~V~~v~~~GifV~lg---~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~  156 (179)
T TIGR00448        80 ELGEIVEGEVIEIVEFGAFVSLG---PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP  156 (179)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEeC---CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC
Confidence            37999999999999999999994   48999999998865432           234789999999999999984     


Q ss_pred             -CCceeeecccccch
Q psy18072         78 -EKVMTTVTPEKADG   91 (174)
Q Consensus        78 -~~~l~ls~~~k~~g   91 (174)
                       ...+.+|.+.+-+|
T Consensus       157 ~~~~I~lt~k~~~LG  171 (179)
T TIGR00448       157 EGSKIGLTMRQPLLG  171 (179)
T ss_pred             CcceEEEEeccCcCC
Confidence             23567777666555

This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.

>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]

Probab=98.78  E-value=1.1e-08  Score=81.62  Aligned_cols=76  Identities=20%  Similarity=0.380  Sum_probs=60.5

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-----------ccccccCCCCEEEEEEEEEeCCC--
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-----------SINKLIRVGKTEPVVVIRVDKEK--   79 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-----------~~~~~l~vGd~V~vrVi~Vd~~~--   79 (174)
                      |..|++|.|.|+++.+||+||.|.+   ..||||+|++.+.++.           .-...+++|+.|+|||+++....  
T Consensus        79 P~~gEVV~GeVv~~~~~G~fV~igp---~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~  155 (183)
T COG1095          79 PFRGEVVEGEVVEVVEFGAFVRIGP---LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR  155 (183)
T ss_pred             eccccEEEEEEEEEeecceEEEecc---ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCc
Confidence            4579999999999999999999986   8999999999987432           13348999999999999988754  


Q ss_pred             ----ceeeecccccch
Q psy18072         80 ----VMTTVTPEKADG   91 (174)
Q Consensus        80 ----~l~ls~~~k~~g   91 (174)
                          .+.+|.+.+-+|
T Consensus       156 ~~~~~I~lTmrq~~LG  171 (183)
T COG1095         156 PRESKIGLTMRQPGLG  171 (183)
T ss_pred             cccceEEEEeccccCC
Confidence                345555555333

>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain

Probab=98.74  E-value=5.3e-08  Score=69.22  Aligned_cols=75  Identities=12%  Similarity=0.042  Sum_probs=62.3

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEK   88 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k   88 (174)
                      ..|++||.|.|+|+.+....++|.|..  .+.|++|.+.+... .+..+..|++||.|.|||.++++.....+++.++
T Consensus         2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s--~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~   76 (86)
T cd05790           2 YVPAKGDHVIGIVVAKAGDFFKVDIGG--SEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRDMEPELSCVDS   76 (86)
T ss_pred             CcCCCCCEEEEEEEEEcCCeEEEEcCC--CcceEechHHcccc-cccccccCCCCCEEEEEEEecCCCCCeEEEEeCC
Confidence            356799999999999999999999988  68999999887432 3334678999999999999999877677777653

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases

Probab=98.74  E-value=2.8e-08  Score=93.07  Aligned_cols=73  Identities=27%  Similarity=0.493  Sum_probs=61.1

Q ss_pred             cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-----------hccccccCCCCEEEEE
Q psy18072          3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-----------RSINKLIRVGKTEPVV   71 (174)
Q Consensus         3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-----------~~~~~~l~vGd~V~vr   71 (174)
                      +.|+|+.++   +|.++.|+|++|+++|+||.|.++ +++||||++++.++++           ++....|++||.|+|+
T Consensus       563 ~~~~yl~~~---iG~~~~g~I~~v~~~GifV~L~~~-~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vk  638 (654)
T TIGR00358       563 LKCRYLLDK---VGTEFSGEISSVTRFGMFVRLDDN-GIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVK  638 (654)
T ss_pred             HHHHhhhhC---CCcEEEEEEEeEEcCcEEEEecCC-ceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEE
Confidence            358876663   699999999999999999999854 5999999999987652           2234789999999999


Q ss_pred             EEEEeCCC
Q psy18072         72 VIRVDKEK   79 (174)
Q Consensus        72 Vi~Vd~~~   79 (174)
                      |++||..+
T Consensus       639 i~~vd~~~  646 (654)
T TIGR00358       639 LTEVNMET  646 (654)
T ss_pred             EEEEeccc
Confidence            99998754

This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.

>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []

Probab=98.66  E-value=7e-08  Score=67.99  Aligned_cols=64  Identities=22%  Similarity=0.325  Sum_probs=43.9

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCC----------------CCeEEEEEceecchhhhh--ccccccCCCCEEEEEEE
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEY----------------NNIEGMILLSELSRRRIR--SINKLIRVGKTEPVVVI   73 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~----------------~~~~GlI~iSels~~~v~--~~~~~l~vGd~V~vrVi   73 (174)
                      +|++|++|.|+|+++++.-|++.|...                ..+.|+||.+++......  .+.+.|++||.|+|+|+
T Consensus         1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~Vi   80 (82)
T PF10447_consen    1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVI   80 (82)
T ss_dssp             ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEE
T ss_pred             CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEe
Confidence            478999999999999999999888654                147999999988754433  35789999999999999


Q ss_pred             EE
Q psy18072         74 RV   75 (174)
Q Consensus        74 ~V   75 (174)
                      +.
T Consensus        81 Sl   82 (82)
T PF10447_consen   81 SL   82 (82)
T ss_dssp             EE
T ss_pred             eC
Confidence            74

The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.

>KOG1067|consensus

Probab=98.53  E-value=9.5e-08  Score=87.21  Aligned_cols=68  Identities=24%  Similarity=0.317  Sum_probs=62.3

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeee
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTV   84 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls   84 (174)
                      .|-+|+|+|+++.++|+||.|.+  ...||+|+|+|+.+++.++.+.+.+||.|.|+.+..|+.+.+.++
T Consensus       668 ~g~vy~~tIt~~rd~G~~V~l~p--~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~~~ls  735 (760)
T KOG1067|consen  668 FGGVYTATITEIRDTGVMVELYP--MQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLS  735 (760)
T ss_pred             eeeEEEEEEeeecccceEEEecC--CchhhccchhcccccccChHHHHhhcceeEEEEEeecCccceeeh
Confidence            68889999999999999999977  899999999999999999999999999999999999987755443

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.48  E-value=6.6e-07  Score=81.05  Aligned_cols=94  Identities=18%  Similarity=0.199  Sum_probs=69.8

Q ss_pred             hhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC---ceeee
Q psy18072          8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK---VMTTV   84 (174)
Q Consensus         8 ~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~---~l~ls   84 (174)
                      |...-.+.|++|+|+|.++.++|+||.|.   +++||||.++++      ++..|++||.|+|.|++|+..+   .+-+|
T Consensus       127 ~~eyk~~~GeIV~G~V~ri~~~giiVDLg---gvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilS  197 (470)
T PRK09202        127 YEEYKDRVGEIITGVVKRVERGNIIVDLG---RAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILS  197 (470)
T ss_pred             HHHHHhhcCCEEEEEEEEEecCCEEEEEC---CeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEE
Confidence            33333358999999999999999999993   699999999985      5688999999999999999864   35555


Q ss_pred             cccccchHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072         85 TPEKADGLKALQEAIDTIKAKIEQLGGVFQVQ  116 (174)
Q Consensus        85 ~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k  116 (174)
                      ...+  .  .+...++  .++=+...|.+.++
T Consensus       198 Rt~p--~--~l~~Lf~--~EVPEI~~G~ieIk  223 (470)
T PRK09202        198 RTHP--E--FLKKLFE--QEVPEIADGLIEIK  223 (470)
T ss_pred             eCcH--H--HHHHHHH--HhCcccccCeEEEE
Confidence            5544  3  2333332  23335567887775

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=98.38  E-value=6.9e-06  Score=73.43  Aligned_cols=61  Identities=21%  Similarity=0.275  Sum_probs=52.3

Q ss_pred             cCCCCCCEEEEEEEEEecc--eEEEEECCCCCeEEEEEceecchh------------hhhccccccCCCCEEEEEEEE
Q psy18072         11 KYPEVEDVVMVTVISIAEM--GAYVHLLEYNNIEGMILLSELSRR------------RIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~--GafV~L~~~~~~~GlI~iSels~~------------~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      ..+ +|++|.|+|.+|.+.  ||||.|..  +..||||++++.+.            +..++.+.+++||.|.|+|++
T Consensus        22 ~~~-vGnIY~GrV~~i~p~l~aAFVdiG~--~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K   96 (414)
T TIGR00757        22 RQL-KGNIYKGRVTRILPSLQAAFVDIGL--EKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK   96 (414)
T ss_pred             cCC-CCCEEEEEEeeecCCCceEEEEcCC--CceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee
Confidence            344 899999999999998  99999987  78999999998643            234566789999999999998

The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.

>PRK05054 exoribonuclease II; Provisional

Probab=98.34  E-value=1.3e-06  Score=81.93  Aligned_cols=75  Identities=24%  Similarity=0.298  Sum_probs=57.6

Q ss_pred             cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh--hh----------ccccccCCCCEEEE
Q psy18072          3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR--IR----------SINKLIRVGKTEPV   70 (174)
Q Consensus         3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~--v~----------~~~~~l~vGd~V~v   70 (174)
                      +.|+|+.+. +-.|..+.|.|++|+++|+||+|.++ +++||||++.+...+  +.          .-.+.|++||.|+|
T Consensus       550 ~~~~y~~~~-~G~~~~f~g~I~~v~~~G~fV~l~~~-~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V  627 (644)
T PRK05054        550 LYARYLKDK-AGTDTRFAAEIIDISRGGMRVRLLEN-GAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDV  627 (644)
T ss_pred             HHHHHHhhc-cCCCeEEEEEEEeeecCcEEEEEeCC-ceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEE
Confidence            367866653 21245999999999999999999874 599999999986531  11          11257999999999


Q ss_pred             EEEEEeCCC
Q psy18072         71 VVIRVDKEK   79 (174)
Q Consensus        71 rVi~Vd~~~   79 (174)
                      +|.+||..+
T Consensus       628 ~v~~vd~~~  636 (644)
T PRK05054        628 TLAEVRMET  636 (644)
T ss_pred             EEEEEcccc
Confidence            999999753

>KOG1070|consensus

Probab=98.30  E-value=1.2e-06  Score=86.35  Aligned_cols=75  Identities=25%  Similarity=0.323  Sum_probs=66.3

Q ss_pred             hhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeecc
Q psy18072          8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTP   86 (174)
Q Consensus         8 ~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~   86 (174)
                      |.+..  +|.++.|+|-.+.++||||++.+  ++.||.|.|++++.++.+...+|.+||+|.|+|+++|.++ .+.++++
T Consensus       594 ~~~~~--pg~~~~G~l~~~~~~g~~V~F~g--~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r  669 (1710)
T KOG1070|consen  594 FEQAI--PGKITKGTLCAIKENGAFVTFTG--GLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLR  669 (1710)
T ss_pred             hhhcC--CCceEEEEEeeeccCCeEEEecC--ccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhh
Confidence            44443  59999999999999999999977  9999999999999999999999999999999999999876 4555543

>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain

Probab=98.25  E-value=6.6e-06  Score=58.49  Aligned_cols=61  Identities=13%  Similarity=0.109  Sum_probs=50.1

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhc-----------cccccCCCCEEEEEEEEEeCC
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRS-----------INKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~-----------~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      +|+++.|+|+++.++|+||.+.+   +.+|+|.+.+......+           -...+.+|+.|++||+.+..+
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gp---l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~   72 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGP---LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVD   72 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcC---ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEc
Confidence            48999999999999999999976   88999999886543211           245699999999999998764

RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.19  E-value=8.2e-06  Score=71.79  Aligned_cols=92  Identities=20%  Similarity=0.209  Sum_probs=68.1

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC---ceeeecc
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK---VMTTVTP   86 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~---~l~ls~~   86 (174)
                      ....+.|++|+|+|.++.+.|+||.|.   +++|+||.+++.      ++..|++||.++|.|++|+..+   .+.+|..
T Consensus       129 ef~~k~GeiV~G~V~~~~~~~~~Vdlg---~vEa~LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt  199 (362)
T PRK12327        129 EFSEREGDIVTGVVQRRDNRFVYVNLG---KIEAVLPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT  199 (362)
T ss_pred             HHHHhcCCEEEEEEEEEeCCcEEEEeC---CeEEEecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence            333358999999999999999999994   599999988764      3578999999999999999654   4666665


Q ss_pred             cccchHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072         87 EKADGLKALQEAIDTIKAKIEQLGGVFQVQ  116 (174)
Q Consensus        87 ~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k  116 (174)
                      .+  .  .+...++  .++=+...|.+.++
T Consensus       200 ~p--~--~v~~Lfe--~EVPEI~~G~VeIk  223 (362)
T PRK12327        200 HP--G--LVKRLFE--LEVPEIYDGTVEIK  223 (362)
T ss_pred             CH--H--HHHHHHH--HhCccccCCeEEEE
Confidence            55  3  2333332  23335567877775

>TIGR01953 NusA transcription termination factor NusA

Probab=98.19  E-value=9.7e-06  Score=70.80  Aligned_cols=88  Identities=19%  Similarity=0.273  Sum_probs=65.8

Q ss_pred             CCCCEEEEEEEEEecce-EEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC---ceeeeccccc
Q psy18072         14 EVEDVVMVTVISIAEMG-AYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK---VMTTVTPEKA   89 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~G-afV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~---~l~ls~~~k~   89 (174)
                      +.|++|+|+|.++.+.| +||.| +  +.+|+||.++..      +...|++||.++|.|++|+...   .+.+|...+ 
T Consensus       130 k~GeiV~G~V~~v~~~g~v~Vdi-G--~~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~-  199 (341)
T TIGR01953       130 KEGEIISGTVKRVNRRGNLYVEL-G--KTEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP-  199 (341)
T ss_pred             hcCCEEEEEEEEEecCCcEEEEE-C--CeEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH-
Confidence            58999999999999888 69999 4  699999999877      3467999999999999999653   356665555 


Q ss_pred             chHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072         90 DGLKALQEAIDTIKAKIEQLGGVFQVQ  116 (174)
Q Consensus        90 ~g~~~i~~~~~~i~~~l~~~~g~l~~k  116 (174)
                       .  .+...++  .++=+..+|.+.++
T Consensus       200 -~--~v~~Lfe--~EVPEI~dG~VeI~  221 (341)
T TIGR01953       200 -E--FVKELLK--LEVPEIADGIIEIK  221 (341)
T ss_pred             -H--HHHHHHH--HhCccccCCeEEEE
Confidence             3  2333333  23335577887774

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

>TIGR02062 RNase_B exoribonuclease II

Probab=98.08  E-value=8.1e-06  Score=76.56  Aligned_cols=75  Identities=25%  Similarity=0.347  Sum_probs=57.2

Q ss_pred             cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch--hhh-----h---cc--ccccCCCCEEEE
Q psy18072          3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR--RRI-----R---SI--NKLIRVGKTEPV   70 (174)
Q Consensus         3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~--~~v-----~---~~--~~~l~vGd~V~v   70 (174)
                      +.|+|+.++.- .|..+.|+|++++.+|+||.|.+. +++||||++.+..  .++     .   .+  ...|++||.|+|
T Consensus       546 ~~~~yl~~~~g-~~~~f~g~I~~v~~~g~~v~l~~~-~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V  623 (639)
T TIGR02062       546 LYARFLADKAA-KNTRFAAEIVDISRGGMRVRLLEN-GAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDV  623 (639)
T ss_pred             HHHHHHhhccC-CCcEEEEEEEeeeCCcEEEEEecC-ceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEE
Confidence            35776666421 355999999999999999999763 6999999999865  222     1   11  136999999999


Q ss_pred             EEEEEeCCC
Q psy18072         71 VVIRVDKEK   79 (174)
Q Consensus        71 rVi~Vd~~~   79 (174)
                      +|.+||..+
T Consensus       624 ~v~~vd~~~  632 (639)
T TIGR02062       624 VLTEVRMET  632 (639)
T ss_pred             EEEEecccc
Confidence            999998653

This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=98.05  E-value=8.1e-06  Score=77.28  Aligned_cols=72  Identities=25%  Similarity=0.414  Sum_probs=59.9

Q ss_pred             cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-----------hccccccCCCCEEEEE
Q psy18072          3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-----------RSINKLIRVGKTEPVV   71 (174)
Q Consensus         3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-----------~~~~~~l~vGd~V~vr   71 (174)
                      +.|+|+...   +|..+.|+|++++.||+||.|+++ +++|+||++.+...++           ......+++||.|+|+
T Consensus       613 ~~~~~m~~~---vg~~f~g~V~~v~~~g~~V~l~~~-~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~  688 (706)
T COG0557         613 LKAEYMKKR---VGEEFDGVVTGVTSFGFFVELPEL-GLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVK  688 (706)
T ss_pred             HHHHHHHHh---cCCEEEEEEEEEEeccEEEEeccc-ccccceEcccCCCceeeeccccceeeccccccccccCCEEEEE
Confidence            367765553   699999999999999999999985 3999999999986543           2345689999999999


Q ss_pred             EEEEeCC
Q psy18072         72 VIRVDKE   78 (174)
Q Consensus        72 Vi~Vd~~   78 (174)
                      |++++..
T Consensus       689 v~~v~~~  695 (706)
T COG0557         689 VTSVDLD  695 (706)
T ss_pred             EEEEccc
Confidence            9999874

>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional

Probab=98.01  E-value=3.2e-05  Score=61.65  Aligned_cols=62  Identities=11%  Similarity=0.130  Sum_probs=51.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh-----------h-hccccccCCCCEEEEEEEEEeCC
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR-----------I-RSINKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~-----------v-~~~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      -+|+++.|+|+++.++|+||++..   ++++||.+++....           . .+-...+..|+.|++||+.+..+
T Consensus        80 f~gEVv~g~V~~v~~~G~~v~~Gp---~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~  153 (176)
T PTZ00162         80 FKDEVLDAIVTDVNKLGFFAQAGP---LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYD  153 (176)
T ss_pred             CCCCEEEEEEEEEecceEEEEeeC---eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEec
Confidence            379999999999999999999965   77999999987431           1 12246899999999999998764

>KOG1070|consensus

Probab=97.80  E-value=7.6e-05  Score=74.19  Aligned_cols=72  Identities=21%  Similarity=0.298  Sum_probs=65.3

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeeccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTPE   87 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~~   87 (174)
                      +.|++|.|.|..+.+.|+||.|..  +++|++++|+++..+...+.+.|.+|+.|.+||++++... .+.++++.
T Consensus      1161 k~g~iv~G~V~nv~~~glfi~ls~--~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~ 1233 (1710)
T KOG1070|consen 1161 KIGDIVRGFVKNVETKGLFIALSR--KVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKN 1233 (1710)
T ss_pred             ccCceeEEEEEEecCCcEEEEEcc--ceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEec
Confidence            489999999999999999999988  8999999999999999999999999999999999999876 55555544

>KOG3409|consensus

Probab=97.78  E-value=8.2e-05  Score=59.10  Aligned_cols=85  Identities=22%  Similarity=0.232  Sum_probs=65.6

Q ss_pred             hhccCCCCCCEEEEEEEEEecceEEEEECC-----C-CCeEEEEEceecchh--hhhccccccCCCCEEEEEEEEEeCCC
Q psy18072          8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLE-----Y-NNIEGMILLSELSRR--RIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus         8 ~~~~~p~~GdiV~G~V~~i~~~GafV~L~~-----~-~~~~GlI~iSels~~--~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      +..-+|..|++|.++|..+...-|-|.|..     + ..+.|+||...+...  ---.+.+.|++||.|.|+|++.....
T Consensus        61 ~~~~LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~  140 (193)
T KOG3409|consen   61 FNELLPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGS  140 (193)
T ss_pred             hhhcCCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCC
Confidence            345678899999999999987777666653     2 147999998876531  11235678999999999999977777


Q ss_pred             ceeeecccccchH
Q psy18072         80 VMTTVTPEKADGL   92 (174)
Q Consensus        80 ~l~ls~~~k~~g~   92 (174)
                      .+-|++...++|.
T Consensus       141 ~y~LTtAeneLGV  153 (193)
T KOG3409|consen  141 NYLLTTAENELGV  153 (193)
T ss_pred             cEEEEEecccceE
Confidence            8899998888885

>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.66  E-value=0.00026  Score=48.68  Aligned_cols=56  Identities=18%  Similarity=0.214  Sum_probs=49.4

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh---hccccccCCCCEE-EEEEE
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI---RSINKLIRVGKTE-PVVVI   73 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v---~~~~~~l~vGd~V-~vrVi   73 (174)
                      |++|.|+|..-++.+++|+|.++ ++.|+||..++++ .+   +..-..+++||.+ .+.|+
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~~-~l~a~l~~~HLsD-~~~k~~~~~~klrvG~~L~~~lvL   60 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILPE-EIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCL   60 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCC-CcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE
Confidence            78999999999999999999986 5999999999998 43   3355789999999 99999

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=97.53  E-value=0.00058  Score=45.14  Aligned_cols=60  Identities=25%  Similarity=0.338  Sum_probs=34.7

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVT   85 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~   85 (174)
                      +|++.+.+|..+.++|+|+....  .-+-+||.+++.        ..+++||.|.|-|-. |..+.+.+|+
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~--~~~vlLp~~e~~--------~~~~~Gd~v~VFvY~-D~~~rl~AT~   60 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGE--GKEVLLPKSEVP--------EPLKVGDEVEVFVYL-DKEGRLVATT   60 (61)
T ss_dssp             --------EEEE-SSEEEEEETT---EEEEEEGGG--------------TTSEEEEEEEE--TTS-EEEE-
T ss_pred             CCCCcceEEEEEeCCEEEEECCC--CCEEEechHHcC--------CCCCCCCEEEEEEEE-CCCCCEEEec
Confidence            48899999999999999999766  689999999887        569999999998754 5555565554

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.53  E-value=0.00043  Score=61.14  Aligned_cols=94  Identities=15%  Similarity=0.226  Sum_probs=66.8

Q ss_pred             hhccCCCCCCEEEEEEEEEecc-eEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCc----ee
Q psy18072          8 YAEKYPEVEDVVMVTVISIAEM-GAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKV----MT   82 (174)
Q Consensus         8 ~~~~~p~~GdiV~G~V~~i~~~-GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~----l~   82 (174)
                      |.....++|++|.|+|.++... ++||.|.   +.+|+||.++..      ++..|++||.++|.|.+|.....    +-
T Consensus       131 ~~ey~~~~Geiv~g~V~r~~~~~~i~vdlg---~~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~Ii  201 (374)
T PRK12328        131 FEKYKKKVGKIVFGTVVRVDNEENTFIEID---EIRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIE  201 (374)
T ss_pred             HHHHHHhcCcEEEEEEEEEecCCCEEEEcC---CeEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEE
Confidence            3344446899999999999764 5899985   599999988755      45889999999999999988643    34


Q ss_pred             eecccccchHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072         83 TVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQ  116 (174)
Q Consensus        83 ls~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k  116 (174)
                      +|...+  +  .+...++  .++=+..+|.+.++
T Consensus       202 lSRt~p--~--~v~~Lfe--~EVPEI~dG~VeIk  229 (374)
T PRK12328        202 LSRTSP--K--FLEALLE--LEVPEIKDGEVIII  229 (374)
T ss_pred             EEcCCH--H--HHHHHHH--HhCccccCCeEEEE
Confidence            444444  3  2333333  23335577887774

>KOG1856|consensus

Probab=97.52  E-value=0.00016  Score=70.83  Aligned_cols=63  Identities=33%  Similarity=0.452  Sum_probs=56.8

Q ss_pred             CCCEEEEEEEEEecce---EEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         15 VEDVVMVTVISIAEMG---AYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~G---afV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      .|.+|.++|++|+..-   +-|.+.+  ++.|+||.+.+|.+.+++|...+++||+|.+||++++..+
T Consensus       985 ~g~iV~~~V~~vt~rr~~Cv~v~ld~--G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~ 1050 (1299)
T KOG1856|consen  985 EGAIVPVTVTKVTHRRGICVRVRLDC--GVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKER 1050 (1299)
T ss_pred             cCceEEEeeeEEEecccceeEEEecC--CCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhh
Confidence            7999999999996543   4567777  8999999999999999999999999999999999999887

>PRK11712 ribonuclease G; Provisional

Probab=97.47  E-value=0.002  Score=58.96  Aligned_cols=59  Identities=20%  Similarity=0.303  Sum_probs=48.0

Q ss_pred             CCCEEEEEEEEEec--ceEEEEECCCCCeEEEEEceecchh------------hhhccccccCCCCEEEEEEEEE
Q psy18072         15 VEDVVMVTVISIAE--MGAYVHLLEYNNIEGMILLSELSRR------------RIRSINKLIRVGKTEPVVVIRV   75 (174)
Q Consensus        15 ~GdiV~G~V~~i~~--~GafV~L~~~~~~~GlI~iSels~~------------~v~~~~~~l~vGd~V~vrVi~V   75 (174)
                      +|++|.|+|.+|.+  .+|||.|..  +..||+|++++...            ....+.+.+++||.|-|+|++-
T Consensus        38 vGnIY~G~V~~v~pg~~AAFVdIG~--~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke  110 (489)
T PRK11712         38 VGNIYKGRVSRVLPGMQAAFVDIGL--DKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD  110 (489)
T ss_pred             cccEEEEEEeecCCCCceeEEeeCC--CccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence            89999999999965  389999988  89999999987321            1223456799999999999983

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=97.42  E-value=0.00095  Score=60.10  Aligned_cols=97  Identities=14%  Similarity=0.123  Sum_probs=68.9

Q ss_pred             hhccCCCCCCEEEEEEEEEecceEEEEECC-CCC--eEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC----c
Q psy18072          8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLE-YNN--IEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK----V   80 (174)
Q Consensus         8 ~~~~~p~~GdiV~G~V~~i~~~GafV~L~~-~~~--~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~----~   80 (174)
                      |.....++|++|+|+|.++...+++|.|.. ++.  .+|+||.++..      ++..|++|+.|+|.|.+|....    .
T Consensus       145 ~~ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpq  218 (449)
T PRK12329        145 QEEFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQ  218 (449)
T ss_pred             HHHHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCE
Confidence            334444689999999999988899999942 223  89999988754      4588999999999999997752    3


Q ss_pred             eeeecccccchHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072         81 MTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQ  116 (174)
Q Consensus        81 l~ls~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k  116 (174)
                      +.+|...+  +  .+...++  .++=+...|.+.++
T Consensus       219 IilSRt~p--~--lv~~Lfe--~EVPEI~dG~VeIk  248 (449)
T PRK12329        219 LFVSRANA--G--LVVYLFE--NEVPEIEEGVVRIV  248 (449)
T ss_pred             EEEEcCCH--H--HHHHHHH--hhCcccccCeEEEE
Confidence            55555555  4  2333333  23335577888775

>PRK10811 rne ribonuclease E; Reviewed

Probab=97.23  E-value=0.00067  Score=65.95  Aligned_cols=61  Identities=18%  Similarity=0.285  Sum_probs=49.6

Q ss_pred             CCCCCEEEEEEEEEec--ceEEEEECCCCCeEEEEEceecchhhhh---------ccccccCCCCEEEEEEEEE
Q psy18072         13 PEVEDVVMVTVISIAE--MGAYVHLLEYNNIEGMILLSELSRRRIR---------SINKLIRVGKTEPVVVIRV   75 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~--~GafV~L~~~~~~~GlI~iSels~~~v~---------~~~~~l~vGd~V~vrVi~V   75 (174)
                      +.+|+||.|+|.+|.+  .+|||.|..  +..||||++++...++.         ++...+++||.|-|.|.+-
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDIG~--gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE  107 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDYGA--ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE  107 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEecC--CcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence            3489999999999954  488999998  89999999998644321         3456799999999999983

>KOG3013|consensus

Probab=96.56  E-value=0.0029  Score=53.31  Aligned_cols=81  Identities=22%  Similarity=0.259  Sum_probs=67.0

Q ss_pred             hccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch------hh----hhccccccCCCCEEEEEEEEEeCC
Q psy18072          9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR------RR----IRSINKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus         9 ~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~------~~----v~~~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      ....|++||+|.|+|..|.+.-|=|++..  +..+.+..|.+.-      ++    -...+.+|+.||.|.|.|-.+-.+
T Consensus        79 ~rY~pEvGDvVVgRV~eVq~KRWkvd~ns--k~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~d  156 (301)
T KOG3013|consen   79 SRYAPEVGDVVVGRVIEVQQKRWKVDLNS--KQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHD  156 (301)
T ss_pred             hhcCCccCCEEEEEeeeeecceeEEeccc--ccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccC
Confidence            45567899999999999999999999988  8999999887642      11    124678999999999999999999


Q ss_pred             Cceeeecccccch
Q psy18072         79 KVMTTVTPEKADG   91 (174)
Q Consensus        79 ~~l~ls~~~k~~g   91 (174)
                      +.+++.++....|
T Consensus       157 Gs~sLhTRS~KYG  169 (301)
T KOG3013|consen  157 GSLSLHTRSLKYG  169 (301)
T ss_pred             CeEEEEecchhcc
Confidence            9998888776444

>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]

Probab=96.42  E-value=0.035  Score=50.83  Aligned_cols=62  Identities=23%  Similarity=0.313  Sum_probs=51.3

Q ss_pred             CCCEEEEEEEEEecc--eEEEEECCCCCeEEEEEceecchhhhhc-----cccccCCCCEEEEEEEEEeCCC
Q psy18072         15 VEDVVMVTVISIAEM--GAYVHLLEYNNIEGMILLSELSRRRIRS-----INKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~--GafV~L~~~~~~~GlI~iSels~~~v~~-----~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      +|.+|.|+|++|.+.  .|||.+..  .-.||+|.+++.+ +++.     +...++.||.+-|.|++-....
T Consensus        37 ~gniy~grv~~i~p~~~aafvdig~--~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~  105 (487)
T COG1530          37 VGNIYKGRVTRVLPSLEAAFVDIGL--ERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPRGT  105 (487)
T ss_pred             ecCceEEEecccCccchhheeeccC--CccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecCcc
Confidence            799999999999654  78999987  7899999999998 4433     3468999999999999855443

>KOG3298|consensus

Probab=95.66  E-value=0.058  Score=42.59  Aligned_cols=61  Identities=15%  Similarity=0.103  Sum_probs=42.3

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch-----------hhhhccccccCCCCEEEEEEEEEeCC
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR-----------RRIRSINKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~-----------~~v~~~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      .|++|.|+|+.+...|+|+++.+   ++-++..--...           .+..+-...+.+|..|+++|+.+.-+
T Consensus        81 KGEVvdgvV~~Vnk~G~F~~~GP---l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~  152 (170)
T KOG3298|consen   81 KGEVVDGVVTKVNKMGVFARSGP---LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVD  152 (170)
T ss_pred             CCcEEEEEEEEEeeeeEEEeccc---eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEe
Confidence            69999999999999999999977   333332111111           11112223799999999999987654

>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit

Probab=94.02  E-value=0.37  Score=36.28  Aligned_cols=61  Identities=20%  Similarity=0.081  Sum_probs=43.5

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchh-h-----------h-hccccccCCCCEEEEEEEEEeC
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRR-R-----------I-RSINKLIRVGKTEPVVVIRVDK   77 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~-~-----------v-~~~~~~l~vGd~V~vrVi~Vd~   77 (174)
                      +|+++.|+|.+.+..|+.|.|.-|  -+=+||.+.|... +           + ....-.+..|+.|+.||.++..
T Consensus         3 ~gEvl~g~I~~~~~~Gi~vslgFF--ddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f   76 (122)
T PF08292_consen    3 VGEVLTGKIKSSTAEGIRVSLGFF--DDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF   76 (122)
T ss_dssp             TT-EEEEEEEEEETTEEEEEECCE--EEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred             CCCEEEEEEEecCCCcEEEEeccc--ccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence            699999999999999999999653  3567777766531 1           1 2334467999999999999876

Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.

>KOG1004|consensus

Probab=92.86  E-value=0.55  Score=38.74  Aligned_cols=65  Identities=15%  Similarity=0.060  Sum_probs=48.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      .|.+||.|.|+|+.-...+.-|.|..  .--|+|+.-.+...- +.-+-.+++||.|-|||...+++.
T Consensus        62 iP~~~D~VIGiV~~~~gd~ykVDigg--~~~a~L~~laFe~At-krNrPnl~vGdliyakv~~a~~~~  126 (230)
T KOG1004|consen   62 IPVKGDHVIGIVTSKSGDIYKVDIGG--SEPASLSYLAFEGAT-KRNRPNLQVGDLIYAKVVDANKDM  126 (230)
T ss_pred             cCCCCCEEEEEEEeccCceEEEecCC--CCeeeeeeccccCcc-ccCCCccccccEEEEEEEecCCCc
Confidence            45689999999999888888999976  567777765554321 112246999999999999876544

>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=92.33  E-value=0.96  Score=33.16  Aligned_cols=51  Identities=6%  Similarity=0.089  Sum_probs=43.5

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      .|.+|.|+|..|...-+||.+..  +..++++......       +.|..|..|.+|+..
T Consensus        23 ~gk~V~G~I~hvv~ddLYIDfG~--KFhcVc~rp~~~~-------~~y~~G~rV~lrLkd   73 (104)
T PF10246_consen   23 EGKIVIGKIFHVVDDDLYIDFGG--KFHCVCKRPAVNG-------EKYVRGSRVRLRLKD   73 (104)
T ss_pred             cCCEEEEEEEEEecCceEEEeCC--ceeEEEecccccc-------cccccCCEEEEEECC
Confidence            79999999999988899999988  8999998665432       468889999999874

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 [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].

>PRK15464 cold shock-like protein CspH; Provisional

Probab=89.95  E-value=1.2  Score=30.17  Aligned_cols=51  Identities=12%  Similarity=0.173  Sum_probs=38.8

Q ss_pred             EEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         19 VMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        19 V~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      ++|+|+... ..|. ||..+. ++-+-|+|+|.+.....    +.+.+||.|...|..
T Consensus         5 ~~G~Vk~fn~~KGfGFI~~~~-g~~DvFvH~s~l~~~g~----~~l~~G~~V~f~v~~   57 (70)
T PRK15464          5 MTGIVKTFDRKSGKGFIIPSD-GRKEVQVHISAFTPRDA----EVLIPGLRVEFCRVN   57 (70)
T ss_pred             ceEEEEEEECCCCeEEEccCC-CCccEEEEehhehhcCC----CCCCCCCEEEEEEEE
Confidence            479999984 4676 787765 24689999999964322    468999999998876

>PRK15463 cold shock-like protein CspF; Provisional

Probab=89.06  E-value=1.5  Score=29.65  Aligned_cols=51  Identities=14%  Similarity=0.149  Sum_probs=38.6

Q ss_pred             EEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         19 VMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        19 V~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      ++|+|+... ..|. ||.... ++-+-|+|+|.+.....    ..+++|+.|...|..
T Consensus         5 ~~G~Vk~fn~~kGfGFI~~~~-g~~DvFvH~sal~~~g~----~~l~~G~~V~f~v~~   57 (70)
T PRK15463          5 MTGIVKTFDGKSGKGLITPSD-GRKDVQVHISALNLRDA----EELTTGLRVEFCRIN   57 (70)
T ss_pred             ceEEEEEEeCCCceEEEecCC-CCccEEEEehhhhhcCC----CCCCCCCEEEEEEEE
Confidence            479999984 4676 777765 24789999999975422    468899999998775

>TIGR00008 infA translation initiation factor IF-1

Probab=88.79  E-value=2.1  Score=29.03  Aligned_cols=54  Identities=15%  Similarity=0.016  Sum_probs=38.9

Q ss_pred             EEEEEEEEEecceEEE-EECCCCCeEEEEEcee-cchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072         18 VVMVTVISIAEMGAYV-HLLEYNNIEGMILLSE-LSRRRIRSINKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus        18 iV~G~V~~i~~~GafV-~L~~~~~~~GlI~iSe-ls~~~v~~~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      .+.|+|+..-+.+.|- .|.+  +..=+.|+|= +...+     -.+.+||.|.|.+...+..
T Consensus         6 e~~G~V~e~L~~~~f~V~l~n--g~~vla~i~GKmr~~r-----I~I~~GD~V~Ve~spyd~t   61 (68)
T TIGR00008         6 EMEGKVTESLPNAMFRVELEN--GHEVLAHISGKIRMHY-----IRILPGDKVKVELSPYDLT   61 (68)
T ss_pred             EEEEEEEEECCCCEEEEEECC--CCEEEEEecCcchhcc-----EEECCCCEEEEEECcccCC
Confidence            4789999997777764 8877  7777777773 22122     3588999999987765543

This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=88.15  E-value=2  Score=30.60  Aligned_cols=55  Identities=18%  Similarity=0.111  Sum_probs=39.6

Q ss_pred             EEEEEEEEEecceEE-EEECCCCCeEEEEEcee-cchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         18 VVMVTVISIAEMGAY-VHLLEYNNIEGMILLSE-LSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        18 iV~G~V~~i~~~Gaf-V~L~~~~~~~GlI~iSe-ls~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      .+.|+|+.+-+.+.| |.|.+  +..=+-|+|= +...+     -.+.+||.|.|.+...|..+
T Consensus         8 e~~G~V~e~Lp~~~frV~Len--G~~vla~isGKmR~~r-----IrIl~GD~V~VE~spYDltk   64 (87)
T PRK12442          8 ELDGIVDEVLPDSRFRVTLEN--GVEVGAYASGRMRKHR-----IRILAGDRVTLELSPYDLTK   64 (87)
T ss_pred             EEEEEEEEECCCCEEEEEeCC--CCEEEEEeccceeeee-----EEecCCCEEEEEECcccCCc
Confidence            589999999777766 48887  6666777662 22222     34789999999998777654

>PRK09890 cold shock protein CspG; Provisional

Probab=87.35  E-value=2.8  Score=28.23  Aligned_cols=51  Identities=4%  Similarity=0.117  Sum_probs=37.7

Q ss_pred             EEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         19 VMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        19 V~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      ++|+|.... ..|. ||.-.+ ++-+-|+|+|.+...-+    ..+.+|+.|...+..
T Consensus         5 ~~G~Vk~f~~~kGfGFI~~~~-g~~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~   57 (70)
T PRK09890          5 MTGLVKWFNADKGFGFITPDD-GSKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQ   57 (70)
T ss_pred             ceEEEEEEECCCCcEEEecCC-CCceEEEEEeeeccCCC----CCCCCCCEEEEEEEE
Confidence            479999884 3565 777665 14789999999975432    468899999997765

>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []

Probab=87.30  E-value=5.5  Score=25.87  Aligned_cols=51  Identities=16%  Similarity=0.125  Sum_probs=35.4

Q ss_pred             EEEEEEEEec-ceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         19 VMVTVISIAE-MGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        19 V~G~V~~i~~-~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      .+|+|....+ .|. ||.-.+- .-+=++|.|.+....    ...++.|+.|...+..
T Consensus         1 ~~G~V~~~~~~kgyGFI~~~~~-~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~   53 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYGFITSDDG-GEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE   53 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTS-SSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred             CeEEEEEEECCCCceEEEEccc-ceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence            4799999854 233 5555541 458999999998543    2568899999999987

During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....

>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS)

Probab=86.61  E-value=3.5  Score=29.60  Aligned_cols=53  Identities=19%  Similarity=0.305  Sum_probs=34.7

Q ss_pred             EEEEEEEEEecce--EEEEECCCC-CeEEEEEceecchhhhhccccccCCCCEEEE
Q psy18072         18 VVMVTVISIAEMG--AYVHLLEYN-NIEGMILLSELSRRRIRSINKLIRVGKTEPV   70 (174)
Q Consensus        18 iV~G~V~~i~~~G--afV~L~~~~-~~~GlI~iSels~~~v~~~~~~l~vGd~V~v   70 (174)
                      .+.|.|.++...|  +||.|.... .++.++..+......+......+++|+.|.|
T Consensus         3 ~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v   58 (108)
T cd04322           3 SVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGV   58 (108)
T ss_pred             EEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEE
Confidence            4789999997654  799997622 3566665554433333333344899999866

These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein

>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein

Probab=86.48  E-value=1.2  Score=33.99  Aligned_cols=20  Identities=30%  Similarity=0.421  Sum_probs=14.4

Q ss_pred             HHHHHHHHHhcccccCCCCc
Q psy18072        131 ARQMERAEAENAEVAADDDE  150 (174)
Q Consensus       131 k~~~~~l~k~~~e~~gd~~~  150 (174)
                      ++--.+|..-+++||.|+++
T Consensus       101 ~kyk~rLk~LG~eVSddE~~  120 (136)
T PF04871_consen  101 KKYKERLKELGEEVSDDEDS  120 (136)
T ss_pred             HHHHHHHHHcCCCccCCccc
Confidence            33446677889999988765

This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane

>TIGR00638 Mop molybdenum-pterin binding domain

Probab=85.58  E-value=2.6  Score=27.34  Aligned_cols=55  Identities=13%  Similarity=0.100  Sum_probs=33.8

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEE-EEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGM-ILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~Gl-I~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      ...+.|+|.++...|.++.+.-  .+.|. .-.+.++......  -.|++|+.|.+.+-.
T Consensus         6 ~N~l~g~I~~i~~~g~~~~v~l--~~~~~~~l~a~i~~~~~~~--l~l~~G~~v~~~ik~   61 (69)
T TIGR00638         6 RNQLKGKVVAIEDGDVNAEVDL--LLGGGTKLTAVITLESVAE--LGLKPGKEVYAVIKA   61 (69)
T ss_pred             ccEEEEEEEEEEECCCeEEEEE--EECCCCEEEEEecHHHHhh--CCCCCCCEEEEEEEC
Confidence            3578999999987777665532  12222 2233444433332  348999999998754

This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=84.56  E-value=0.034  Score=48.34  Aligned_cols=47  Identities=13%  Similarity=0.084  Sum_probs=27.8

Q ss_pred             hccCCCCCCEEEEEEEEE-ecceEEEE------ECCCCCeEEEEEceecchhhhhcc
Q psy18072          9 AEKYPEVEDVVMVTVISI-AEMGAYVH------LLEYNNIEGMILLSELSRRRIRSI   58 (174)
Q Consensus         9 ~~~~p~~GdiV~G~V~~i-~~~GafV~------L~~~~~~~GlI~iSels~~~v~~~   58 (174)
                      ...|+ .|++|.|+|..+ ..+|+|++      ..+  .++++.|+++++...+.++
T Consensus       100 ~e~~~-~g~~v~~~V~~ia~~~g~~~eely~~i~~p--l~~~~gh~y~af~~~v~~~  153 (319)
T PTZ00248        100 EEKFS-KSKKVHSIMRHIAQKHGMSVEELYTKIIWP--LYKKYGHALDALKEALTNP  153 (319)
T ss_pred             HHhCc-CCCEEEEEEEEchhhcCCCHHHHHHHHHHH--HHHhcCCHHHHHHHHhcCc
Confidence            44554 677777777777 34677765      222  4566667666665544433

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]

Probab=84.52  E-value=5.2  Score=34.26  Aligned_cols=51  Identities=16%  Similarity=0.277  Sum_probs=35.4

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEE
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV   72 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrV   72 (174)
                      ++|.+....|.+.++||+|+.=.++. -.=++|.++.-.       +.+.+||.|+|-|
T Consensus         4 ~iG~~~~l~V~~~~~~g~fL~~~~~~-~~ilL~k~~~~~-------~e~evGdev~vFi   54 (287)
T COG2996           4 KIGQINSLEVVEFSDFGYFLDAGEDG-TTILLPKSEPEE-------DELEVGDEVTVFI   54 (287)
T ss_pred             cccceEEEEEEEeeceeEEEecCCCc-eEEeccccCCcC-------CccccCcEEEEEE
Confidence            37999999999999999999876631 255666664321       3455666666543

>PRK10354 RNA chaperone/anti-terminator; Provisional

Probab=84.22  E-value=4.8  Score=27.01  Aligned_cols=51  Identities=10%  Similarity=0.141  Sum_probs=37.4

Q ss_pred             EEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         19 VMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        19 V~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      +.|+|.... ..|. ||.-.. ++-+-|+|+|.+.....    ..+++|+.|...+..
T Consensus         5 ~~G~Vk~f~~~kGfGFI~~~~-g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~   57 (70)
T PRK10354          5 MTGIVKWFNADKGFGFITPDD-GSKDVFVHFSAIQNDGY----KSLDEGQKVSFTIES   57 (70)
T ss_pred             ceEEEEEEeCCCCcEEEecCC-CCccEEEEEeeccccCC----CCCCCCCEEEEEEEE
Confidence            479998884 3455 676655 14789999999974322    468999999998775

>PRK09507 cspE cold shock protein CspE; Reviewed

Probab=82.33  E-value=6.3  Score=26.40  Aligned_cols=53  Identities=9%  Similarity=0.119  Sum_probs=38.7

Q ss_pred             EEEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072         18 VVMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV   75 (174)
Q Consensus        18 iV~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V   75 (174)
                      .++|+|+... ..|. ||..++ ++-+-|+|+|.+.....    ..+.+|+.|...+..-
T Consensus         3 ~~~G~Vk~f~~~kGyGFI~~~~-g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~~   57 (69)
T PRK09507          3 KIKGNVKWFNESKGFGFITPED-GSKDVFVHFSAIQTNGF----KTLAEGQRVEFEITNG   57 (69)
T ss_pred             ccceEEEEEeCCCCcEEEecCC-CCeeEEEEeecccccCC----CCCCCCCEEEEEEEEC
Confidence            4679999884 3566 777655 14689999999874322    4688999999987753

>PRK10943 cold shock-like protein CspC; Provisional

Probab=82.05  E-value=5.3  Score=26.78  Aligned_cols=53  Identities=11%  Similarity=0.135  Sum_probs=38.9

Q ss_pred             EEEEEEEEEec-ceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072         18 VVMVTVISIAE-MGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV   75 (174)
Q Consensus        18 iV~G~V~~i~~-~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V   75 (174)
                      .++|+|+.... .|. ||.-.. ++-+-|+|+|.+.....    ..+..|+.|...+..-
T Consensus         3 ~~~G~Vk~f~~~kGfGFI~~~~-g~~dvFvH~s~l~~~g~----~~l~~G~~V~f~~~~~   57 (69)
T PRK10943          3 KIKGQVKWFNESKGFGFITPAD-GSKDVFVHFSAIQGNGF----KTLAEGQNVEFEIQDG   57 (69)
T ss_pred             ccceEEEEEeCCCCcEEEecCC-CCeeEEEEhhHccccCC----CCCCCCCEEEEEEEEC
Confidence            36899998843 565 776654 14799999999874422    4688999999988763

>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional

Probab=80.64  E-value=6.9  Score=26.73  Aligned_cols=52  Identities=12%  Similarity=0.050  Sum_probs=38.2

Q ss_pred             EEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEe
Q psy18072         20 MVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD   76 (174)
Q Consensus        20 ~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd   76 (174)
                      +|+|+-.. ..|. ||..+. ++-+-|+|+|.+...-.    ..+..||.|...+..-.
T Consensus         3 ~G~Vkwfn~~KGfGFI~~~~-gg~dVFvH~s~i~~~g~----~~l~~G~~V~f~~~~~~   56 (74)
T PRK09937          3 KGTVKWFNNAKGFGFICPEG-GGEDIFAHYSTIQMDGY----RTLKAGQSVQFDVHQGP   56 (74)
T ss_pred             CeEEEEEeCCCCeEEEeeCC-CCccEEEEEeeccccCC----CCCCCCCEEEEEEEECC
Confidence            48888874 3566 776654 25799999999974422    46889999999887643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	174
1q8k_A	308	Solution Structure Of Alpha Subunit Of Human Eif2 L		1e-22
1q8k_A	308	Solution Structure Of Alpha Subunit Of Human Eif2 L		3e-12
1q46_A	175	Crystal Structure Of The Eif2 Alpha Subunit From Sa		1e-19
2a19_A	175	Pkr Kinase Domain- Eif2alpha- Amp-Pnp Complex. Leng		1e-19
1kl9_A	182	Crystal Structure Of The N-Terminal Segment Of Huma		5e-17

>pdb|1Q8K|A Chain A, Solution Structure Of Alpha Subunit Of Human Eif2 Length = 308

Iteration: 1
 Score =  102 bits (254), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 54/92 (58%), Positives = 60/92 (65%), Gaps = 5/92 (5%)
Query: 3  LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXNKLI 62
          +SCRFY  K+PEVEDVVMV V SI EMGAYV LLEYNNIEGM              NKLI
Sbjct: 1  MSCRFYQHKFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLI 60
Query: 63 RVGKTEPVVVIRVDKEK-----VMTTVTPEKA 89
          R+G+ E V VIRVDKEK         V+PE+A
Sbjct: 61 RIGRNECVKVIRVDKEKGYIDLSKRRVSPEEA 92

>pdb|1Q8K|A Chain A, Solution Structure Of Alpha Subunit Of Human Eif2 Length = 308

Iteration: 1
 Score = 67.8 bits (164), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 34/55 (61%), Positives = 40/55 (72%)
Query: 80  VMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQM 134
           VMTT T E+ +GL  L +A+  IK KIE+  GVF VQM PKVVT +DE ELARQM
Sbjct: 233 VMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQM 287

>pdb|1Q46|A Chain A, Crystal Structure Of The Eif2 Alpha Subunit From Saccharomyces Cerevisia Length = 175

Iteration: 1
 Score = 92.4 bits (228), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 45/75 (60%), Positives = 51/75 (68%)
Query: 5  CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXNKLIRV 64
          CRFY  KYPE++D+VMV V  IAEMGAYV LLEY+NIEGM               KLIRV
Sbjct: 5  CRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRV 64
Query: 65 GKTEPVVVIRVDKEK 79
          GK +  VV+RVDKEK
Sbjct: 65 GKNDVAVVLRVDKEK 79

>pdb|2A19|A Chain A, Pkr Kinase Domain- Eif2alpha- Amp-Pnp Complex. Length = 175

Iteration: 1
 Score = 92.4 bits (228), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 45/75 (60%), Positives = 51/75 (68%)
Query: 5  CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXNKLIRV 64
          CRFY  KYPE++D+VMV V  IAEMGAYV LLEY+NIEGM               KLIRV
Sbjct: 5  CRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRV 64
Query: 65 GKTEPVVVIRVDKEK 79
          GK +  VV+RVDKEK
Sbjct: 65 GKNDVAVVLRVDKEK 79

>pdb|1KL9|A Chain A, Crystal Structure Of The N-Terminal Segment Of Human Eukaryotic Initiation Factor 2alpha Length = 182

Iteration: 1
 Score = 83.6 bits (205), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 54/92 (58%), Positives = 59/92 (64%), Gaps = 5/92 (5%)
Query: 3  LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMXXXXXXXXXXXXXXNKLI 62
          LSCRFY  K+PEVEDVV V V SIAE GAYV LLEYNNIEG               NKLI
Sbjct: 3  LSCRFYQHKFPEVEDVVXVNVRSIAEXGAYVSLLEYNNIEGXILLSELSRRRIRSINKLI 62
Query: 63 RVGKTEPVVVIRVDKEK-----VMTTVTPEKA 89
          R+G+ E VVVIRVDKEK         V+PE+A
Sbjct: 63 RIGRNECVVVIRVDKEKGYIDLSKRRVSPEEA 94

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	174
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	2e-31
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	1e-29
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	2e-26
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	5e-19
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	2e-25
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	4e-04
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	4e-21
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	4e-09
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	1e-11
1yz7_A	188	Probable translation initiation factor 2 alpha sub	2e-10
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	3e-08
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	5e-08
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	1e-06
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	2e-04
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	2e-04
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	5e-04

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 Length = 182

 Score =  110 bits (277), Expect = 2e-31
 Identities = 67/78 (85%), Positives = 70/78 (89%)

Query: 2  PLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKL 61
           LSCRFY  K+PEVEDVVMV V SIAEMGAYV LLEYNNIEGMILLSELSRRRIRSINKL
Sbjct: 2  GLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKL 61

Query: 62 IRVGKTEPVVVIRVDKEK 79
          IR+G+ E VVVIRVDKEK
Sbjct: 62 IRIGRNECVVVIRVDKEK 79

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A Length = 175

 Score =  105 bits (264), Expect = 1e-29
 Identities = 59/77 (76%), Positives = 65/77 (84%)

Query: 3  LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLI 62
            CRFY  KYPE++D+VMV V  IAEMGAYV LLEY+NIEGMILLSELSRRRIRSI KLI
Sbjct: 3  SHCRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLI 62

Query: 63 RVGKTEPVVVIRVDKEK 79
          RVGK +  VV+RVDKEK
Sbjct: 63 RVGKNDVAVVLRVDKEK 79

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1 Length = 308

 Score =  101 bits (252), Expect = 2e-26
 Identities = 63/77 (81%), Positives = 67/77 (87%)

Query: 3  LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLI 62
          +SCRFY  K+PEVEDVVMV V SI EMGAYV LLEYNNIEGMI LSELSRRRIRSINKLI
Sbjct: 1  MSCRFYQHKFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLI 60

Query: 63 RVGKTEPVVVIRVDKEK 79
          R+G+ E V VIRVDKEK
Sbjct: 61 RIGRNECVKVIRVDKEK 77

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1 Length = 308

 Score = 81.2 bits (200), Expect = 5e-19
 Identities = 48/117 (41%), Positives = 63/117 (53%), Gaps = 6/117 (5%)

Query: 41  IEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD------KEKVMTTVTPEKADGLKA 94
           I   I ++      I ++ + +R G       + +          VMTT T E+ +GL  
Sbjct: 188 IRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTLERTEGLSV 247

Query: 95  LQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADDDED 151
           L +A+  IK KIE+  GVF VQM PKVVT +DE ELARQMER E ENAEV  D +  
Sbjct: 248 LSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQMERLERENAEVDGDLEHH 304

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B* Length = 266

 Score = 97.8 bits (243), Expect = 2e-25
 Identities = 21/74 (28%), Positives = 42/74 (56%)

Query: 6  RFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVG 65
           +   K P   ++++ TV  + + G+YV L EY  ++  +  SE+S + +++I  +++  
Sbjct: 2  IYSRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKEN 61

Query: 66 KTEPVVVIRVDKEK 79
          +   V VIRVD+ K
Sbjct: 62 RKVIVKVIRVDRRK 75

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B* Length = 266

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 5/38 (13%), Positives = 12/38 (31%)

Query: 80  VMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQM 117
            +  V     +  +AL + I  +    ++      V  
Sbjct: 228 RVDVVGTNPKEASEALNQIISNLIKIGKEENVDISVVK 265

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Length = 275

 Score = 86.2 bits (213), Expect = 4e-21
 Identities = 25/74 (33%), Positives = 39/74 (52%)

Query: 6  RFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVG 65
             A +YPE  + V+ TV  I   GA++ L EY   E  + +SE++   +R+I   ++ G
Sbjct: 2  PRKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEG 61

Query: 66 KTEPVVVIRVDKEK 79
          +     VIRVD  K
Sbjct: 62 QKVVAKVIRVDPRK 75

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Length = 275

 Score = 53.1 bits (127), Expect = 4e-09
 Identities = 8/50 (16%), Positives = 19/50 (38%)

Query: 80  VMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAE 129
            +    P+     + L++  + I   I+Q GG   +    K +    + +
Sbjct: 225 RIDITAPDYYKAEEVLEDIAEEILRVIKQAGGEATLLRKEKRIRKVKKRK 274

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5 Length = 88

 Score = 57.3 bits (138), Expect = 1e-11
 Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 3/69 (4%)

Query: 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLS-ELSRRRIRSINKLIRVGKTEPV 70
           P   DV+   V    +   Y++L +Y + E ++  S ++   R       + VGKT  V
Sbjct: 8  LPNAGDVIKGRV-YEKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKV 65

Query: 71 VVIRVDKEK 79
           VIRVD  K
Sbjct: 66 KVIRVDYTK 74

>1yz7_A Probable translation initiation factor 2 alpha subunit; helical domain, alpha-beta domain; 2.26A {Pyrococcus abyssi} Length = 188

 Score = 55.6 bits (134), Expect = 2e-10
 Identities = 7/50 (14%), Positives = 18/50 (36%)

Query: 80  VMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAE 129
            +    P+     + L+   + I   I++ GG   +    K +    + +
Sbjct: 138 RIDITAPDYYKAEEVLESIAEEILRVIKEAGGEATLLRKEKRIKKVKKRK 187

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115

 Score = 48.8 bits (117), Expect = 3e-08
 Identities = 18/72 (25%), Positives = 40/72 (55%), Gaps = 4/72 (5%)

Query: 9  AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS-RRRIRSINKLIRVGKT 67
          A++YP     +   V ++ + G +V + E   +EG++ +SE+    +    +K++ VG  
Sbjct: 25 AKRYP-EGTKLTGRVTNLTDYGCFVEIEE--GVEGLVHVSEMDWTNKNIHPSKVVNVGDV 81

Query: 68 EPVVVIRVDKEK 79
            V+V+ +D+E+
Sbjct: 82 VEVMVLDIDEER 93

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 47.6 bits (114), Expect = 5e-08
 Identities = 17/72 (23%), Positives = 29/72 (40%), Gaps = 3/72 (4%)

Query: 8  YAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKT 67
          +         +V   V ++   GA V L +   +EG +  SE SR R+     ++ VG  
Sbjct: 25 WVALNK-KGAIVTGKVTAVDAKGATVELAD--GVEGYLRASEASRDRVEDATLVLSVGDE 81

Query: 68 EPVVVIRVDKEK 79
                 VD++ 
Sbjct: 82 VEAKFTGVDRKN 93

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130

 Score = 44.3 bits (105), Expect = 1e-06
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
           EV  V    V  +   GA+V L E    +G++ +SE++   ++ IN+ + VG    V V
Sbjct: 5  FEVGSVYTGKVTGLQAYGAFVALDE--ETQGLVHISEVTHGFVKDINEHLSVGDEVQVKV 62

Query: 73 IRVDKEK 79
          + VD+EK
Sbjct: 63 LAVDEEK 69

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 13/65 (20%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 13  PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
            EV  +    V+ + + GA+V+       +G++ +S++S  R+   + +++ G+   V +
Sbjct: 635 AEVGKIYDGKVVKVVDFGAFVNFF--GAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKL 692

Query: 73  IRVDK 77
           +  D 
Sbjct: 693 LGFDD 697

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 13 PEVEDVVMVTVISIAEMGAYVHLLEY-NNIEGMILLSELS-RRRIRSINKLIRVGKTEPV 70
          P + D+    V SI + G +V L       EG++ +SEL    R+ ++  ++  G+   V
Sbjct: 10 PTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKV 69

Query: 71 VVIRVDKEKV 80
           V+     K 
Sbjct: 70 KVLSFTGTKT 79

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 38.6 bits (91), Expect = 5e-04
 Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 13  PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
            EV  V    V  I + GA+V +      EG++ +S+++ +R+  +   +++G+  PV V
Sbjct: 625 IEVGRVYTGKVTRIVDFGAFVAIG--GGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKV 682

Query: 73  IRVDK 77
           + VD+
Sbjct: 683 LEVDR 687

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	174
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.93
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.93
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.85
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.83
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.75
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.72
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.7
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.64
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.63
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.62
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.58
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.58
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.57
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	99.54
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.44
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.43
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	99.39
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	99.38
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.37
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	99.34
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	99.33
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.32
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.27
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	99.23
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.22
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	99.22
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.19
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	99.18
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	99.18
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	99.15
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	99.13
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.96
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	98.95
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	98.94
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	98.83
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.79
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.61
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.6
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	98.57
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	98.55
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	98.53
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	98.51
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.51
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	98.36
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	98.09
1jjg_A	102	M156R; beta barrel, S1 motif, OB fold, MYXV156R, N	97.74
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.08
1yz7_A	188	Probable translation initiation factor 2 alpha sub	96.54
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	96.38
2qn6_B	93	Translation initiation factor 2 alpha subunit; ini	95.99
2r7d_A	469	Ribonuclease II family protein; structural genomic	95.25
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	94.02
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	92.85
3h8z_A	128	FragIle X mental retardation syndrome-related Pro;	89.22
1wfq_A	89	UNR protein; beta-barrel, translational regulation	88.16
2k5n_A	74	Putative cold-shock protein; GFT protein structure	87.59
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	87.47
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	86.15
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	85.25
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	84.94
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	84.57
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	81.71
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	81.34
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	81.01
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	80.49
3cam_A	67	Cold-shock domain family protein; cold shock prote	80.25

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=99.93  E-value=1.5e-26  Score=195.11  Aligned_cols=120  Identities=15%  Similarity=0.199  Sum_probs=112.1

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEE-EECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC-CCceeeeccc
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYV-HLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK-EKVMTTVTPE   87 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV-~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~-~~~l~ls~~~   87 (174)
                      ..|+ +|++|.|+|+++++||+|| .|.+  ++.||||+|+++        ..+++||.|+|+|++|++ ++++++|++.
T Consensus       148 ~~~~-~G~~V~g~V~~i~~~G~fV~~i~~--g~~Glih~SEl~--------~~l~~Gd~v~~~V~~id~~d~kI~LSlk~  216 (285)
T 3go5_A          148 YNNM-QNQNWPAIVYRLKLSGTFVYLPEN--NMLGFIHPSERY--------AEPRLGQVLDARVIGFREVDRTLNLSLKP  216 (285)
T ss_dssp             CSCC-TTCEEEEEEEEEETTEEEEEETTT--TEEEEECGGGCS--------SCCCTTCEEEEEEEEEETTTTEEEEECSC
T ss_pred             hhCC-CCCEEEEEEEEEeCCcEEEEEeCC--CeEEEEEHHHcc--------ccCCCCCEEEEEEEEEECCCCeEEEEeCh
Confidence            4665 8999999999999999999 9988  899999999998        579999999999999999 8899999977


Q ss_pred             ccchHHHHHHHHHHHHHHHhhhCCeeEE--eeCceeEe---ccCHHHHHHHHHHHHHhcc
Q psy18072         88 KADGLKALQEAIDTIKAKIEQLGGVFQV--QMAPKVVT---ASDEAELARQMERAEAENA  142 (174)
Q Consensus        88 k~~g~~~i~~~~~~i~~~l~~~~g~l~~--k~~P~~i~---~~~~~~~k~~~~~l~k~~~  142 (174)
                      .  ++.++..+++.|++.|+.+||+||+  ||+|+.|+   ++||++||||+|+|+|++.
T Consensus       217 ~--~~~~~~~~a~~il~~L~~~~G~l~~~DkS~pe~I~~~f~~SK~~FKrAiG~L~K~~~  274 (285)
T 3go5_A          217 R--SFEMLENDAQMILTYLESNGGFMTLNDKSSPDDIKATFGISKGQFKKALGGLMKAGK  274 (285)
T ss_dssp             C--CCCCCCHHHHHHHHHHHHTTTEESCCTTSCHHHHHHHHSSCHHHHHHHHHHHHHTTC
T ss_pred             h--hhhccchHHHHHHHHHHhcCCeeccCCCCCHHHHHHHhCcCHHHHHHHHHHHhhCCc
Confidence            7  7778999999999999999999999  89999999   9999999999999999873

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1

Probab=99.93  E-value=4.2e-26  Score=194.05  Aligned_cols=145  Identities=73%  Similarity=1.027  Sum_probs=137.8

Q ss_pred             cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC---
Q psy18072          3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK---   79 (174)
Q Consensus         3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~---   79 (174)
                      +.||||...+|++|++|.|+|++|++|||||.|.+|++++||||+|++++.+++++.+.|++||.|.|+|+++++.+   
T Consensus         1 ~~~~f~~~~~~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI   80 (308)
T 1q8k_A            1 MSCRFYQHKFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYI   80 (308)
T ss_dssp             CCCCSSSSCCCSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEE
T ss_pred             CceEehhhcCCCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEE
Confidence            46999999999999999999999999999999985547999999999999999999999999999999999999854   


Q ss_pred             --------------------------------------------------------------------------------
Q psy18072         80 --------------------------------------------------------------------------------   79 (174)
Q Consensus        80 --------------------------------------------------------------------------------   79 (174)
                                                                                                      
T Consensus        81 ~LSlK~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~~G~fi~~~~e~l~~~i~~~l~~~~g~~~~~~y~af~~a~~~~~~l  160 (308)
T 1q8k_A           81 DLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSIL  160 (308)
T ss_dssp             EEECSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSHHHHHHHHHTHHHHHHHTTCSSHHHHHHHHHTTTCGGGG
T ss_pred             EEEEEecccChHHHHHHHccCCCeeEEEEEEcccccCCccCCCHHHHHHHHHHHHHHHhCCcchhHHHHHHHHcCChhhh
Confidence                                                                                            


Q ss_pred             ------------------------------------------------------------------------ceeeeccc
Q psy18072         80 ------------------------------------------------------------------------VMTTVTPE   87 (174)
Q Consensus        80 ------------------------------------------------------------------------~l~ls~~~   87 (174)
                                                                                              .+++++.+
T Consensus       161 ~~~~i~~~~~~~l~~~~~~~l~~~~vkI~~~iel~~~~~dGIe~Ik~aL~~~~~~~~~~~~i~i~~v~~P~Y~i~~~~~d  240 (308)
T 1q8k_A          161 DSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTLE  240 (308)
T ss_dssp             GGCCCCHHHHHHHHHHHHHHTSCCCCEEEECCCEECCSTTTHHHHHHHHHHHHHSSBTTBCEEEEEEETTEEEEEEECSS
T ss_pred             hhcCCCHHHHHHHHHHHHHhccCCCceEEEEEEEEecCCChHHHHHHHHHHhhhccCcCccEEEEEECCCEEEEEEEeCC
Confidence                                                                                    57888999


Q ss_pred             ccchHHHHHHHHHHHHHHHhhhCCeeEEeeCceeEeccCHHHHHHHHHHHHHhcccccCC
Q psy18072         88 KADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAAD  147 (174)
Q Consensus        88 k~~g~~~i~~~~~~i~~~l~~~~g~l~~k~~P~~i~~~~~~~~k~~~~~l~k~~~e~~gd  147 (174)
                      +..|...|+++++.|.+.|++.||.+.|+..|++++..++..|.++|+++.++|+|++||
T Consensus       241 ~k~~~~~l~~~~~~i~~~i~~~gG~~~~~~~p~~v~~~~~~~~~~~~~~~~~~~~~~~~~  300 (308)
T 1q8k_A          241 RTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQMERLERENAEVDGD  300 (308)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTSCEECCSSCCEECCSSHHHHHHHHCCSGGGCCCCCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCEEEEEECCEecChhhHHHHHHHHHHhhhhhcccccc
Confidence            999999999999999999999999999999999999999999999999999999999988

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5

Probab=99.85  E-value=4.4e-21  Score=152.28  Aligned_cols=88  Identities=75%  Similarity=1.053  Sum_probs=67.2

Q ss_pred             CCcccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-C
Q psy18072          1 MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-K   79 (174)
Q Consensus         1 ~~~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~   79 (174)
                      |+|+||||..++|++|++|.|+|++|++|||||+|.++++++||||+|++++.++.++++.|++||.|+|+|+++|.. +
T Consensus         1 ~~~~~~~~~~~~p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~   80 (182)
T 1kl9_A            1 PGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKG   80 (182)
T ss_dssp             --CCCCSSSSSSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTT
T ss_pred             CCeeeEeccccCCCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCC
Confidence            789999999999999999999999999999999996444899999999999999999999999999999999999974 5


Q ss_pred             ceeeecccc
Q psy18072         80 VMTTVTPEK   88 (174)
Q Consensus        80 ~l~ls~~~k   88 (174)
                      .+++|.+..
T Consensus        81 rI~LSlk~~   89 (182)
T 1kl9_A           81 YIDLSKRRV   89 (182)
T ss_dssp             EEEEESTTC
T ss_pred             EEEEEEeec
Confidence            678877654

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A

Probab=99.83  E-value=7.7e-20  Score=144.25  Aligned_cols=86  Identities=67%  Similarity=1.034  Sum_probs=70.1

Q ss_pred             cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cce
Q psy18072          3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVM   81 (174)
Q Consensus         3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l   81 (174)
                      ..|+||.++||++|++|.|+|++|++|||||+|.++++++||||+|++++.++.++++.|++||.|+|+|+++|.. +.+
T Consensus         3 ~~~~~~~~~~p~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I   82 (175)
T 2a19_A            3 SHCRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYI   82 (175)
T ss_dssp             CCCCSSSSSSCCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEE
T ss_pred             cceEEhhhcCCCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeE
Confidence            3699999999999999999999999999999996434799999999999999999999999999999999999985 467


Q ss_pred             eeecccc
Q psy18072         82 TTVTPEK   88 (174)
Q Consensus        82 ~ls~~~k   88 (174)
                      ++|++..
T Consensus        83 ~LSlk~~   89 (175)
T 2a19_A           83 DLSKRRV   89 (175)
T ss_dssp             EEESTTC
T ss_pred             EEEEEec
Confidence            8877654

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A

Probab=99.75  E-value=2e-18  Score=144.71  Aligned_cols=84  Identities=29%  Similarity=0.413  Sum_probs=71.8

Q ss_pred             cchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC-CCceee
Q psy18072          5 CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK-EKVMTT   83 (174)
Q Consensus         5 ~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~-~~~l~l   83 (174)
                      ++||.+.+|++|++|.|+|++|.+|||||.|.+|++++||||+|++++.++.++.+.|++||.|.|+|+++|. .+.+.+
T Consensus         1 ~~~~~~~~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~L   80 (275)
T 3aev_A            1 MPRKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDL   80 (275)
T ss_dssp             ------CCCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEE
T ss_pred             CCcccccCCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEE
Confidence            4789999999999999999999999999999865579999999999999999999999999999999999998 567788


Q ss_pred             ecccc
Q psy18072         84 VTPEK   88 (174)
Q Consensus        84 s~~~k   88 (174)
                      |.+..
T Consensus        81 Slk~~   85 (275)
T 3aev_A           81 SLRRV   85 (275)
T ss_dssp             ESTTC
T ss_pred             EEeec
Confidence            77653

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*

Probab=99.72  E-value=1.9e-18  Score=144.25  Aligned_cols=129  Identities=20%  Similarity=0.326  Sum_probs=98.6

Q ss_pred             chhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC-CCceeee
Q psy18072          6 RFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK-EKVMTTV   84 (174)
Q Consensus         6 r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~-~~~l~ls   84 (174)
                      |||...+|++|++|.|+|++|.+|||||.|.+|++++||||+|++++.++.++++.|++||.|.|+|++++. .+.+.+|
T Consensus         2 r~~~~~~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LS   81 (266)
T 3cw2_C            2 IYSRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVS   81 (266)
T ss_dssp             CCCSSSSCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEE
T ss_pred             CccccccCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEE
Confidence            799999999999999999999999999999844489999999999999999999999999999999999997 5677777


Q ss_pred             cccccc-hHHHH------HHHHHHHHHHHhhhCCeeEEeeCceeE----e---ccCHHHHHHHHH
Q psy18072         85 TPEKAD-GLKAL------QEAIDTIKAKIEQLGGVFQVQMAPKVV----T---ASDEAELARQME  135 (174)
Q Consensus        85 ~~~k~~-g~~~i------~~~~~~i~~~l~~~~g~l~~k~~P~~i----~---~~~~~~~k~~~~  135 (174)
                      .+.... .+..+      ......+...+...-+ +..++.|..+    .   +.+.++||+|++
T Consensus        82 lk~~~~~~~~~~~~~~~~~~~~~~iv~~lae~~~-~~~ee~~~~i~~~l~~~~~~~~~aFk~a~~  145 (266)
T 3cw2_C           82 LKKVTDDERRKKNLQWKKIQRLDKILELVSQKLK-LSEKDAWEQVAWKLEAKYGDPITAIEKAVK  145 (266)
T ss_dssp             STTSCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCHHHHHHHTHHHHHTTSSCHHHHHHHHHH
T ss_pred             EEecchhhHHHHHHhccccCccceeeeehhhhCC-CCHHHHHHHHHHHHHHHHhhHHHHHHHHhc
Confidence            765421 22111      1133344444442222 2235666444    2   678899999998

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=99.70  E-value=5.9e-17  Score=114.32  Aligned_cols=74  Identities=27%  Similarity=0.376  Sum_probs=65.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEce-ecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLS-ELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE   87 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iS-els~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~   87 (174)
                      .|++|+++.|+|+ |++|||||+|.++++++||||+| +++++++.++++.+ +||.|+|+|+++|.. +.+.+|.+.
T Consensus         8 ~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lslk~   83 (88)
T 1luz_A            8 LPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKR   83 (88)
T ss_dssp             CCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEE
T ss_pred             CCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEEee
Confidence            3568999999999 99999999998654699999999 99999999999999 999999999999984 567776643

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}

Probab=99.64  E-value=8.7e-16  Score=115.39  Aligned_cols=71  Identities=28%  Similarity=0.431  Sum_probs=66.2

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC-CCceeeecc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK-EKVMTTVTP   86 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~-~~~l~ls~~   86 (174)
                      ++|++|.|+|++|++|||||.|.+  +++||||+|++++.++.++.+.|++||.|+|+|++|+. .+.+.+|++
T Consensus         6 ~vG~iv~G~V~~i~~~G~FV~l~~--~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk   77 (130)
T 2k4k_A            6 EVGSVYTGKVTGLQAYGAFVALDE--ETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIR   77 (130)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEEET--TEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESH
T ss_pred             CCCCEEEEEEEEEeCCeEEEEECC--CcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence            499999999999999999999988  89999999999999999999999999999999999998 667777764

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}

Probab=99.63  E-value=1.5e-15  Score=104.79  Aligned_cols=69  Identities=22%  Similarity=0.279  Sum_probs=62.4

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPEK   88 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~k   88 (174)
                      ++|++|.|+|+++++|||||.|.+  +++||||+|++++.++    +.|++||.|+|+|++++.+ +.+.+|.+..
T Consensus         4 ~~G~iv~G~V~~v~~~G~fV~l~~--~~~Gllh~sel~~~~~----~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~~   73 (80)
T 2k52_A            4 EPGKFYKGVVTRIEKYGAFINLNE--QVRGLLRPRDMISLRL----ENLNVGDEIIVQAIDVRPEKREIDFKYIPL   73 (80)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEEET--TEEEEECGGGCSSCCG----GGCCTTCEEEEEEEEEETTTTEEEEEECSC
T ss_pred             CCCCEEEEEEEEEeCCEEEEEECC--CCEEEEEHHHCCcccc----eeeCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence            589999999999999999999988  8999999999997765    6899999999999999997 7788877554

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.3e-15  Score=109.97  Aligned_cols=74  Identities=23%  Similarity=0.405  Sum_probs=65.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCC-CeEEEEEceec-chhhhhccccccCCCCEEEEEEEEEeCCCceeeeccc
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYN-NIEGMILLSEL-SRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPE   87 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~-~~~GlI~iSel-s~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~   87 (174)
                      +++|++|.|+|++|++|||||+|.++. +++||||+|++ ++.++.++.+.|++||.|+|+|++++. +.+.+|.+.
T Consensus        10 ~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~-~~i~LSlk~   85 (103)
T 2eqs_A           10 PTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG-TKTSLSMKD   85 (103)
T ss_dssp             CCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET-TEEEEESTT
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC-CeeEEEEee
Confidence            459999999999999999999998642 69999999999 666788888999999999999999998 567777654

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=99.58  E-value=2.2e-15  Score=109.63  Aligned_cols=72  Identities=24%  Similarity=0.354  Sum_probs=66.7

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeeccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTPE   87 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~~   87 (174)
                      ++|++|.|+|++|.+|||||.|.+  +++||||+|++++.++.++.+.|++||.|+|+|++++..+ .+.+|.+.
T Consensus        30 ~~G~iv~G~V~~v~~~G~fV~l~~--~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~~~~ki~LS~k~  102 (109)
T 2khj_A           30 KKGAIVTGKVTAVDAKGATVELAD--GVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDRKNRAISLSVRA  102 (109)
T ss_dssp             CSSSEEEEEEEEECSSCEEEECST--TCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEETTTTEEEEETTS
T ss_pred             CCCCEEEEEEEEEECCeEEEEECC--CCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            499999999999999999999987  8999999999999999999999999999999999999875 68887754

>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=2.6e-15  Score=111.30  Aligned_cols=75  Identities=15%  Similarity=0.268  Sum_probs=65.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC---Cceeeeccc
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE---KVMTTVTPE   87 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~---~~l~ls~~~   87 (174)
                      .+++|++|.|+|++|++|||||.|.++ +++||||+|++++.++.++.+.|++||.|+|+|++++..   +.+.++++.
T Consensus        19 ~~~vG~iv~G~V~~I~~fGaFV~l~g~-~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~~~~i~LSlk~   96 (119)
T 2cqo_A           19 LPALYTIFQGEVAMVTDYGAFIKIPGC-RKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKV   96 (119)
T ss_dssp             SCCTTCEEEEEEEEEETTEEEEECTTC-SSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECSSCEEEEEESTT
T ss_pred             ccCCCCEEEEEEEEEeCceEEEEECCC-cEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEeccccCceEEEEEee
Confidence            346899999999999999999999652 269999999999999999999999999999999999975   367777654

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=99.57  E-value=1.1e-14  Score=107.08  Aligned_cols=73  Identities=19%  Similarity=0.358  Sum_probs=65.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchh-hhhccccccCCCCEEEEEEEEEeC-CCceeeeccc
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRR-RIRSINKLIRVGKTEPVVVIRVDK-EKVMTTVTPE   87 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~-~v~~~~~~l~vGd~V~vrVi~Vd~-~~~l~ls~~~   87 (174)
                      +++|++|.|+|++|++||+||.|.+  +++||||+|++++. ++.++.+.|++||.|+|+|++++. .+.+.++++.
T Consensus        28 ~~~G~~~~G~V~~v~~~G~FV~l~~--~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~rI~lslk~  102 (115)
T 2khi_A           28 YPEGTKLTGRVTNLTDYGCFVEIEE--GVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRRISLGLKQ  102 (115)
T ss_dssp             SCSSCEEEEEEEEEETTEEEEECST--TCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEETTTTEEEECCCC
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECC--CCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEECCCCEEEEEEEe
Confidence            4599999999999999999999988  89999999999874 778888999999999999999998 4577777654

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=99.54  E-value=6.2e-16  Score=122.06  Aligned_cols=97  Identities=18%  Similarity=0.234  Sum_probs=84.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCC--------CCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCcee
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEY--------NNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMT   82 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~--------~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~   82 (174)
                      ..|+ |++|.|+|++|.++||||+|..+        .+++|+||+|++++.++.++.+.|++||.|.|+|++    +.+.
T Consensus        54 y~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~----~~i~  128 (179)
T 3m7n_A           54 EIVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG----DNLR  128 (179)
T ss_dssp             CCCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE----TTTE
T ss_pred             ccCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC----CeEE
Confidence            5787 99999999999999999999752        148999999999999999999999999999999998    6799


Q ss_pred             eecccccchHHHHHHHHHHHHHHHhhhCCeeE
Q psy18072         83 TVTPEKADGLKALQEAIDTIKAKIEQLGGVFQ  114 (174)
Q Consensus        83 ls~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~  114 (174)
                      ||++...+|  ++.+.|..|+..|...+..|+
T Consensus       129 LS~k~~~lG--vv~a~~~~~g~~m~~~~~~~~  158 (179)
T 3m7n_A          129 LSTKEEEMG--VLRALCSNCKTEMVREGDILK  158 (179)
T ss_dssp             EECCSTTCE--EEECBCTTTCCBCEECSSSEE
T ss_pred             EEEecCCCC--EEEecccccCCceEECCCEEE
Confidence            999998777  788888888887766554443

>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2

Probab=99.44  E-value=1.9e-13  Score=110.34  Aligned_cols=89  Identities=25%  Similarity=0.263  Sum_probs=76.8

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCC------CCeEEEEEceecchhhhh--ccccccCCCCEEEEEEEEEeCCC-ce
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEY------NNIEGMILLSELSRRRIR--SINKLIRVGKTEPVVVIRVDKEK-VM   81 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~------~~~~GlI~iSels~~~v~--~~~~~l~vGd~V~vrVi~Vd~~~-~l   81 (174)
                      ..|++|++|.|+|++|+++||||.|..+      .+++|+||+|++++.++.  ++.+.|++||.|+|+|++++..+ .+
T Consensus        77 y~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i  156 (209)
T 2nn6_I           77 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNY  156 (209)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEE
T ss_pred             CCCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeE
Confidence            3578999999999999999999998521      157999999999988887  89999999999999999999875 59


Q ss_pred             eeecccccchHHHHHHHHHH
Q psy18072         82 TTVTPEKADGLKALQEAIDT  101 (174)
Q Consensus        82 ~ls~~~k~~g~~~i~~~~~~  101 (174)
                      .||++...+|  ++.+.|+.
T Consensus       157 ~LS~k~~~lG--Vv~A~c~~  174 (209)
T 2nn6_I          157 LLTTAENELG--VVVAHSES  174 (209)
T ss_dssp             EEECCSSSCE--ECCCBCSS
T ss_pred             EEEEecCCCc--EEEEEcCC
Confidence            9999998777  66776654

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=99.43  E-value=5.7e-13  Score=105.07  Aligned_cols=87  Identities=16%  Similarity=0.362  Sum_probs=71.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-----------ccccccCCCCEEEEEEEEEeCC---
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-----------SINKLIRVGKTEPVVVIRVDKE---   78 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-----------~~~~~l~vGd~V~vrVi~Vd~~---   78 (174)
                      |.+|++|.|+|+++++||+||+|.+   .+||||+|++++.++.           ++...|++||.|+|+|++++..   
T Consensus        79 ~~~Gev~~G~V~~v~~~G~fV~l~~---~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~  155 (187)
T 1go3_E           79 PEMYELIEGEVVDVVEFGSFVRLGP---LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAER  155 (187)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECSS---SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC--
T ss_pred             cCCCCEEEEEEEEEeCcEEEEEEcC---ccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccCC
Confidence            4589999999999999999999954   8999999999987765           6788999999999999999974   


Q ss_pred             ---CceeeecccccchHHHHHHHHHHHHHHHhh
Q psy18072         79 ---KVMTTVTPEKADGLKALQEAIDTIKAKIEQ  108 (174)
Q Consensus        79 ---~~l~ls~~~k~~g~~~i~~~~~~i~~~l~~  108 (174)
                         ..+.+|.+...+|.      ++|..+..++
T Consensus       156 p~~~~I~lS~k~~~LG~------~~w~~~~~~~  182 (187)
T 1go3_E          156 KRGSKIALTMRQPYLGK------LEWIEEEKAK  182 (187)
T ss_dssp             ---CEEEEECCSTTCEE------HHHHHHHHHH
T ss_pred             CCccEEEEEEcCCCCCc------HHHHhhhhhh
Confidence               26788887776663      3555544443

>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C

Probab=99.39  E-value=4.6e-13  Score=110.83  Aligned_cols=79  Identities=20%  Similarity=0.260  Sum_probs=72.1

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh---hccccccCCCCEEEEEEEEEeCCCceeeeccc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI---RSINKLIRVGKTEPVVVIRVDKEKVMTTVTPE   87 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v---~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~   87 (174)
                      ..|++||+|.|+|+++.++||||.|..  .+.|+||+|+++..++   .++++.|++||.|.|+|++++.++.+.||++.
T Consensus        70 y~p~~GDiV~G~V~~v~~~ga~VdI~~--~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r~  147 (251)
T 2je6_I           70 YYPKINDIVIGLVEDVEIYGWVVDIKA--PYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKG  147 (251)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSS--SSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCS
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEcCC--CeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECCCCcEEEEEcc
Confidence            467899999999999999999999987  7899999999998776   77889999999999999999988889999988


Q ss_pred             ccch
Q psy18072         88 KADG   91 (174)
Q Consensus        88 k~~g   91 (174)
                      +.+|
T Consensus       148 ~~lG  151 (251)
T 2je6_I          148 KDLG  151 (251)
T ss_dssp             TTCE
T ss_pred             ccCC
Confidence            7666

>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=99.38  E-value=1.3e-12  Score=106.79  Aligned_cols=79  Identities=19%  Similarity=0.247  Sum_probs=71.7

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchh-hhhccccccCCCCEEEEEEEEEeCCCceeeeccccc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRR-RIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKA   89 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~-~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k~   89 (174)
                      ..|++||+|.|+|+++.++||||.|..  .+.|+||+|+++.. +..++++.|++||.|.|+|++++.++.+.||++.+.
T Consensus        53 y~p~~GDiV~G~V~~v~~~~a~V~I~~--~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~~~  130 (229)
T 2ba0_A           53 YTPSVGDVVIGIIREVAANGWAVDIYS--PYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRI  130 (229)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSS--SSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCSSS
T ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECCCCcEEEEEcccc
Confidence            468899999999999999999999987  68999999999964 677889999999999999999998888999998876


Q ss_pred             ch
Q psy18072         90 DG   91 (174)
Q Consensus        90 ~g   91 (174)
                      +|
T Consensus       131 lG  132 (229)
T 2ba0_A          131 CR  132 (229)
T ss_dssp             CE
T ss_pred             CC
Confidence            66

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=99.37  E-value=2.3e-12  Score=94.88  Aligned_cols=78  Identities=15%  Similarity=0.149  Sum_probs=61.8

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecc-hhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecccccc
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS-RRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPEKAD   90 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels-~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~k~~   90 (174)
                      +++|++|.|+|++|++|||||+|.. ++..||+|.++.. +.++.++.+.|++||.|+|+|++++.. +.+.++.+....
T Consensus        19 l~~G~i~~G~V~~v~~fG~fV~l~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~Lslk~~~l   97 (119)
T 1wi5_A           19 LKPGMLLTGTVSSLEDHGYLVDIGV-DGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV   97 (119)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECCC-SSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCCCS
T ss_pred             CCCCCEEEEEEEEEeCceEEEEECC-CCeEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCCCCEEEEEEchhhc
Confidence            4599999999999999999999982 1566666655532 334557889999999999999999975 578888877655


Q ss_pred             h
Q psy18072         91 G   91 (174)
Q Consensus        91 g   91 (174)
                      +
T Consensus        98 ~   98 (119)
T 1wi5_A           98 S   98 (119)
T ss_dssp             C
T ss_pred             c
Confidence            5

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E

Probab=99.34  E-value=2.8e-12  Score=100.59  Aligned_cols=76  Identities=22%  Similarity=0.389  Sum_probs=64.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-----------hccccccCCCCEEEEEEEEEeCCC--
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-----------RSINKLIRVGKTEPVVVIRVDKEK--   79 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-----------~~~~~~l~vGd~V~vrVi~Vd~~~--   79 (174)
                      |.+|+++.|+|+++++||+||++..   .+||+|+|+++++++           ++....+++||.|+|||++++.+.  
T Consensus        79 p~~Gev~~G~V~~v~~~G~fv~l~~---~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~~~  155 (180)
T 4ayb_E           79 PVVQEVVEGEVLQVDNYGVFVNLGP---MDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTG  155 (180)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECSS---SEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC----
T ss_pred             ccCCCEEEEEEeeeccceEEEEECC---ccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCCCCc
Confidence            4589999999999999999999864   799999999998876           466788999999999999998642  


Q ss_pred             ---ceeeecccccch
Q psy18072         80 ---VMTTVTPEKADG   91 (174)
Q Consensus        80 ---~l~ls~~~k~~g   91 (174)
                         .+.+|.+.+.+|
T Consensus       156 ~~~rI~ls~k~~gLG  170 (180)
T 4ayb_E          156 RLPRIALTMRQPYLG  170 (180)
T ss_dssp             ---CEEEECCSTTCE
T ss_pred             ccCcEEEEcCCCCCC
Confidence               577777776555

>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1

Probab=99.33  E-value=1.9e-12  Score=106.00  Aligned_cols=79  Identities=19%  Similarity=0.296  Sum_probs=69.9

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchh----hhhccccccCCCCEEEEEEEEEeCCCceeeecc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRR----RIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTP   86 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~----~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~   86 (174)
                      ..|++||+|.|+|+++.++||||.|..  .+.|+||+|+++.+    +..++++.|++||.|.|+|++++.++.+.||++
T Consensus        62 y~p~~GDiV~G~V~~v~~~~~~V~I~~--~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k  139 (235)
T 2z0s_A           62 YVPQAGDVVIGLIQSVGIMNWFVDINS--PYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQ  139 (235)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECSS--SSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECC
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECCCCcEEEEEe
Confidence            468899999999999999999999987  79999999999863    456788899999999999999998878888887


Q ss_pred             cccch
Q psy18072         87 EKADG   91 (174)
Q Consensus        87 ~k~~g   91 (174)
                      .+.+|
T Consensus       140 ~~~lG  144 (235)
T 2z0s_A          140 GEGLG  144 (235)
T ss_dssp             SSSCE
T ss_pred             cccCc
Confidence            77555

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=99.32  E-value=1.4e-13  Score=128.14  Aligned_cols=72  Identities=18%  Similarity=0.380  Sum_probs=0.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecc
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTP   86 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~   86 (174)
                      +++|++|.|+|++|.+|||||+|.+  +++||||+|++++.|+.++.+.|++||.|+|||+++|..+++++|.+
T Consensus       635 ~~vG~v~~G~V~~I~~fGaFVel~~--g~eGLvHiSels~~rv~~~~d~~kvGD~V~VkVi~iD~~grI~LS~K  706 (726)
T 4aid_A          635 AEVGKIYDGKVVKVVDFGAFVNFFG--AKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMK  706 (726)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             hcCCcEEEEEEEEEeccEEEEEECC--CcEEEEEHHHcCcccccCccccCCCCCEEEEEEEEECCCCcEEEEEe
Confidence            3599999999999999999999988  89999999999999999999999999999999999998777777654

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=99.27  E-value=3.9e-13  Score=125.26  Aligned_cols=72  Identities=25%  Similarity=0.469  Sum_probs=0.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecc
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTP   86 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~   86 (174)
                      +++|++|.|+|++|.+||+||+|.+  +++||||+|++++.|+.++.+.|++||.|+|||++++..+++++|.+
T Consensus       625 ~~vG~i~~G~V~~i~~fGaFVel~~--g~eGLvHiSel~~~~v~~~~~~~~vGd~V~VkVi~vd~~grI~LS~k  696 (723)
T 3cdi_A          625 IEVGRVYTGKVTRIVDFGAFVAIGG--GKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIK  696 (723)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             hhcCcEEEEEEEEEecceEEEEeCC--CceEEEEHHHcCCccccCcccccCCCCEEEEEEEEECCCCcEEEEEE
Confidence            3599999999999999999999987  89999999999999999999999999999999999998777777765

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...

Probab=99.23  E-value=2.3e-11  Score=94.84  Aligned_cols=64  Identities=16%  Similarity=0.107  Sum_probs=53.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh----hcc------ccccCCCCEEEEEEEEEeCCC
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI----RSI------NKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v----~~~------~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      |.+|+++.|+|+++++||+||+|..   .+||||+|++++.+.    .++      .+.+++||.|+|||++++.+.
T Consensus        81 ~~~Gev~~G~V~~v~~fG~FV~l~~---~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~  154 (171)
T 1y14_B           81 PFKGEVVDGTVVSCSQHGFEVQVGP---MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQV  154 (171)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETT---EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEET
T ss_pred             CCCCCEEEEEEEEEecCEEEEEecC---eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEEcCC
Confidence            3489999999999999999999964   899999999975432    111      267999999999999999764

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}

Probab=99.22  E-value=1.4e-11  Score=120.01  Aligned_cols=73  Identities=16%  Similarity=0.150  Sum_probs=66.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh-hhccccccCCCCEEEEEEEEEeCC-Cceeeecccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR-IRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPEK   88 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~-v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~k   88 (174)
                      ++|++|.|+|++|++|||||.|..  +++||||+|++++.+ +.++.+.|++||.|+|+|++||.. +.+.+|++..
T Consensus       901 ~~G~iv~G~V~~V~~fGaFV~L~~--gveGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~  975 (1219)
T 3psi_A          901 FKGSIIPVRVERFWHNDIICTTNS--EVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDH  975 (1219)
T ss_dssp             CTTCEEEEEEEEECSSCEEEECTT--SCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEECCHH
T ss_pred             CCCCEEEEEEEEEecceEEEEeCC--CceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEecHH
Confidence            489999999999999999999987  899999999999998 789999999999999999999964 5677776544

>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1

Probab=99.22  E-value=3.1e-11  Score=94.06  Aligned_cols=64  Identities=13%  Similarity=0.188  Sum_probs=53.2

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh----h--------ccccccCCCCEEEEEEEEEeCCC
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI----R--------SINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v----~--------~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      |.+|+++.|+|+++++||+||+|..   .+||||+|++++.+.    .        .....+++||.|+|||++++...
T Consensus        79 ~~~Gev~~G~V~~v~~fG~fV~l~~---~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~  154 (172)
T 2c35_B           79 PFKGEVVDAVVTQVNKVGLFTEIGP---MSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDK  154 (172)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETT---EEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEET
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEECC---EEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCC
Confidence            3589999999999999999999953   779999999975432    1        11458999999999999999764

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=99.19  E-value=5.9e-13  Score=124.54  Aligned_cols=74  Identities=22%  Similarity=0.513  Sum_probs=37.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceec----chhhhhccccccCCCCEEEEEEEEEeCCCceeeecccc
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSEL----SRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEK   88 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSel----s~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k   88 (174)
                      +++|++|.|+|++|.+||+||+|.+  +++||||+|++    ++.|+.++.+.|++||.|+|+|+++|..++++++.+..
T Consensus       665 ~~vG~i~~G~V~~i~~fGaFV~l~~--g~eGLvHiSel~~~~s~~rv~~~~~~~~vGd~V~VkVi~vd~~grI~LS~k~~  742 (757)
T 1e3p_A          665 PEVGERILGSVVKTTTFGAFVSLLP--GKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGKLSLIPVIE  742 (757)
T ss_dssp             --------CBEEECC-CSCEECCC-----CCCCC-------------------CCSSCBCCCCCCCCCSSCC--------
T ss_pred             cccccEEEEEEEEccccEEEEEEcC--CcEEEEEhHHhccccCCCcccCcccccCCCCEEEEEEEEECCCCCEEEEEecC
Confidence            4599999999999999999999987  89999999999    99999999999999999999999999877787776543

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A

Probab=99.18  E-value=6.4e-12  Score=117.92  Aligned_cols=72  Identities=19%  Similarity=0.306  Sum_probs=66.0

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE   87 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~   87 (174)
                      ++|++|.|+|++|++||+||.|..  +++||||+|++++.++.++.+.|++||.|+|+|++||.. +.+.+|++.
T Consensus       653 ~vG~iv~G~V~~V~~fGaFV~l~~--~~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~LSlk~  725 (785)
T 3bzc_A          653 KPGMVLEGVVTNVTNFGAFVDIGV--HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRM  725 (785)
T ss_dssp             CTTCBCCCEEEEEETTEEEEECSS--SSEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEECCSS
T ss_pred             CCCCEEEEEEEEEecCCeEEEeCC--CcEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEEEec
Confidence            489999999999999999999977  799999999999999999999999999999999999984 567777764

>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1

Probab=99.18  E-value=3.7e-11  Score=97.33  Aligned_cols=74  Identities=15%  Similarity=0.071  Sum_probs=58.6

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhcc----------ccccCCCCEEEEEEEEEeCCC----
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSI----------NKLIRVGKTEPVVVIRVDKEK----   79 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~----------~~~l~vGd~V~vrVi~Vd~~~----   79 (174)
                      ++|+++.|+|+++++||+||+|..   .+||||+|++++.+..++          .+.+++||.|+|||++++.+.    
T Consensus        82 ~vGev~~G~V~~vt~fG~FVelg~---~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~~i~  158 (215)
T 2b8k_G           82 FKGEVVDGTVVSCSQHGFEVQVGP---MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIH  158 (215)
T ss_dssp             CTTEEEEEEEEEEETTEEEEECTT---SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETTEEE
T ss_pred             CCCCEEEEEEEEEecceEEEEecC---cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcCCCccE
Confidence            589999999999999999999964   799999999975433111          267999999999999999864    


Q ss_pred             ceeeecccccch
Q psy18072         80 VMTTVTPEKADG   91 (174)
Q Consensus        80 ~l~ls~~~k~~g   91 (174)
                      .+. |.+...+|
T Consensus       159 ~Ig-Smk~~~LG  169 (215)
T 2b8k_G          159 AIG-SIKEDYLG  169 (215)
T ss_dssp             EEE-ECCSTTCE
T ss_pred             EEE-EcCCCCCC
Confidence            344 55554444

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}

Probab=99.15  E-value=3.8e-12  Score=122.24  Aligned_cols=73  Identities=16%  Similarity=0.154  Sum_probs=0.0

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh-hhccccccCCCCEEEEEEEEEeC-CCceeeecccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR-IRSINKLIRVGKTEPVVVIRVDK-EKVMTTVTPEK   88 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~-v~~~~~~l~vGd~V~vrVi~Vd~-~~~l~ls~~~k   88 (174)
                      ++|++|.|+|++|++|||||.|..  +++||||+|++++.+ +.++.+.|++||.|+|+|++|+. .+.+.+|++..
T Consensus       904 ~~G~iv~G~V~~V~~fGaFV~L~~--gveGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~  978 (1030)
T 3psf_A          904 FKGSIIPVRVERFWHNDIICTTNS--EVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDH  978 (1030)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             cCCCEEEEEEEEEccCeEEEEeCC--CcEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEechH
Confidence            489999999999999999999987  899999999999998 88999999999999999999995 45677776544

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=99.13  E-value=2.3e-11  Score=95.16  Aligned_cols=64  Identities=13%  Similarity=0.214  Sum_probs=54.5

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh----------hccccccCCCCEEEEEEEEEeCCC
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI----------RSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v----------~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      |.+|+++.|+|+++++||+||+|..   .+||||+|++++.+.          ++....+++||.|+|||++++.+.
T Consensus        82 p~~Gev~~G~V~~v~~fG~FV~l~~---~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~~~  155 (172)
T 3h0g_G           82 PFRGEVVDAIVTTVNKMGFFANIGP---LNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDA  155 (172)
T ss_dssp             CCTTCEEECCCCEEETTEEECCBTT---BCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEESS
T ss_pred             cCCCCEEEEEEEEEEcceEEEEeCC---eEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEECCC
Confidence            3489999999999999999999964   679999999975533          233578999999999999999875

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=98.96  E-value=1.4e-09  Score=87.11  Aligned_cols=70  Identities=9%  Similarity=0.087  Sum_probs=58.3

Q ss_pred             cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-------------------hccccccC
Q psy18072          3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-------------------RSINKLIR   63 (174)
Q Consensus         3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-------------------~~~~~~l~   63 (174)
                      ++|.|+.+   .+|+++.|+|++++++|+||+| +  .++||+|++++..+++                   ++....++
T Consensus        72 fk~~~f~p---~~GEv~~G~Vs~vt~~GifV~l-g--~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~  145 (203)
T 3ayh_B           72 FRLIIFRP---FRGEVMLGKIKSCSEEGIRVTI-S--FFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFD  145 (203)
T ss_dssp             EEEEEECC---CTTCEEEEEEEEEETTEEEEEC-S--SCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECC
T ss_pred             EEEEEEcc---CCCCEEEEEEEEEeccEEEEEE-e--CceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEc
Confidence            35665553   4799999999999999999999 4  4899999999977654                   44567899


Q ss_pred             CCCEEEEEEEEEeCC
Q psy18072         64 VGKTEPVVVIRVDKE   78 (174)
Q Consensus        64 vGd~V~vrVi~Vd~~   78 (174)
                      +||.|++||++++..
T Consensus       146 ~Gd~VrvrV~~v~~~  160 (203)
T 3ayh_B          146 IDEEIRFQIESEDFV  160 (203)
T ss_dssp             TTCEEEEEEEEEEEC
T ss_pred             CCCEEEEEEEEEEcc
Confidence            999999999999874

>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=98.95  E-value=6.9e-10  Score=94.22  Aligned_cols=79  Identities=18%  Similarity=0.192  Sum_probs=66.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchh----hh------hccccccCCCCEEEEEEEEEeCCCc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRR----RI------RSINKLIRVGKTEPVVVIRVDKEKV   80 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~----~v------~~~~~~l~vGd~V~vrVi~Vd~~~~   80 (174)
                      ..|++||+|.|+|+++.+++|||.|..  ...|++|+|+++..    |.      ..++..|++||.|.|||++++.+..
T Consensus        91 Y~P~vGDvViG~Vt~V~~~~a~VdI~s--~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~~~~  168 (308)
T 2nn6_H           91 YIGEVGDIVVGRITEVQQKRWKVETNS--RLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGA  168 (308)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSS--SSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTE
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEECC--CcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCCCCC
Confidence            478899999999999999999999986  57899999998642    22      2456899999999999999998888


Q ss_pred             eeeecccccch
Q psy18072         81 MTTVTPEKADG   91 (174)
Q Consensus        81 l~ls~~~k~~g   91 (174)
                      +.+|++...+|
T Consensus       169 i~LStr~~~LG  179 (308)
T 2nn6_H          169 VSLHTRSLKYG  179 (308)
T ss_dssp             EEEECCSSTTC
T ss_pred             EEEEecCcCCc
Confidence            99988877555

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=98.94  E-value=1e-09  Score=89.04  Aligned_cols=72  Identities=10%  Similarity=0.104  Sum_probs=59.0

Q ss_pred             cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh--------------hccccccCCCCEE
Q psy18072          3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI--------------RSINKLIRVGKTE   68 (174)
Q Consensus         3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v--------------~~~~~~l~vGd~V   68 (174)
                      ++|.||.+ +  +|+++.|+|++++++|+||+|.+  .++||+|++++..+++              +.....|++||.|
T Consensus        72 fk~~~f~p-~--vGEv~~G~Is~Vt~fGifVeL~g--~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~V  146 (218)
T 2ckz_B           72 FRAVVFKP-F--LGEIVTGWISKCTAEGIKVSLLG--IFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKI  146 (218)
T ss_dssp             EEEEEECC-C--TTCEEEEEEEEEETTEEEEECTT--SCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEE
T ss_pred             EEEEEecC-C--CCCEEEEEEEEEccCcEEEEccC--ccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEE
Confidence            35665544 3  79999999999999999999976  5899999999976553              3346789999999


Q ss_pred             EEEEEEEeCCC
Q psy18072         69 PVVVIRVDKEK   79 (174)
Q Consensus        69 ~vrVi~Vd~~~   79 (174)
                      ++||++++...
T Consensus       147 rvrV~~v~~~~  157 (218)
T 2ckz_B          147 RFRIEREVFVD  157 (218)
T ss_dssp             EEEEEEEEECC
T ss_pred             EEEEEEEEccc
Confidence            99999999764

>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1

Probab=98.83  E-value=8.8e-09  Score=80.91  Aligned_cols=72  Identities=17%  Similarity=0.140  Sum_probs=62.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeee
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTV   84 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls   84 (174)
                      +.|++||+|.|+|+.+..++|+|.|..+ .+.|+||++.+. ...+..+..|++||.|.|||.+++.+..+.++
T Consensus         3 Y~P~~gDvViG~V~~v~~~~~~VdI~~~-~~~a~L~~s~~~-g~~k~~r~~l~~GDlV~ArV~~~~~~~~~~Lt   74 (175)
T 2ja9_A            3 YIPSVNDFVIGVIIGTFSDSYKVSLQNF-SSSVSLSYMAFP-NASKKNRPTLQVGDLVYARVCTAEKELEAEIE   74 (175)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESSTT-SCCEEEETTSST-TCCSSSCCCCCTTCEEEEEEEECCTTSCCEEE
T ss_pred             ccCCCcCEEEEEEEEEECcEEEEEECCC-CccEEEEHHHCC-chhhhhhccCCCCCEEEEEEEEecCCCceEEE
Confidence            4577999999999999999999999752 378999999886 33456778999999999999999987777887

>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A

Probab=98.79  E-value=1.3e-08  Score=93.84  Aligned_cols=78  Identities=17%  Similarity=0.215  Sum_probs=62.5

Q ss_pred             ccchhhccCCCCCC--EEEEEEEEEecceEEEEECCCCCeEEEEEceecch--hhhh----------ccccccCCCCEEE
Q psy18072          4 SCRFYAEKYPEVED--VVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR--RRIR----------SINKLIRVGKTEP   69 (174)
Q Consensus         4 ~~r~~~~~~p~~Gd--iV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~--~~v~----------~~~~~l~vGd~V~   69 (174)
                      .|+|+...   +|+  ++.|+|++|++||+||.|.++ +++||||+|+++.  +++.          +....|++||.|+
T Consensus       550 ~~~~l~~~---vGe~~~f~g~V~~V~~~G~fV~L~~~-gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~  625 (644)
T 2id0_A          550 YARFLKDK---AGTDTRFAAEIVDISRGGMRVRLVDN-GAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVID  625 (644)
T ss_dssp             HHHHHGGG---TTSCCCEEEEEEEEETTEEEEEETTT-CCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEE
T ss_pred             HHHHhhhc---cCCCceEEEEEEEEeCCceEEEEcCC-cEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEE
Confidence            57877663   688  999999999999999999754 6999999999973  3321          3356799999999


Q ss_pred             EEEEEEeCC-Cceeeec
Q psy18072         70 VVVIRVDKE-KVMTTVT   85 (174)
Q Consensus        70 vrVi~Vd~~-~~l~ls~   85 (174)
                      |+|++|+.. +.+.++.
T Consensus       626 VkV~~vd~~~~~I~~~l  642 (644)
T 2id0_A          626 VTIAEVRMETRSIIARP  642 (644)
T ss_dssp             EEEEEEETTTTEEEEEE
T ss_pred             EEEEEEeCCCCEEEEEE
Confidence            999999985 4565553

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=98.61  E-value=2.4e-07  Score=79.61  Aligned_cols=89  Identities=16%  Similarity=0.101  Sum_probs=66.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC---ceeeeccccc
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK---VMTTVTPEKA   89 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~---~l~ls~~~k~   89 (174)
                      .+.|++|+|+|.++.++|+||.|.   +.+|+||.++++      ++..|++||.|+|.|++++...   .+.+|...+ 
T Consensus       132 ~~~GeIV~G~V~ri~~~~v~VDlG---k~EgiLp~sE~i------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p-  201 (344)
T 1hh2_P          132 ELKGTVTTAEVIRVMGEWADIRIG---KLETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVP-  201 (344)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEET---TEEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESSSH-
T ss_pred             hcCCCEEEEEEEEEecCcEEEEeC---CeEEEEeHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEeecc-
Confidence            358999999999999999999994   599999999987      4578999999999999999653   355554444 


Q ss_pred             chHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072         90 DGLKALQEAIDTIKAKIEQLGGVFQVQ  116 (174)
Q Consensus        90 ~g~~~i~~~~~~i~~~l~~~~g~l~~k  116 (174)
                       .  .+....+  .+.=+...|.+.++
T Consensus       202 -~--~lk~Lfe--lEVPEI~dG~VeI~  223 (344)
T 1hh2_P          202 -E--FVIGLMK--LEIPEVENGIVEIK  223 (344)
T ss_dssp             -H--HHHHHHH--HHCHHHHHSSEEEE
T ss_pred             -H--HHHHHHH--hhcccceeeeEEEE
Confidence             3  2333333  23334467777664

>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A

Probab=98.60  E-value=9.3e-08  Score=86.13  Aligned_cols=64  Identities=17%  Similarity=0.298  Sum_probs=56.0

Q ss_pred             CCCCCEEEEEEEEEecc--eEEEEECCCCCeEEEEEceecchhhh---------hccccccCCCCEEEEEEEEEeCC
Q psy18072         13 PEVEDVVMVTVISIAEM--GAYVHLLEYNNIEGMILLSELSRRRI---------RSINKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~--GafV~L~~~~~~~GlI~iSels~~~v---------~~~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      +.+|++|.|+|++|.++  ||||.|..  +..||||+|++++.++         .++.+.+++||.|.|+|++....
T Consensus        43 ~~vGnIY~GkV~rv~p~~~aAFVdiG~--gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g  117 (517)
T 2bx2_L           43 QKKANIYKGKITRIEPSLEAAFVDYGA--ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERG  117 (517)
T ss_dssp             CCTTCEEEEEEEEEETTTTEEEEESSS--SSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCT
T ss_pred             CCCCCEEEEEEEEeccCCceEEEEeCC--CcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeeccc
Confidence            35899999999999999  99999988  8899999999987763         34668899999999999996644

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=98.57  E-value=7.5e-08  Score=90.27  Aligned_cols=77  Identities=17%  Similarity=0.138  Sum_probs=56.5

Q ss_pred             ccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecc--hhhh-----------hc----cccccCCCC
Q psy18072          4 SCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS--RRRI-----------RS----INKLIRVGK   66 (174)
Q Consensus         4 ~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels--~~~v-----------~~----~~~~l~vGd   66 (174)
                      .|+|+...   + .++.|+|++|+++|+||.|.++ +++|+||+|+++  ..++           .+    ....|++||
T Consensus       662 ~~~~l~~~---~-~~~~g~V~~V~~~G~fV~l~~~-giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD  736 (760)
T 2vnu_D          662 VGQVMRNN---E-STETGYVIKVFNNGIVVLVPKF-GVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFD  736 (760)
T ss_dssp             HHHHHHTC---C-SEEEEEEEEEETTEEEEEETTT-TEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTC
T ss_pred             HHHHhhcC---c-eEEEEEEEEEECCeEEEEEeCC-CcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCC
Confidence            57766653   3 6999999999999999999876 599999999996  4442           12    257899999


Q ss_pred             EEEEEEEEEeCC----Cceeeec
Q psy18072         67 TEPVVVIRVDKE----KVMTTVT   85 (174)
Q Consensus        67 ~V~vrVi~Vd~~----~~l~ls~   85 (174)
                      .|+|+|++++..    +++.+++
T Consensus       737 ~V~VkV~~vd~~~~~~~kI~lsl  759 (760)
T 2vnu_D          737 KVEVQVRSVMDPITSKRKAELLL  759 (760)
T ss_dssp             EEEEEEC--------CCEEEC--
T ss_pred             EEEEEEEEEECccccCCcEEEEe
Confidence            999999999876    5666554

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=98.55  E-value=1.8e-07  Score=78.51  Aligned_cols=67  Identities=15%  Similarity=0.144  Sum_probs=55.0

Q ss_pred             CCCCEEEEEEEEEe-cceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecc
Q psy18072         14 EVEDVVMVTVISIA-EMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTP   86 (174)
Q Consensus        14 ~~GdiV~G~V~~i~-~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~   86 (174)
                      ++|+++.|+|++++ ++||||.+.. .+.+||||+|+++|.+.    ..+++||.+.|+ +.+|+.+.+.+|.+
T Consensus        68 ~~G~~~~g~V~~v~~~~GaFVdiG~-~~~d~lvp~sel~~~~~----~~~~~Gd~v~v~-l~iD~~~Ri~ls~k  135 (285)
T 3go5_A           68 TQDQFGWGRVTEVRKDLGVFVDTGL-PDKEIVVSLDILPELKE----LWPKKGDQLYIR-LEVDKKDRIWGLLA  135 (285)
T ss_dssp             CSSSCEEEEEEEEETTTEEEEECSC-TTCCEEEEGGGSCSSGG----GSCCTTCEEEEE-EEECTTSCEEEEEC
T ss_pred             cCCCEEEEEEEEEccCceEEEEECC-CCcEEEEEHHHCCcccc----cccCCCCEEEEE-EEECCCCcEEEEeh
Confidence            48999999999999 7999999952 03799999999997543    357999999766 68998777877764

>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=98.53  E-value=1.4e-07  Score=79.47  Aligned_cols=72  Identities=13%  Similarity=-0.014  Sum_probs=63.1

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVT   85 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~   85 (174)
                      +.|++||+|.|+|+++....|.|.|..  .+.|+||.+.+. ...+.++..|++||.|.|||+++..+..+.|++
T Consensus       123 YiP~vGDiVIG~Vt~v~~~~~~VdI~s--~~~a~L~~~~f~-Gatk~~r~~f~~GDlV~ArV~s~~~~~~~eLsc  194 (289)
T 2nn6_G          123 YVPVKGDHVIGIVTAKSGDIFKVDVGG--SEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANKDMEPEMVC  194 (289)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSS--SSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCTTSCCEEEC
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEECC--CceeEEehhhcC-cchhhhhhhcCCCCEEEEEEEEcCCCCceEEEe
Confidence            468899999999999999999999987  789999999875 234567789999999999999999877778887

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=98.51  E-value=1e-07  Score=91.52  Aligned_cols=77  Identities=18%  Similarity=0.161  Sum_probs=62.0

Q ss_pred             ccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecc--hhhh-----------hc----cccccCCCC
Q psy18072          4 SCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS--RRRI-----------RS----INKLIRVGK   66 (174)
Q Consensus         4 ~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels--~~~v-----------~~----~~~~l~vGd   66 (174)
                      .|+|+...    |.++.|+|++|+++|+||.|.++ +++|+||+|+++  .+++           ++    ....|++||
T Consensus       879 ~~~~l~~~----ge~~~g~V~~V~~~G~fV~L~~~-giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD  953 (977)
T 2wp8_J          879 VGQVMRNN----ESTETGYVIKVFNNGIVVLVPKF-GVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFD  953 (977)
T ss_dssp             HHHHHHHT----TCEEEEEEEEECSSEEEEECTTT-CCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTC
T ss_pred             Hhhhhccc----ceEEEEEEEEEcCCeEEEEEcCC-CeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCC
Confidence            57877663    78999999999999999999876 599999999997  5442           11    347899999


Q ss_pred             EEEEEEEEEeCC----Cceeeec
Q psy18072         67 TEPVVVIRVDKE----KVMTTVT   85 (174)
Q Consensus        67 ~V~vrVi~Vd~~----~~l~ls~   85 (174)
                      .|+|+|++++..    +++.+++
T Consensus       954 ~V~VkV~~vd~~~~~~~kI~Lsl  976 (977)
T 2wp8_J          954 KVEVQVRSVMDPITSKRKAELLL  976 (977)
T ss_dssp             EEEEEECCCCCSSSCCCCCCEEE
T ss_pred             EEEEEEEEEcCcccCCCceEEEe
Confidence            999999999862    4566654

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}

Probab=98.51  E-value=6.9e-08  Score=69.19  Aligned_cols=42  Identities=29%  Similarity=0.481  Sum_probs=37.9

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI   55 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v   55 (174)
                      .|++|+.|.+.|.++++||+||+|.+  +++||||+|++++.++
T Consensus        58 ~l~~Ge~V~g~V~~i~~fG~fv~l~~--~~eGlvhis~i~~~~~   99 (101)
T 2bh8_A           58 NPQQGDRVEGKIKSITDFGIFIGLDG--GIDGLVHLSDISWAQA   99 (101)
T ss_dssp             CCCTTCEEEEEEEECCSEEEEECTTS--CEEEEEEEEEEEECCC
T ss_pred             CCCCCCEEEEEEEEeCCcEEEEEcCC--CceEEEEHHHCccCcC
Confidence            34599999999999999999999987  8999999999997654

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=98.36  E-value=1.1e-06  Score=75.90  Aligned_cols=97  Identities=15%  Similarity=0.119  Sum_probs=69.4

Q ss_pred             hhccCCCCCCEEEEEEEE----EecceEEEEECC-CCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC---
Q psy18072          8 YAEKYPEVEDVVMVTVIS----IAEMGAYVHLLE-YNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK---   79 (174)
Q Consensus         8 ~~~~~p~~GdiV~G~V~~----i~~~GafV~L~~-~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~---   79 (174)
                      |.+...+.|++|+|+|.+    +.+.++||.|.. -.+.+|+||.+++.      ++..|++||.|+|.|++|+...   
T Consensus       123 ~~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi------P~E~~~~GDrVkvyV~~V~~~~kgp  196 (366)
T 1k0r_A          123 YGEFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREP  196 (366)
T ss_dssp             ----CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSC
T ss_pred             HHHHHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC------CCccCCCCCEEEEEEEEEecCCCcc
Confidence            444445689999999999    999999999953 01389999999986      3589999999999999999863   


Q ss_pred             ceeeecccccchHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072         80 VMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQ  116 (174)
Q Consensus        80 ~l~ls~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k  116 (174)
                      .+.+|...+  +  .+...++  .++=+...|.+.++
T Consensus       197 qI~LSRT~p--~--lv~~Lfe--~EVPEI~dG~VeIk  227 (366)
T 1k0r_A          197 LITLSRTHP--N--LVRKLFS--LEVPEIADGSVEIV  227 (366)
T ss_dssp             EEEEESSCH--H--HHHHHHH--HHCHHHHTTSEEEE
T ss_pred             EEEEEeCCh--H--HHHHHHH--hcchhhcCCeEEEE
Confidence            355555444  3  3344433  33345577888775

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=98.09  E-value=1.9e-05  Score=65.07  Aligned_cols=91  Identities=14%  Similarity=0.102  Sum_probs=68.0

Q ss_pred             CCCCEEEEEEEE----EecceEEEEECC-CCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC---ceeeec
Q psy18072         14 EVEDVVMVTVIS----IAEMGAYVHLLE-YNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK---VMTTVT   85 (174)
Q Consensus        14 ~~GdiV~G~V~~----i~~~GafV~L~~-~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~---~l~ls~   85 (174)
                      +.|++|+|+|.+    +....+||.|.. -.+.+|+||.+++.      +++.|++||.|+|.|++|+...   .+.+|.
T Consensus         6 r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqi------p~E~~~~GDrIkayV~~V~~~~~gpqIiLSR   79 (251)
T 2asb_A            6 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITLSR   79 (251)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEEES
T ss_pred             cCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcC------CCccCCCCCEEEEEEEEEEcCCCCCEEEEEe
Confidence            489999999999    788899999952 01389999999976      4589999999999999999863   455665


Q ss_pred             ccccchHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072         86 PEKADGLKALQEAIDTIKAKIEQLGGVFQVQ  116 (174)
Q Consensus        86 ~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k  116 (174)
                      ..+  .  .+...++  .++=+...|.+.++
T Consensus        80 t~p--~--lvk~Lfe--~EVPEI~dG~veI~  104 (251)
T 2asb_A           80 THP--N--LVRKLFS--LEVPEIADGSVEIV  104 (251)
T ss_dssp             SCH--H--HHHHHHH--HHCHHHHTTSEEEE
T ss_pred             ccH--H--HHHHHHH--hcchHhhcCeEEEE
Confidence            544  3  3344443  33445678888875

>1jjg_A M156R; beta barrel, S1 motif, OB fold, MYXV156R, NESG project, structural genomics, EIF-2A homolog, PSI, protein structure initiative; NMR {Myxoma virus} SCOP: b.40.4.5

Probab=97.74  E-value=6.8e-05  Score=52.74  Aligned_cols=62  Identities=21%  Similarity=0.212  Sum_probs=51.7

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEce-ecchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLS-ELSRRRIRSINKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iS-els~~~v~~~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      +|++.+|+|+ +.+.-++|.|.+|.+.+|+|--+ .+..++...+++.+ +|.+|+|+|+++|.-
T Consensus        32 ~g~VtkGiVy-~kd~~fyV~L~dY~glEaii~dYvnv~~dr~~klkkkL-VGKtIkVqVIRvD~l   94 (102)
T 1jjg_A           32 PGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADGL   94 (102)
T ss_dssp             SSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECSS
T ss_pred             CCceEeeEEE-EeCCEEEEEecCCCCceeeeehhhhhhHHHHHHHHHHh-cCceEEEEEEEeccE
Confidence            7999999998 68889999999997799998755 34445666677777 899999999999863

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}

Probab=97.08  E-value=0.0012  Score=46.86  Aligned_cols=61  Identities=8%  Similarity=0.007  Sum_probs=45.8

Q ss_pred             CCCEEEEEEEEE---ecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         15 VEDVVMVTVISI---AEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        15 ~GdiV~G~V~~i---~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      .++.++|+|+.+   +.|| ||.... ++.+.|+|+|.+++..+  +...+++|+.|...|.++.+-+
T Consensus        13 ~~~~~~G~Vk~fn~~kGfG-FI~~~~-gg~dvfvH~s~l~~~~~--~~~~l~~Ge~V~g~V~~i~~fG   76 (101)
T 2bh8_A           13 QSGKMTGIVKWFNADKGFG-FITPDD-GSKDVFVHFSAGSSGAA--VRGNPQQGDRVEGKIKSITDFG   76 (101)
T ss_dssp             ---CEEEEEEEEEGGGTEE-EEEESS-SSCEEEEECCCSCSSSC--CCCCCCTTCEEEEEEEECCSEE
T ss_pred             ccccceeEEEEEECCCCCE-EEEeCC-CCcEEEEEEEEEecCCc--cccCCCCCCEEEEEEEEeCCcE
Confidence            678899999988   5688 887654 25899999999987543  1246889999999999987543

>1yz7_A Probable translation initiation factor 2 alpha subunit; helical domain, alpha-beta domain; 2.26A {Pyrococcus abyssi}

Probab=96.54  E-value=0.0011  Score=52.29  Aligned_cols=85  Identities=13%  Similarity=0.140  Sum_probs=57.6

Q ss_pred             eEEEEEceecchhhhhccccccCCC-------CEEEEEEEEEeC-CCceeeecccccchHHHHHHHHHHHHHHHhhhCCe
Q psy18072         41 IEGMILLSELSRRRIRSINKLIRVG-------KTEPVVVIRVDK-EKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGV  112 (174)
Q Consensus        41 ~~GlI~iSels~~~v~~~~~~l~vG-------d~V~vrVi~Vd~-~~~l~ls~~~k~~g~~~i~~~~~~i~~~l~~~~g~  112 (174)
                      +.|.|.++-++.+-+..+...|+-|       +.+.++|.-|-+ --.+++++.++..|...|+.+++.|.+.|++.||.
T Consensus        91 Ira~ieltc~~~dGIe~IK~AL~~a~~~~~~~~~~~ikI~lvgaP~Y~i~~~~~Dkk~g~~~L~~aie~i~~~I~~~gG~  170 (188)
T 1yz7_A           91 IDAEFEITVPKPNGVEIIKEALIRARDRANKEKDVEVKFTYLGAPRYRIDITAPDYYKAEEVLESIAEEILRVIKEAGGE  170 (188)
T ss_dssp             EEEEEEEECCSTTHHHHHHHHHHHHHHHHHTSTTCEEEEEECSTTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHTTCE
T ss_pred             EEEEEEEEeCCCchHHHHHHHHHHHHhcccCCCCCcEEEEEEcCcEEEEEEeeCCHHHHHHHHHHHHHHHHHHHHHhCCE
Confidence            5666666655555555444444322       223333333333 23689999999999999999999999999999999


Q ss_pred             eEEeeCceeEecc
Q psy18072        113 FQVQMAPKVVTAS  125 (174)
Q Consensus       113 l~~k~~P~~i~~~  125 (174)
                      +.|+..++.|+..
T Consensus       171 ~~v~r~~~~~~~~  183 (188)
T 1yz7_A          171 ATLLRKEKRIKKV  183 (188)
T ss_dssp             EEEECCCCC----
T ss_pred             EEEEEcHHHHHHH
Confidence            9999888877643

>3d0f_A Penicillin-binding 1 transmembrane protein MRCA; BIG_1156.2, STR genomics, PSI-2, protein structure initiative; 1.64A {Nitrosomonas europaea atcc 19718}

Probab=96.38  E-value=0.013  Score=41.44  Aligned_cols=60  Identities=17%  Similarity=0.042  Sum_probs=50.3

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-----hc-cccccCCCCEEEEE
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-----RS-INKLIRVGKTEPVV   71 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-----~~-~~~~l~vGd~V~vr   71 (174)
                      ..++..|+.+.+.|+++.+.++-|.+.+  +..+.|+.+.+.+.+-     +. +.+.|++||.|.|+
T Consensus        28 ~~~~~~~~~~~AvV~~v~~~~~~v~~~~--g~~~~l~~~~~~WA~~~~~~~~~~~~~~l~~GdvI~V~   93 (106)
T 3d0f_A           28 QDIGNSDDILAAVVLSATPGAVEAFRKN--GETIRITGDGLKAAHRFLSNDPKIGEKRIRPGALIRVK   93 (106)
T ss_dssp             TTSCTTTTCEEEEEEEEETTEEEEEETT--SCEEEECGGGGSTTGGGTTTCTTTGGGSCCTTEEEEEE
T ss_pred             hccCccCCeEEEEEEEeCCCeEEEEEcC--CCeEEEcHHHChhhhhcccccccchhccCCCCCEEEEE
Confidence            4466679999999999999999999977  6778899999988752     33 66789999999998

>2qn6_B Translation initiation factor 2 alpha subunit; initiation of translation, GTP-binding, nucleotide-binding, protein biosynthesis; HET: GDP; 2.15A {Sulfolobus solfataricus} SCOP: d.58.51.1 PDB: 2qmu_B* 3qsy_B*

Probab=95.99  E-value=0.0023  Score=44.99  Aligned_cols=76  Identities=12%  Similarity=0.148  Sum_probs=53.4

Q ss_pred             eEEEEEceecchhhhhccccccCCCC---------EEEEEEEEEeCCC-ceeeecccccchHHHHHHHHHHHHHHHhhhC
Q psy18072         41 IEGMILLSELSRRRIRSINKLIRVGK---------TEPVVVIRVDKEK-VMTTVTPEKADGLKALQEAIDTIKAKIEQLG  110 (174)
Q Consensus        41 ~~GlI~iSels~~~v~~~~~~l~vGd---------~V~vrVi~Vd~~~-~l~ls~~~k~~g~~~i~~~~~~i~~~l~~~~  110 (174)
                      +.|.|.++-+..+-+..+.+.|+-|.         .+.++|--|-+-. .+++++.++..|...|+++++.|.+.++++|
T Consensus         6 Ira~iel~c~~~dGIe~IK~AL~~a~~~~~~~~~~~~~vkI~~vgaP~Y~i~~~~~D~k~ge~~L~~ai~~i~~~i~~~g   85 (93)
T 2qn6_B            6 MSGLITVRTNEPLGVEKIKEVISKALENIEQDYESLLNIKIYTIGAPRYRVDVVGTNPKEASEALNQIISNLIKIGKEEN   85 (93)
T ss_dssp             EEEEEEEEECCTTTHHHHHHHHHHHHTTHHHHCTTEEEEEEEESSTTEEEEEEEESCHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             EEEEEEEEeCCCchHHHHHHHHHHHHhhcccccCccceEEEEEEcCCeEEEEEEecCHHHHHHHHHHHHHHHHHHHHHhC
Confidence            56666666666555554444443221         1345554443322 6789999999999999999999999999999


Q ss_pred             CeeEEe
Q psy18072        111 GVFQVQ  116 (174)
Q Consensus       111 g~l~~k  116 (174)
                      |.+.|+
T Consensus        86 G~~~v~   91 (93)
T 2qn6_B           86 VDISVV   91 (93)
T ss_dssp             EEEEEC
T ss_pred             CEEEEE
Confidence            999884

>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure initiative, northeast structural genomics consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5 b.40.4.16 PDB: 2r7f_A

Probab=95.25  E-value=0.022  Score=50.54  Aligned_cols=59  Identities=20%  Similarity=0.253  Sum_probs=42.2

Q ss_pred             ccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072          4 SCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus         4 ~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      .|+|+.+   ++|..+.|.|+.+.         .   ..|+||++.+...  ......+++||.|+|+|.+||..+
T Consensus       395 ~~~~l~~---~~g~~f~g~vv~l~---------~---~~glV~v~~l~~d--~~~~~~~~lGd~V~V~v~~vd~~~  453 (469)
T 2r7d_A          395 TLRFIAA---QPERVWDAVVVDRR---------G---AQATLLIPDLAFD--VQVNTPAAPGTALQVQFADIDLPQ  453 (469)
T ss_dssp             HHHHHHT---CTTCCEEEEEEEEE---------T---TEEEEEEGGGTEE--EEEECCCCTTCEEEEEEEEEETTT
T ss_pred             HHHHHHh---CCCCEEEEEEEEEe---------C---cEEEEEECCCCeE--EecCCcCCCCCEEEEEEEEEccCC
Confidence            5776665   37999999876543         2   3577777766543  123467999999999999999865

>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae}

Probab=94.02  E-value=0.11  Score=41.34  Aligned_cols=65  Identities=11%  Similarity=0.038  Sum_probs=46.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh--hcc----------ccccCCCCEEEEEEEEEeCCC
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI--RSI----------NKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v--~~~----------~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      |.+|+++.|+|+.+.+.|+.+-+.+  -+..+|+...+...+.  .+-          .+--++|+.|+.||.+++..+
T Consensus       127 Pf~GevL~G~V~~~s~~~Ig~~~~G--~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~~~~~~~  203 (214)
T 2rf4_A          127 PQVGDVLEGYIFIQSASHIGLLIHD--AFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTG  203 (214)
T ss_dssp             CCTTCEEEEEECCCCSSCEEEEETT--TEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEEEEECCS
T ss_pred             cCCCCEEEEEEEEECCCcEEEEEeC--CEEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEEEEEecC
Confidence            4589999999999999777776544  5778999988753321  100          011236999999999998755

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*

Probab=92.85  E-value=0.019  Score=47.35  Aligned_cols=77  Identities=12%  Similarity=0.138  Sum_probs=54.7

Q ss_pred             CeEEEEEceecchhhhhccccccCCCCE---------EEEEEEEEeC-CCceeeecccccchHHHHHHHHHHHHHHHhhh
Q psy18072         40 NIEGMILLSELSRRRIRSINKLIRVGKT---------EPVVVIRVDK-EKVMTTVTPEKADGLKALQEAIDTIKAKIEQL  109 (174)
Q Consensus        40 ~~~GlI~iSels~~~v~~~~~~l~vGd~---------V~vrVi~Vd~-~~~l~ls~~~k~~g~~~i~~~~~~i~~~l~~~  109 (174)
                      ++.|.|.++-++...+..+.+.|+.|..         +.++|.-|-+ .-.+++++.++..|...|+++++.|.+.|+++
T Consensus       178 ki~~~i~~~~~~~~Gi~~Ik~aL~~~~~~~~~~~~~~~~i~i~~v~~P~Y~i~~~~~d~k~~~~~l~~~~~~~~~~i~~~  257 (266)
T 3cw2_C          178 KMSGLITVRTNEPLGVEKIKEVISKALENIEQDYESLLNIKIYTIGAPRYRVDVVGTNPKEASEALNQIISNLIKIGKEE  257 (266)
T ss_dssp             EEEEEEEECCCCTTHHHHHHHHHHHHHTTCTTTSCSEEEEECBBSSSSEEEEEEEESCHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             EEEEEEEEEecCCChHHHHHHHHHHhhhhcccccCccceEEEEEEcCCEEEEEEEeCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            3677777777766666555555543311         2233333332 22678899999999999999999999999999


Q ss_pred             CCeeEEe
Q psy18072        110 GGVFQVQ  116 (174)
Q Consensus       110 ~g~l~~k  116 (174)
                      ||.+.|+
T Consensus       258 ~g~~~~~  264 (266)
T 3cw2_C          258 NVDISVV  264 (266)
T ss_dssp             TCCEEEC
T ss_pred             CCEEEEE
Confidence            9999874

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

Probab=89.22  E-value=0.87  Score=33.52  Aligned_cols=58  Identities=16%  Similarity=0.024  Sum_probs=39.1

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEE
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV   72 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrV   72 (174)
                      .|..+.|+|..|.+.+++|...+.-...--+|.+++.--.-......|.+||.|.|-.
T Consensus        14 ~G~~y~a~V~~v~~d~~~V~f~n~w~~~~~vp~~~vRlpP~~~~~~~f~~gd~VEV~~   71 (128)
T 3h8z_A           14 NGAFYKGFVKDVHEDSVTIFFENNWQSERQIPFGDVRLPPPADYNKEITEGDEVEVYS   71 (128)
T ss_dssp             TSCEEEEEEEEECSSEEEEEETTCTTCCEEEEGGGEECCCCC----CCCTTCEEEEEE
T ss_pred             CCCEEEEEEEEEeCCcEEEEEccccCcceEechhhEEcCCCcccccCCCCCCEEEEEe
Confidence            5999999999999999999997611124567777664221112235789999998844

>1wfq_A UNR protein; beta-barrel, translational regulation, RNA chaperone, RNA/DN binding, QB fold, greek-KEY topology, structur genomics; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=88.16  E-value=2.4  Score=29.00  Aligned_cols=55  Identities=9%  Similarity=0.011  Sum_probs=41.8

Q ss_pred             CCCEEEEEEEEEecceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEe
Q psy18072         15 VEDVVMVTVISIAEMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD   76 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd   76 (174)
                      ......|+|+.+. .|. ||.-.+ ++-+=|+|+|.|...     .+.++.||.|...|..-.
T Consensus        15 ~~~~~~G~Vkwf~-KGfGFI~~dd-gg~DVFvH~s~i~~~-----~~~L~~G~~V~F~v~~~~   70 (89)
T 1wfq_A           15 AALRETGVIEKLL-TSYGFIQCSE-RQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDR   70 (89)
T ss_dssp             CCCEEEEEEEEEC-SSEEEEEETT-TTEEEEEETTTCSSC-----TTTCCTTCCEEEEEEECS
T ss_pred             cccccceEEEEEe-CCeeEEecCC-CCccEEEEhHHhhCc-----cCCCCCCCEEEEEEEECC
Confidence            4567899999984 555 666665 137999999998753     257899999999987643

>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, cold shock structural genomics; NMR {Pectobacterium atrosepticum}

Probab=87.59  E-value=2.7  Score=27.75  Aligned_cols=48  Identities=8%  Similarity=0.058  Sum_probs=35.2

Q ss_pred             EEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         19 VMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        19 V~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      ..|+|+... ..|. ||.-.+- +-. |+|+|.|....      .++.||.|...+..
T Consensus         3 ~~G~Vkwfn~~KGfGFI~~~dg-~~d-FvH~s~i~~~g------~l~~G~~V~F~~~~   52 (74)
T 2k5n_A            3 MNGTITTWFKDKGFGFIKDENG-DNR-YFHVIKVANPD------LIKKDAAVTFEPTT   52 (74)
T ss_dssp             EEEEEEEEETTTTEEEEEESSS-CEE-EEEGGGBSSGG------GCCTTCEEEEEEEE
T ss_pred             cceEEEEEECCCCeEEEecCCC-Cce-EEEHhHcccCC------CCCCCCEEEEEEEe
Confidence            579999883 3455 6665541 356 99999997432      68999999998875

>1c9o_A CSPB, cold-shock protein; beta barrel, homodimer, transcription; 1.17A {Bacillus caldolyticus} SCOP: b.40.4.5 PDB: 2hax_A 1hz9_A 1hzb_A 1i5f_A 1hza_A 1hzc_A 3pf4_A 1csq_A 1nmf_A 1nmg_A 1csp_A 2f52_A 2es2_A 3pf5_A 2i5m_X 2i5l_X

Probab=87.47  E-value=1.9  Score=27.64  Aligned_cols=51  Identities=10%  Similarity=0.163  Sum_probs=37.7

Q ss_pred             EEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072         19 VMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV   75 (174)
Q Consensus        19 V~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V   75 (174)
                      ..|+|+... ..|. ||.-.+  +-+=|+|+|.+.....    +.++.||.|...+..-
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~--g~dvFvH~s~i~~~g~----~~l~~G~~V~f~~~~~   54 (66)
T 1c9o_A            2 QRGKVKWFNNEKGYGFIEVEG--GSDVFVHFTAIQGEGF----KTLEEGQEVSFEIVQG   54 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETT--EEEEEEEGGGBCSSSC----CCCCTTCEEEEEEEEE
T ss_pred             CceEEEEEECCCCeEEEecCC--CccEEEEHHHccccCC----CCCCCCCEEEEEEEEC
Confidence            479999884 4455 676666  5788999999874322    4688999999988653

>3i2z_B RNA chaperone, negative regulator of CSPA transcription; beta barrel, DNA binding protein/transcription, cytoplasm, gene regulation; 1.10A {Salmonella typhimurium} SCOP: b.40.4.5 PDB: 2l15_A 1mjc_A 3mef_A

Probab=86.15  E-value=1.9  Score=28.15  Aligned_cols=53  Identities=9%  Similarity=0.119  Sum_probs=37.4

Q ss_pred             EEEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072         18 VVMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV   75 (174)
Q Consensus        18 iV~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V   75 (174)
                      ...|+|+... ..|. ||.-.+ ++-+=|+|.|.+.....    +.++.||.|...+..-
T Consensus         5 ~~~G~Vk~fn~~kGfGFI~~~~-g~~dvFvH~s~i~~~g~----~~l~~G~~V~f~~~~~   59 (71)
T 3i2z_B            5 KIKGNVKWFNESKGFGFITPED-GSKDVFVHFSAIQTNGF----KTLAEGQRVEFEITNG   59 (71)
T ss_dssp             CEEEEEEEEETTTTEEEEEETT-CCCCEEEEGGGBCCSSC----CCCCTTCEEEEEEEEE
T ss_pred             cccEEEEEEECCCCcEEEecCC-CCccEEEEhHHcccccC----cCCCCCCEEEEEEEEC
Confidence            3689999884 3344 666555 13678999999874322    4688999999988753

>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural genomics, NPPSFA; 1.65A {Thermus thermophilus}

Probab=85.25  E-value=1.5  Score=28.76  Aligned_cols=51  Identities=10%  Similarity=0.092  Sum_probs=37.5

Q ss_pred             EEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072         19 VMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV   75 (174)
Q Consensus        19 V~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V   75 (174)
                      ..|+|+... ..|. ||.-.+  +-+=|+|+|.+....+    ..++.||.|...+..-
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~--g~dvFvH~s~i~~~g~----~~l~~G~~V~f~~~~~   54 (73)
T 3a0j_A            2 QKGRVKWFNAEKGYGFIEREG--DTDVFVHYTAINAKGF----RTLNEGDIVTFDVEPG   54 (73)
T ss_dssp             EEEEEEEEETTTTEEEEECTT--SCCEEEEGGGBCSSSC----SSCCTTCEEEEEEECC
T ss_pred             CCEEEEEEECCCCEEEEecCC--CCcEEEEhhhccccCC----CCCCCCCEEEEEEEEC
Confidence            479999884 4455 676665  5788999999874322    4688999999988653

>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral twinning, leucine-rich repeat protein, LRR, merohedral twinning; 2.2A {Schizosaccharomyces pombe} SCOP: c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A

Probab=84.94  E-value=0.32  Score=40.32  Aligned_cols=11  Identities=9%  Similarity=0.142  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHH
Q psy18072        128 AELARQMERAE  138 (174)
Q Consensus       128 ~~~k~~~~~l~  138 (174)
                      ..+..++.++.
T Consensus       323 ~~l~~~l~~~~  333 (386)
T 2ca6_A          323 DEIREVFSTRG  333 (386)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHhhhcC
Confidence            45555555543

>2kcm_A Cold shock domain family protein; nucleic acid binding protein, beta barrel, structural genomi 2, protein structure initiative; NMR {Shewanella oneidensis}

Probab=84.57  E-value=1.5  Score=29.07  Aligned_cols=49  Identities=12%  Similarity=0.020  Sum_probs=36.8

Q ss_pred             EEEEEEEe-cceE-EEEECCCCCeEEEEEceecc-hhhhhccccccCCCCEEEEEEEE
Q psy18072         20 MVTVISIA-EMGA-YVHLLEYNNIEGMILLSELS-RRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        20 ~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels-~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      +|+|+... ..|. ||.-.+  +-+=|+|+|.+. ...+    ..++.||.|...+..
T Consensus         2 ~G~Vkwfn~~KGfGFI~~~d--G~DvFvH~s~i~~~~g~----~~l~~G~~V~F~~~~   53 (74)
T 2kcm_A            2 KGKVVSYLAAKKYGFIQGDD--GESYFLHFSELLDKKDE----GKLVKGSMVHFDPTP   53 (74)
T ss_dssp             EEEEEEEETTTTEEEEEETT--SCEECCCGGGSSCSGGG----TTCCTTSEEEEEEEC
T ss_pred             CEEEEEEECCCCEEEEecCC--CceEEEEhhhcccCCCC----CCCCCCCEEEEEEEE
Confidence            68999884 4455 676666  578899999987 4433    468899999998863

>1g6p_A Cold shock protein TMCSP; greek-KEY, beta barrel, OB-fold, structural genomics; NMR {Thermotoga maritima} SCOP: b.40.4.5

Probab=81.71  E-value=0.77  Score=29.57  Aligned_cols=49  Identities=12%  Similarity=0.109  Sum_probs=35.8

Q ss_pred             EEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         20 MVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        20 ~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      +|+|+... ..|. ||.-.+  +-+=++|+|.+....+    ..++.||.|...+..
T Consensus         2 ~G~Vk~fn~~kGfGFI~~~~--g~dvFvH~s~i~~~g~----~~l~~G~~V~f~~~~   52 (66)
T 1g6p_A            2 RGKVKWFDSKKGYGFITKDE--GGDVFVHWSAIEMEGF----KTLKEGQVVEFEIQE   52 (66)
T ss_dssp             CEEEEEEETTTTEEEEEETT--SCBCBBCSSSSCCSSC----CCCCSSSEEEEEEEC
T ss_pred             cEEEEEEECCCCEEEEecCC--CceEEEEhHHccccCC----CCCCCCCEEEEEEEE
Confidence            58888884 3455 666665  5788999999874322    468899999988764

>1h95_A CSD, Y-box binding protein; translation factor, transcription factor, OB-fold, 5- stranded anti-parallel beta-barrel, single stranded DNA binding; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=81.34  E-value=4.9  Score=26.63  Aligned_cols=58  Identities=14%  Similarity=0.169  Sum_probs=39.5

Q ss_pred             CCEEEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         16 EDVVMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        16 GdiV~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      ...+.|+|+... ..|. ||.-.+ ++-+=|+|+|.|.....+.-.+.++.||.|...+..
T Consensus         6 ~~~~~G~Vkwfn~~kGfGFI~~~~-gg~DvFvH~s~i~~~~~~~g~~~l~~G~~V~f~~~~   65 (79)
T 1h95_A            6 ATKVLGTVKWFNVRNGYGFINRND-TKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVE   65 (79)
T ss_dssp             EEEEEEEEEEEETTTTEEEEEEGG-GTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEE
T ss_pred             ccccceEEEEEECCCCcEEEecCC-CCccEEEEhHHccccccccccccCCCCCEEEEEEEE
Confidence            456889999984 3444 555543 147899999999753111112568899999998875

>2ytx_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational REGU RNA chaperone, RNA/DNA binding, QB fold; NMR {Homo sapiens}

Probab=81.01  E-value=1.6  Score=30.30  Aligned_cols=51  Identities=10%  Similarity=0.056  Sum_probs=39.2

Q ss_pred             CCEEEEEEEEEecceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEE
Q psy18072         16 EDVVMVTVISIAEMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI   73 (174)
Q Consensus        16 GdiV~G~V~~i~~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi   73 (174)
                      .....|+|..+ ..|. ||.-.+ ++-+=|+|+|.+...     .+.++.||.|...|.
T Consensus        16 ~~~~~G~Vkwf-~KGfGFI~~dd-g~~DvFvH~s~i~~~-----~~~L~~G~~V~F~v~   67 (97)
T 2ytx_A           16 QARCQGVVCAM-KEAFGFIERGD-VVKEIFFHYSEFKGD-----LETLQPGDDVEFTIK   67 (97)
T ss_dssp             CCCEEEEECCC-CSSEEEEECSS-SCCCEEEETTTCCSC-----TTSCCSCCEEEEEEC
T ss_pred             CcceeEEEEEE-eCCceEEecCC-CCceEEEEehHhccc-----cCCCCCCCEEEEEEE
Confidence            56789999988 5566 666654 136889999999754     257899999999885

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=80.49  E-value=3.5  Score=30.70  Aligned_cols=52  Identities=10%  Similarity=0.135  Sum_probs=37.4

Q ss_pred             EEEEEEEEEe-cceE-EEEEC--------CCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072         18 VVMVTVISIA-EMGA-YVHLL--------EYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV   75 (174)
Q Consensus        18 iV~G~V~~i~-~~Ga-fV~L~--------~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V   75 (174)
                      .++|+|+-+. ..|. ||.-.        .  +-+-|+|+|.|....+    +.|+.|+.|...|..-
T Consensus         9 ~~~G~Vkwfn~~kGfGFI~~~~~~g~p~~~--g~DvFvH~s~i~~~g~----~~l~eG~~V~f~~~~g   70 (148)
T 3ts2_A            9 HGAGICKWFNVRMGFGFLSMTARAGVALDP--PVDVFVHQSKLHMEGF----RSLKEGEAVEFTFKKS   70 (148)
T ss_dssp             EEEEEEEEEETTTTEEEEEEEEETTEEEEE--EEEEEEEGGGBCSSSS----CCCCTTCEEEEEEEEE
T ss_pred             cceeEEEEEECCCCeeEEeeCccccccCCC--CccEEEEhHHhcccCC----ccCCCCCEEEEEEEEc
Confidence            4789999984 3344 55543        3  4688999999874433    4688999999988764

>3cam_A Cold-shock domain family protein; cold shock protein, chain SWAP, STRU genomics, oxford protein production facility, OPPF, gene RE; 2.60A {Neisseria meningitidis MC58}

Probab=80.25  E-value=5.8  Score=25.43  Aligned_cols=52  Identities=13%  Similarity=0.084  Sum_probs=36.9

Q ss_pred             EEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072         19 VMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV   75 (174)
Q Consensus        19 V~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V   75 (174)
                      ..|+|+... ..|. ||.-.+ ++-+=|+|+|.+...-.    +.++.||.|...+..-
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~-gg~dvFvH~s~i~~~g~----~~l~~G~~V~f~~~~~   55 (67)
T 3cam_A            2 ATGIVKWFNDAKGFGFITPDE-GGEDLFAHFSAINMEGF----KTLKEGQRVSFDVTTG   55 (67)
T ss_dssp             EEEEEEEEETTTTEEEEEETT-SCCCEEEEGGGBCGGGG----SSCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEECCCCeEEEecCC-CCccEEEEHHHccccCC----CCCCCCCEEEEEEEEC
Confidence            368999883 3454 565544 14788999999975432    4688999999988753

---

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	174
d1q8ka2	117	d.58.51.1 (A:186-302) eIF-2-alpha, C-terminal doma	8e-20
d1kl9a2	86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	5e-18
d2ahob2	84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	3e-12
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	1e-06
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	4e-06
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	5e-05
d1e3pa2	62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	6e-05
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	4e-04
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	4e-04
d2qn6b1	89	d.58.51.1 (B:176-264) eIF-2-alpha, C-terminal doma	7e-04
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	0.002
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	0.003

>d1q8ka2 d.58.51.1 (A:186-302) eIF-2-alpha, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 117

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: eIF-2-alpha, C-terminal domain
family: eIF-2-alpha, C-terminal domain
domain: eIF-2-alpha, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.9 bits (192), Expect = 8e-20
 Identities = 43/68 (63%), Positives = 49/68 (72%)

Query: 80  VMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEA 139
           VMTT T E+ +GL  L +A+  IK KIE+  GVF VQM PKVVT +DE ELARQMER E 
Sbjct: 50  VMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQMERLER 109

Query: 140 ENAEVAAD 147
           ENAEV  D
Sbjct: 110 ENAEVDGD 117

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.3 bits (177), Expect = 5e-18
 Identities = 67/77 (87%), Positives = 70/77 (90%)

Query: 3  LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLI 62
          LSCRFY  K+PEVEDVVMV V SIAEMGAYV LLEYNNIEGMILLSELSRRRIRSINKLI
Sbjct: 1  LSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLI 60

Query: 63 RVGKTEPVVVIRVDKEK 79
          R+G+ E VVVIRVDKEK
Sbjct: 61 RIGRNECVVVIRVDKEK 77

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Length = 84

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 57.3 bits (138), Expect = 3e-12
 Identities = 21/73 (28%), Positives = 42/73 (57%)

Query: 7  FYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGK 66
          +   K P   ++++ TV  + + G+YV L EY  ++  +  SE+S + +++I  +++  +
Sbjct: 3  YSRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENR 62

Query: 67 TEPVVVIRVDKEK 79
             V VIRVD+ K
Sbjct: 63 KVIVKVIRVDRRK 75

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 88

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 42.6 bits (100), Expect = 1e-06
 Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 6/72 (8%)

Query: 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRS----INKLIRVGKT 67
           P+  DVV+  + S+  M  +V +   +    ++ + +   R        +  L++VG  
Sbjct: 4  VPQAGDVVIGLIQSVGIMNWFVDI--NSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDY 61

Query: 68 EPVVVIRVDKEK 79
              V+  DK +
Sbjct: 62 IKAKVVAFDKTR 73

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Length = 76

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Escherichia coli [TaxId: 562]

 Score = 40.9 bits (96), Expect = 4e-06
 Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72
           EV  V    V  I + GA+V        EG++ +S+++ +R+  +   +++G+  PV V
Sbjct: 3  IEVGRVYTGKVTRIVDFGAFVA--IGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKV 60

Query: 73 IRVDKEK 79
          + VD++ 
Sbjct: 61 LEVDRQG 67

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 87

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 38.1 bits (88), Expect = 5e-05
 Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 5/71 (7%)

Query: 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71
          YP++ D+V+  V  +   G  V +      +  +  S L  R I     L R       V
Sbjct: 4  YPKINDIVIGLVEDVEIYGWVVDI--KAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYV 61

Query: 72 ---VIRVDKEK 79
             +   D+  
Sbjct: 62 IARIENFDRSI 72

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} Length = 62

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 37.4 bits (87), Expect = 6e-05
 Identities = 12/62 (19%), Positives = 31/62 (50%), Gaps = 6/62 (9%)

Query: 22 TVISIAEMGAYVHLLEYNNIEGMILLSELSR----RRIRSINKLIRVGKTEPVVVIRVDK 77
          +V+     GA+V L      +G++ +S++ +    +R+ ++  ++ VG+   V +  +D 
Sbjct: 2  SVVKTTTFGAFVSL--LPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDS 59

Query: 78 EK 79
            
Sbjct: 60 RG 61

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.7 bits (82), Expect = 4e-04
 Identities = 11/77 (14%), Positives = 28/77 (36%), Gaps = 12/77 (15%)

Query: 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS----------RRRIRSINKL 61
            EV D+V+  +  + +    V     + ++ ++LLS ++               ++   
Sbjct: 5  IGEVGDIVVGRITEVQQKRWKVETN--SRLDSVLLLSSMNLPGGELRRRSAEDELAMRGF 62

Query: 62 IRVGKTEPVVVIRVDKE 78
          ++ G      V  V  +
Sbjct: 63 LQEGDLISAEVQAVFSD 79

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 83

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 35.4 bits (81), Expect = 4e-04
 Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRR-RIRSINKLIRVGKTEPV 70
           P V DVV+  +  +A  G  V    Y+  +  + +SE       +  N+++ +G     
Sbjct: 2  TPSVGDVVIGIIREVAANGWAVD--IYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIA 59

Query: 71 VVIRVDKEK 79
           V+ +D + 
Sbjct: 60 KVLNIDPKM 68

>d2qn6b1 d.58.51.1 (B:176-264) eIF-2-alpha, C-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: eIF-2-alpha, C-terminal domain
family: eIF-2-alpha, C-terminal domain
domain: eIF-2-alpha, C-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 34.8 bits (80), Expect = 7e-04
 Identities = 5/36 (13%), Positives = 12/36 (33%)

Query: 80  VMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQV 115
            +  V     +  +AL + I  +    ++      V
Sbjct: 53  RVDVVGTNPKEASEALNQIISNLIKIGKEENVDISV 88

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 106

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 34.2 bits (78), Expect = 0.002
 Identities = 11/78 (14%), Positives = 31/78 (39%), Gaps = 14/78 (17%)

Query: 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEP--- 69
          PE+ +++   V+ + E G++V       ++G+I +S++    +    K   +   E    
Sbjct: 1  PEMYELIEGEVVDVVEFGSFV---RLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKV 57

Query: 70 --------VVVIRVDKEK 79
                    ++ +  + 
Sbjct: 58 LEIGDYVRARIVAISLKA 75

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Tex S1-domain
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 33.3 bits (76), Expect = 0.003
 Identities = 14/66 (21%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73
          +   V+   V ++   GA+V +    + +G++ +S LS + ++   ++++ G    V V+
Sbjct: 17 KPGMVLEGVVTNVTNFGAFVDI--GVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVM 74

Query: 74 RVDKEK 79
           VD  +
Sbjct: 75 EVDIPR 80

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	174
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.89
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.77
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.73
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.73
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.7
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.7
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.61
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.6
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.58
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.47
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.43
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	99.39
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	99.34
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	99.28
d1q8ka2	117	eIF-2-alpha, C-terminal domain {Human (Homo sapien	99.2
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	99.19
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	99.17
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	99.12
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.59
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	98.42
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	98.06
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	98.06
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	97.8
d2qn6b1	89	eIF-2-alpha, C-terminal domain {Sulfolobus solfata	96.31
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	93.49
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	92.53
d2vnud2	88	Exosome complex exonuclease RRP44 {Saccharomyces c	91.38
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	91.11
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	89.45
d1yeza1	68	Hypothetical protein MM1357 {Methanosarcina mazei	89.26
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	88.73
d1yvca1	69	Hypothetical protein MMP0076 {Methanococcus maripa	87.55
d1fr3a_	67	Molybdate/tungstate binding protein MOP {Sporomusa	86.3
d1g6pa_	66	Major cold shock protein {Thermotoga maritima [Tax	86.24
d1e1oa1	143	Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g	83.68
d1uwva1	60	rRNA (Uracil-5-)-methyltransferase RumA, N-termina	80.39

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=4.4e-23  Score=143.27  Aligned_cols=84  Identities=79%  Similarity=1.124  Sum_probs=66.3

Q ss_pred             cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cce
Q psy18072          3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVM   81 (174)
Q Consensus         3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l   81 (174)
                      |.||||.+++|++|++|.|+|++++++|+||+|..+++++||||+|++++.++.++.+.|++||.|.|+|+++|+. +.+
T Consensus         1 ~~cr~~~~~~p~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~ki   80 (86)
T d1kl9a2           1 LSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYI   80 (86)
T ss_dssp             CCCCSSSSSSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEE
T ss_pred             CeeeehhhcCCCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEEECCCCEE
Confidence            7899999999999999999999999999999998665799999999999999999999999999999999999975 477


Q ss_pred             eeecc
Q psy18072         82 TTVTP   86 (174)
Q Consensus        82 ~ls~~   86 (174)
                      .+|.+
T Consensus        81 ~LS~K   85 (86)
T d1kl9a2          81 DLSKR   85 (86)
T ss_dssp             EEEST
T ss_pred             EEEee
Confidence            77764

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.77  E-value=4.5e-19  Score=122.04  Aligned_cols=80  Identities=26%  Similarity=0.497  Sum_probs=68.0

Q ss_pred             hhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeec
Q psy18072          7 FYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVT   85 (174)
Q Consensus         7 ~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~   85 (174)
                      |+.+++|++|++|.|+|++|+++|+||+|..|++++||||.|++++.++.++.+.|++||.|+|+|+++|+.+ .+.+|.
T Consensus         3 ~~~~~~p~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~   82 (84)
T d2ahob2           3 YSRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSL   82 (84)
T ss_dssp             CCSSSSCCTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEES
T ss_pred             cccccCCCCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEE
Confidence            5678899999999999999999999999987668999999999999999999999999999999999999764 677775


Q ss_pred             c
Q psy18072         86 P   86 (174)
Q Consensus        86 ~   86 (174)
                      +
T Consensus        83 K   83 (84)
T d2ahob2          83 K   83 (84)
T ss_dssp             S
T ss_pred             c
Confidence            4

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Escherichia coli [TaxId: 562]

Probab=99.73  E-value=1e-18  Score=118.46  Aligned_cols=72  Identities=26%  Similarity=0.498  Sum_probs=67.8

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeeccc
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPE   87 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~   87 (174)
                      ++|++|.|+|++|.+|||||+|.+  +++||||+|++++.++.++.+.|++||.|+|+|+++|+.+++.+|.++
T Consensus         4 kvG~iv~G~V~~v~~~G~fV~l~~--~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~~~ri~LS~k~   75 (76)
T d1sroa_           4 EVGRVYTGKVTRIVDFGAFVAIGG--GKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKE   75 (76)
T ss_dssp             CTTSEEEEEEEEEETTEEEEECSS--SCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCTTCCCEEEECC
T ss_pred             CCCCEEEEEEEEEeCcEEEEEeCC--CCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECCCCCEEEEEEc
Confidence            599999999999999999999987  899999999999999999999999999999999999988888888753

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.73  E-value=7.2e-18  Score=115.63  Aligned_cols=77  Identities=19%  Similarity=0.283  Sum_probs=70.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh-hhccccccCCCCEEEEEEEEEeCCCceeeecccccc
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR-IRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKAD   90 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~-v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k~~   90 (174)
                      .|++|++|.|+|+++.++||||.|.+  ++.||||+|++++.+ ..++++.|++||.|.|+|+++++++.+.+|++...+
T Consensus         2 ~Pk~Gd~V~G~V~~v~~~g~~V~i~~--~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~i~LS~k~~~~   79 (83)
T d2ba0a1           2 TPSVGDVVIGIIREVAANGWAVDIYS--PYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRIC   79 (83)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSS--SSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCSSSC
T ss_pred             cCCCCCEEEEEEEEEECCEEEEecCC--CeeEEEecccccccccccChhhhcccccEEEEEEEEECCCCCEEEEecCCCC
Confidence            57899999999999999999999988  899999999999864 678899999999999999999988889999887643

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.70  E-value=8.6e-18  Score=116.50  Aligned_cols=79  Identities=19%  Similarity=0.288  Sum_probs=71.3

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh----ccccccCCCCEEEEEEEEEeCCCceeeecc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR----SINKLIRVGKTEPVVVIRVDKEKVMTTVTP   86 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~----~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~   86 (174)
                      +.|++|++|.|+|++++++||||.|..  ++.||||.|++++.+++    ++++.|++||.|.|+|+++++++.+.+|++
T Consensus         3 Y~Pk~GdvV~G~V~~v~~~g~fV~i~~--~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~i~Ls~k   80 (88)
T d2z0sa1           3 YVPQAGDVVIGLIQSVGIMNWFVDINS--PYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQ   80 (88)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECSS--SSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECC
T ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCC--CeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECCCCCEEEEEe
Confidence            467899999999999999999999987  79999999999987654    677899999999999999999999999998


Q ss_pred             cccch
Q psy18072         87 EKADG   91 (174)
Q Consensus        87 ~k~~g   91 (174)
                      .+.+|
T Consensus        81 ~~~~g   85 (88)
T d2z0sa1          81 GEGLG   85 (88)
T ss_dssp             SSSCE
T ss_pred             cCCCc
Confidence            87554

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.70  E-value=1e-17  Score=115.92  Aligned_cols=79  Identities=20%  Similarity=0.260  Sum_probs=70.5

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh---ccccccCCCCEEEEEEEEEeCCCceeeeccc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR---SINKLIRVGKTEPVVVIRVDKEKVMTTVTPE   87 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~---~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~   87 (174)
                      +.|++|++|.|+|++++++||||+|..  +++||||+|++++.++.   ++++.|++||.|.|+|+++++.+.+.+|++.
T Consensus         3 Y~Pk~Gdiv~G~V~~i~~~g~fV~i~~--~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~i~LS~k~   80 (87)
T d2je6i1           3 YYPKINDIVIGLVEDVEIYGWVVDIKA--PYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKG   80 (87)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSS--SSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCS
T ss_pred             ccCCCCCEEEEEEEEEECCEEEEEeCC--CEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECCCCCEEEEEec
Confidence            347899999999999999999999987  89999999999987654   5778999999999999999998889999887


Q ss_pred             ccch
Q psy18072         88 KADG   91 (174)
Q Consensus        88 k~~g   91 (174)
                      ..+|
T Consensus        81 ~~lg   84 (87)
T d2je6i1          81 KDLG   84 (87)
T ss_dssp             TTCE
T ss_pred             CCCc
Confidence            7544

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=2.7e-16  Score=110.64  Aligned_cols=80  Identities=16%  Similarity=0.169  Sum_probs=68.6

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchh----------hhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRR----------RIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~----------~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      .+.|++|++|.|+|+++.++||||.|..  .+.|+||+|++++.          ++.++++.|++||.|.|+|++++.++
T Consensus         3 ~Y~P~vGdiV~G~V~~v~~~g~~V~I~~--~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~dg   80 (95)
T d2nn6h1           3 RYIGEVGDIVVGRITEVQQKRWKVETNS--RLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDG   80 (95)
T ss_dssp             CCCCCSSBCCCEEEEEEETTEEEEECSS--SSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTT
T ss_pred             cccCCCCCEEEEEEEEEecCcEEEEeCC--CceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECCCC
Confidence            3457899999999999999999999987  78999999999642          34567789999999999999999999


Q ss_pred             ceeeecccccch
Q psy18072         80 VMTTVTPEKADG   91 (174)
Q Consensus        80 ~l~ls~~~k~~g   91 (174)
                      .+.||++...+|
T Consensus        81 ~i~Ls~r~~~~g   92 (95)
T d2nn6h1          81 AVSLHTRSLKYG   92 (95)
T ss_dssp             EEEEECCSSTTC
T ss_pred             CEEEEeccccCC
Confidence            999999876544

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.60  E-value=1.6e-15  Score=108.62  Aligned_cols=73  Identities=16%  Similarity=0.413  Sum_probs=63.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-----------hccccccCCCCEEEEEEEEEeCCC--
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-----------RSINKLIRVGKTEPVVVIRVDKEK--   79 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-----------~~~~~~l~vGd~V~vrVi~Vd~~~--   79 (174)
                      |++|++|.|+|++|.+||+||+|.   +++||||+|+|++.++           +++.+.|++||.|+|+|++||.++  
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~---~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~~~~   77 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLG---PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAER   77 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS---SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC--
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEee---CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchhhcc
Confidence            679999999999999999999994   5999999999999876           467799999999999999999875  


Q ss_pred             ----ceeeecccc
Q psy18072         80 ----VMTTVTPEK   88 (174)
Q Consensus        80 ----~l~ls~~~k   88 (174)
                          .+.+|.+..
T Consensus        78 ~~~~~i~ls~K~~   90 (106)
T d1go3e1          78 KRGSKIALTMRQP   90 (106)
T ss_dssp             ---CEEEEECCST
T ss_pred             ccCceeecccccC
Confidence                245555544

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Tex S1-domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.58  E-value=2e-15  Score=105.76  Aligned_cols=76  Identities=18%  Similarity=0.294  Sum_probs=68.3

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC-CCceeeecccc
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK-EKVMTTVTPEK   88 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~-~~~l~ls~~~k   88 (174)
                      +.+. +|++|.|+|++|.++|+||.|.+  +++||||.+++++.++.++.+.|++||.|+|+|+++|. .+.+.+|.+..
T Consensus        14 ~~~k-~G~iv~g~V~~v~~~G~~V~l~~--~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~~i~LS~K~~   90 (94)
T d3bzka4          14 KDLK-PGMVLEGVVTNVTNFGAFVDIGV--HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMS   90 (94)
T ss_dssp             GGCC-TTCEEEEEEEEEETTEEEEECSS--SSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEESCTT
T ss_pred             hcCC-CCCEEEEEEEEEECcEEEEEeCC--CceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEEecc
Confidence            3454 89999999999999999999987  89999999999999999999999999999999999997 45777777543

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Streptomyces antibioticus [TaxId: 1890]

Probab=99.47  E-value=3.4e-16  Score=102.14  Aligned_cols=57  Identities=23%  Similarity=0.557  Sum_probs=35.9

Q ss_pred             EEEEEEecceEEEEECCCCCeEEEEEceecch----hhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         21 VTVISIAEMGAYVHLLEYNNIEGMILLSELSR----RRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        21 G~V~~i~~~GafV~L~~~~~~~GlI~iSels~----~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      |+|++|.+|||||+|.+  +++||||+|++++    .++.++++.|++||.|+|+|+++|+++
T Consensus         1 G~V~~i~~fG~FV~l~~--g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLP--GKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             CBEEECC-CSCEECCC-----CCCCC-------------------CCSSCBCCCCCCCCCSSC
T ss_pred             CEEEEEEeceEEEEecC--CceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCCC
Confidence            78999999999999987  8999999999985    478899999999999999999999764

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=1.9e-13  Score=99.42  Aligned_cols=74  Identities=15%  Similarity=0.160  Sum_probs=64.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEC-CCCCeEEEEEceecchhh-hhccccccCCCCEEEEEEEEEeCCC-ceeeecccc
Q psy18072         13 PEVEDVVMVTVISIAEMGAYVHLL-EYNNIEGMILLSELSRRR-IRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTPEK   88 (174)
Q Consensus        13 p~~GdiV~G~V~~i~~~GafV~L~-~~~~~~GlI~iSels~~~-v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~~k   88 (174)
                      .++|++|.|+|.+|.++|+||.|. .  ++.||||++++++.+ ..++...|++||.|.|+|+++++.+ .+.+|++..
T Consensus        19 l~~G~iv~G~V~~i~~~G~~V~lg~~--~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~k~~   95 (119)
T d1wi5a_          19 LKPGMLLTGTVSSLEDHGYLVDIGVD--GTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHS   95 (119)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECCCS--SCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCC
T ss_pred             cCCCCEEEEEEEEEeccEEEEEEecc--ccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEEecHH
Confidence            359999999999999999999994 5  799999999999874 7788899999999999999999765 577776543

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=2.7e-13  Score=93.94  Aligned_cols=75  Identities=12%  Similarity=-0.013  Sum_probs=67.4

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEK   88 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k   88 (174)
                      +.|++||+|.|+|++++.++|||.|..  .+.|+||++++. .+.++.+..|++||.|.|||.+++.++.+.||+.+.
T Consensus         2 Y~P~~GD~ViG~V~~~~~~~~~VdI~s--~~~a~L~~~~f~-g~~k~~r~~l~~GD~V~arV~~v~~~~~~~Lscvd~   76 (88)
T d2nn6g1           2 YVPVKGDHVIGIVTAKSGDIFKVDVGG--SEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDS   76 (88)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSS--SSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCTTSCCEEECSBT
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEcCC--CeeEEEeHHHcC-ccccccCcccCCCCEEEEEEEEeCCCCCEEEEEEcc
Confidence            467899999999999999999999988  789999999985 467778899999999999999999999888888554

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=99.34  E-value=1.2e-12  Score=91.03  Aligned_cols=79  Identities=18%  Similarity=0.098  Sum_probs=70.8

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccccc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKAD   90 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k~~   90 (174)
                      ..|++||+|.|+|+++..++|||.|..  .+.|++|.+.......+..+..|++||.|.|||.+++.+..+.+|+.++..
T Consensus         3 Y~P~~gD~ViG~V~~~~~~~~~vdI~~--~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~~~~~~Lsc~~~~~   80 (90)
T d2ja9a1           3 YIPSVNDFVIGVIIGTFSDSYKVSLQN--FSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTT   80 (90)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESST--TSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCTTSCCEEESSCTTT
T ss_pred             ccCCCCCEEEEEEEEEeCCcEEEEcCC--cchhhhhhhhccCccccccCCccCCCCEEEEEEEEECCCCCEEEEEecccc
Confidence            457899999999999999999999987  688999998888888888889999999999999999999989999877644


Q ss_pred             h
Q psy18072         91 G   91 (174)
Q Consensus        91 g   91 (174)
                      |
T Consensus        81 g   81 (90)
T d2ja9a1          81 G   81 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=99.28  E-value=5.1e-12  Score=87.20  Aligned_cols=64  Identities=17%  Similarity=0.178  Sum_probs=55.1

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh------------ccccccCCCCEEEEEEEEEeCCC
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR------------SINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~------------~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      .++.+.|+|++|+++|+||+|.+. +++||||+|.|+++++.            +....|++||.|+|+|++|++.+
T Consensus         3 ~~~~F~g~Is~v~~~GifV~L~e~-~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~   78 (87)
T d2ix0a3           3 TDTRFAAEIVDISRGGMRVRLVDN-GAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMET   78 (87)
T ss_dssp             SCCCEEEEEEEEETTEEEEEETTT-CCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTT
T ss_pred             CCCEEEEEEEEEEcCeEEEEEecC-CcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEeccc
Confidence            478899999999999999999763 58999999999987643            12457999999999999999865

>d1q8ka2 d.58.51.1 (A:186-302) eIF-2-alpha, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: eIF-2-alpha, C-terminal domain
family: eIF-2-alpha, C-terminal domain
domain: eIF-2-alpha, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.20  E-value=2.5e-12  Score=93.31  Aligned_cols=107  Identities=46%  Similarity=0.617  Sum_probs=85.7

Q ss_pred             CeEEEEEceecchhhhhccccccCCC-----C--EEEEEEEEEeCCCceeeecccccchHHHHHHHHHHHHHHHhhhCCe
Q psy18072         40 NIEGMILLSELSRRRIRSINKLIRVG-----K--TEPVVVIRVDKEKVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGV  112 (174)
Q Consensus        40 ~~~GlI~iSels~~~v~~~~~~l~vG-----d--~V~vrVi~Vd~~~~l~ls~~~k~~g~~~i~~~~~~i~~~l~~~~g~  112 (174)
                      .++|.|.++-++..-+..+.+.|..|     +  .|+++.+. -|.-.+++++.++..|...|..+++.|.+.|+++||.
T Consensus         4 kIra~ievtc~~~dGIe~IK~AL~aa~~~s~e~~~I~I~~ig-aP~Y~i~v~a~D~k~g~~~l~~a~~~i~~~I~~~gG~   82 (117)
T d1q8ka2           4 KIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIA-PPRYVMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGV   82 (117)
T ss_dssp             EEEECCCEECCSTTTHHHHHHHHHHHHHSSBTTBCEEEEEEE-TTEEEEEEECSSHHHHHHHHHHHHHHHHHHHHTTSCE
T ss_pred             EEEEEEEEEEcCcchHHHHHHHHHHHHhcCCCCCcEEEEEEC-CCeEEEEEecCCHHHHHHHHHHHHHHHHHHHHHcCCE
Confidence            35677777766665555544444421     2  35555443 1333688999999999999999999999999999999


Q ss_pred             eEEeeCceeEeccCHHHHHHHHHHHHHhcccccCC
Q psy18072        113 FQVQMAPKVVTASDEAELARQMERAEAENAEVAAD  147 (174)
Q Consensus       113 l~~k~~P~~i~~~~~~~~k~~~~~l~k~~~e~~gd  147 (174)
                      |.+|+.|++|++.++..|.+.|+++.++|+|++||
T Consensus        83 f~ik~~pk~v~~~d~~~l~~~me~~e~~n~e~~~d  117 (117)
T d1q8ka2          83 FNVQMEPKVVTDTDETELARQMERLERENAEVDGD  117 (117)
T ss_dssp             ECCSSCCEECCSSHHHHHHHHCCSGGGCCCCCCCC
T ss_pred             EEEEECCEEeccccHHHHHHHHHHHHhccccccCC
Confidence            99999999999999999999999999999999997

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.19  E-value=2.8e-11  Score=83.46  Aligned_cols=62  Identities=16%  Similarity=0.109  Sum_probs=54.3

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh----------hccccccCCCCEEEEEEEEEeCCC
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI----------RSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v----------~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      +|+++.|+|++++++|+||+|.   .++||||++++.+.+.          ++..+.+++||.|+|||++|+.+.
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg---~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~   74 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVG---PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQV   74 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET---TEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEET
T ss_pred             CCCEEEEEEEEEEeeEEEEEEc---CeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEeccc
Confidence            6999999999999999999995   4899999999987643          345678999999999999998754

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.17  E-value=3.3e-11  Score=88.21  Aligned_cols=90  Identities=24%  Similarity=0.269  Sum_probs=74.1

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCC------CCeEEEEEceecch--hhhhccccccCCCCEEEEEEEEEeCCC-c
Q psy18072         10 EKYPEVEDVVMVTVISIAEMGAYVHLLEY------NNIEGMILLSELSR--RRIRSINKLIRVGKTEPVVVIRVDKEK-V   80 (174)
Q Consensus        10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~------~~~~GlI~iSels~--~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~   80 (174)
                      ...|++||+|.|+|+++....|+|+|...      ..+.|++|.+++..  ....++++.|++||.|+|+|+++...+ .
T Consensus         2 ~~vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~~   81 (125)
T d2nn6i1           2 QLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSN   81 (125)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTE
T ss_pred             CcCCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCcc
Confidence            35688999999999999999999999541      14789999999843  344568899999999999999998765 5


Q ss_pred             eeeecccccchHHHHHHHHHH
Q psy18072         81 MTTVTPEKADGLKALQEAIDT  101 (174)
Q Consensus        81 l~ls~~~k~~g~~~i~~~~~~  101 (174)
                      +.+|+..+++|  ++.+.|+.
T Consensus        82 ~~Lst~~~~LG--Vv~A~c~~  100 (125)
T d2nn6i1          82 YLLTTAENELG--VVVAHSES  100 (125)
T ss_dssp             EEEECCSSSCE--ECCCBCSS
T ss_pred             EEEEecCCCcE--EEEEECCC
Confidence            89999999888  56776653

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.12  E-value=1.1e-10  Score=80.89  Aligned_cols=62  Identities=11%  Similarity=0.184  Sum_probs=53.9

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh-h-----------hccccccCCCCEEEEEEEEEeCCC
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR-I-----------RSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~-v-----------~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      +|+++.|+|++++++|+||+|.   .++||||++++.+.+ +           ++....+++||.|++||++++.+.
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg---~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~   77 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIG---PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDK   77 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET---TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEET
T ss_pred             CCCEEEEEEEEEEeeEEEEEec---CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCc
Confidence            6999999999999999999995   489999999999875 2           334568999999999999988754

>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Thermotoga maritima [TaxId: 2336]

Probab=98.59  E-value=1.3e-07  Score=62.42  Aligned_cols=59  Identities=20%  Similarity=0.130  Sum_probs=51.3

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      ..+.|++|+|+|.++....++|.|.   +.+|+||.++..      ++..|++||.|+|-|.+|+...
T Consensus         5 ~~~~geiv~G~V~r~~~~~~~Vdlg---~~eaiLp~~eqi------p~E~~~~Gdrik~~i~~V~~~~   63 (72)
T d1hh2p1           5 SELKGTVTTAEVIRVMGEWADIRIG---KLETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTT   63 (72)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEEET---TEEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEET
T ss_pred             hhccCcEEEEEEEEEcCCCEEEEEC---CcEEECCHHHcC------CCCCCCCCCEEEEEEEEEEEcC
Confidence            3458999999999999999999995   599999999865      4589999999999999997643

>d1luza_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Vaccinia virus [TaxId: 10245]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Viral structural mimic of eIF2alpha
species: Vaccinia virus [TaxId: 10245]

Probab=98.42  E-value=6.2e-07  Score=59.93  Aligned_cols=68  Identities=31%  Similarity=0.429  Sum_probs=58.5

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEce-ecchhhhhccccccCCCCEEEEEEEEEeCCCc
Q psy18072         11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLS-ELSRRRIRSINKLIRVGKTEPVVVIRVDKEKV   80 (174)
Q Consensus        11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iS-els~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~   80 (174)
                      .+|.+|++.+|+|+ +.+.-++|.|.+|.+.+|+|--+ ++..++...+++.+ +|.+|+|+|+++|.-+.
T Consensus         4 ~lPnigdVtkGiVy-~kd~~fyV~L~dY~g~ea~l~dy~~~~~d~~~klk~kL-VGKtIkvqVIR~d~lKG   72 (85)
T d1luza_           4 SLPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKG   72 (85)
T ss_dssp             CCCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTT
T ss_pred             ccCCCCceeeeEEE-EeCCEEEEEecCCCCceEEeeehhhhhhHHHHHHHHHh-cCceEEEEEEEEcceee
Confidence            47889999999998 58889999999998899998765 55567778888888 89999999999998763

>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.06  E-value=4.6e-06  Score=55.31  Aligned_cols=60  Identities=15%  Similarity=0.093  Sum_probs=48.7

Q ss_pred             CCCCEEEEEEEEEecc----eEEEEECC-CCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072         14 EVEDVVMVTVISIAEM----GAYVHLLE-YNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK   79 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~----GafV~L~~-~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~   79 (174)
                      +.|++|.|+|.++...    -++|.|.. .++.+|+||.++..      +...|++||.|+|-|..|+...
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqi------p~E~y~~Gdrik~~i~~V~~~~   67 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGA   67 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCS
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcC------CCcccCCCCEEEEEEEEEEecC
Confidence            4899999999998543    27999952 12699999988754      4589999999999999998754

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=98.06  E-value=5.1e-06  Score=56.39  Aligned_cols=56  Identities=20%  Similarity=0.329  Sum_probs=48.0

Q ss_pred             CEEEEEEEEEecc--eEEEEECCCCCeEEEEEceecchhhh---------hccccccCCCCEEEEEEEE
Q psy18072         17 DVVMVTVISIAEM--GAYVHLLEYNNIEGMILLSELSRRRI---------RSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        17 diV~G~V~~i~~~--GafV~L~~~~~~~GlI~iSels~~~v---------~~~~~~l~vGd~V~vrVi~   74 (174)
                      ++|.|+|.+|.+.  +|||.+..  .-.||||.+++...+.         ..+.+.++.||.|-|+|++
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~--~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~K   68 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGA--ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDK   68 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSS--SSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEE
T ss_pred             CcEEEEEEEecCCceEEEEEeCC--CccceeEecccceeeeccccccccccchhhhccCCCeEEEEEee
Confidence            5899999999764  89999987  7899999999887653         2467889999999999997

>d1jjga_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Myxoma virus, m156r [TaxId: 10273]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Viral structural mimic of eIF2alpha
species: Myxoma virus, m156r [TaxId: 10273]

Probab=97.80  E-value=2.2e-05  Score=53.54  Aligned_cols=61  Identities=21%  Similarity=0.230  Sum_probs=51.2

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeEEEEEce-ecchhhhhccccccCCCCEEEEEEEEEeC
Q psy18072         15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLS-ELSRRRIRSINKLIRVGKTEPVVVIRVDK   77 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iS-els~~~v~~~~~~l~vGd~V~vrVi~Vd~   77 (174)
                      +|++.+|+|+ +.++-++|.|.+|.+.+++|--+ ++..++...+++.+ +|.+|+|+|+++|.
T Consensus        32 ~G~V~kGiVy-~rd~~fyV~L~dY~g~eail~dY~n~~~dr~~klkkkL-VGKTIkVqVIRvDk   93 (102)
T d1jjga_          32 PGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADG   93 (102)
T ss_dssp             SSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECS
T ss_pred             CCcEeeeEEE-EeCCEEEEEecCCCCceeeeeehhhhhHHHHHHHHHHh-cCceEEEEEEEecc
Confidence            7999999998 68889999999998899986644 45556666777777 89999999999984

>d2qn6b1 d.58.51.1 (B:176-264) eIF-2-alpha, C-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: eIF-2-alpha, C-terminal domain
family: eIF-2-alpha, C-terminal domain
domain: eIF-2-alpha, C-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=96.31  E-value=0.003  Score=42.39  Aligned_cols=75  Identities=12%  Similarity=0.166  Sum_probs=57.1

Q ss_pred             eEEEEEceecchhhhhccccccCCC---------CEEEEEEEEEeCCC-ceeeecccccchHHHHHHHHHHHHHHHhhhC
Q psy18072         41 IEGMILLSELSRRRIRSINKLIRVG---------KTEPVVVIRVDKEK-VMTTVTPEKADGLKALQEAIDTIKAKIEQLG  110 (174)
Q Consensus        41 ~~GlI~iSels~~~v~~~~~~l~vG---------d~V~vrVi~Vd~~~-~l~ls~~~k~~g~~~i~~~~~~i~~~l~~~~  110 (174)
                      +.|.|.++-...+-+..+.+.|..|         +.+.++|.-+-+-. .+++++.++..|...|+++++.|.+.++++|
T Consensus         4 I~g~i~l~~~~~dGIe~IK~aL~~a~~~~~~~~~~d~~i~i~~igaP~Yri~v~a~D~k~ae~~l~~a~~~i~~~ik~~g   83 (89)
T d2qn6b1           4 MSGLITVRTNEPLGVEKIKEVISKALENIEQDYESLLNIKIYTIGAPRYRVDVVGTNPKEASEALNQIISNLIKIGKEEN   83 (89)
T ss_dssp             EEEEEEEEECCTTTHHHHHHHHHHHHTTHHHHCTTEEEEEEEESSTTEEEEEEEESCHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             EEEEEEEEeCCCccHHHHHHHHHHHHHhcccccCCCccEEEEEecCCeEEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence            6788888877766666555555322         45666666554432 6788889999999999999999999999999


Q ss_pred             CeeEE
Q psy18072        111 GVFQV  115 (174)
Q Consensus       111 g~l~~  115 (174)
                      |.+.+
T Consensus        84 g~~~v   88 (89)
T d2qn6b1          84 VDISV   88 (89)
T ss_dssp             EEEEE
T ss_pred             CEEEe
Confidence            99876

>d1k3ra1 b.40.4.10 (A:93-163) Hypothetical protein MTH1 (MT0001), insert domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Hypothetical protein MTH1 (MT0001), insert domain
domain: Hypothetical protein MTH1 (MT0001), insert domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=93.49  E-value=0.2  Score=31.69  Aligned_cols=59  Identities=15%  Similarity=0.179  Sum_probs=43.8

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeeccc
Q psy18072         12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPE   87 (174)
Q Consensus        12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~   87 (174)
                      -|++|++=.|.+.+-...|+||.+.    ++-+.++.           ..|++|+.+.+||.++  .+.|.....+
T Consensus         7 ~p~vGEiReG~~~rr~~~g~~vDiG----lD~la~~k-----------~~~~~~~r~tfrIvs~--~~pl~VeP~e   65 (71)
T d1k3ra1           7 KPVTGEYRQGLTVKRVKKGTLVDIG----ADKLALCR-----------EKLTVNRIMSFRVVRL--GKEILIEPDE   65 (71)
T ss_dssp             SCCTTCEEEEEEEEECSSSEEEESS----SSCEEECS-----------SCCCSSCEEEEEEEEC--SSSCEEEECC
T ss_pred             CCcccceeeEEEEEecCCcEEEEec----CCceeeee-----------cccccCcEEEEEEEEc--CCceEeecCC
Confidence            4679999999999998899999994    44444433           3588999999999998  2235444433

>d1c9oa_ b.40.4.5 (A:) Major cold shock protein {Bacillus caldolyticus [TaxId: 1394]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Bacillus caldolyticus [TaxId: 1394]

Probab=92.53  E-value=0.16  Score=31.38  Aligned_cols=50  Identities=10%  Similarity=0.177  Sum_probs=37.0

Q ss_pred             EEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072         20 MVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV   75 (174)
Q Consensus        20 ~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V   75 (174)
                      +|+|+-.. ..|. ||...+  +-+-|+|+|.+.....    ..++.|+.|...+..-
T Consensus         3 ~G~Vk~fn~~kGfGFI~~d~--g~DiF~H~s~l~~~~~----~~L~~G~~V~f~~~~~   54 (66)
T d1c9oa_           3 RGKVKWFNNEKGYGFIEVEG--GSDVFVHFTAIQGEGF----KTLEEGQEVSFEIVQG   54 (66)
T ss_dssp             EEEEEEEETTTTEEEEEETT--EEEEEEEGGGBCSSSC----CCCCTTCEEEEEEEEE
T ss_pred             CeEEEEEECCCCEEEEEecC--CceEEEEehhcccccC----CcCCCCCEEEEEEEEC
Confidence            68888873 4455 576666  6789999999974432    4688999999988753

>d2vnud2 b.40.4.5 (D:911-998) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome complex exonuclease RRP44
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=91.38  E-value=0.23  Score=32.65  Aligned_cols=58  Identities=22%  Similarity=0.216  Sum_probs=39.9

Q ss_pred             EEEEEEEEecceEEEEECCCCCeEEEEEceecch-----hh------hh------ccccccCCCCEEEEEEEEEeC
Q psy18072         19 VMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR-----RR------IR------SINKLIRVGKTEPVVVIRVDK   77 (174)
Q Consensus        19 V~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~-----~~------v~------~~~~~l~vGd~V~vrVi~Vd~   77 (174)
                      =.|.|.+|.++|+.|-++.| +++|.|.......     .+      ++      +-.-.+++=|.|+|+|.++..
T Consensus         4 EegyV~~Vr~NGivVfVPky-GiEG~v~l~~~~~~~~~~~~De~~~~l~~~~~~~~~~~~~~vFD~V~V~is~vkd   78 (88)
T d2vnud2           4 ETGYVIKVFNNGIVVLVPKF-GVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMD   78 (88)
T ss_dssp             EEEEEEEEETTEEEEEETTT-TEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC----
T ss_pred             eEEEEEEEecccEEEEEecc-ceeEEEEEeccCCCCcceEEcchheEEEEecccCCCcEEEEecceEEEEEEEEEC
Confidence            46999999999999999999 5999999865321     01      00      012356677999999988743

>d1mjca_ b.40.4.5 (A:) Major cold shock protein {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Escherichia coli [TaxId: 562]

Probab=91.11  E-value=0.28  Score=30.56  Aligned_cols=52  Identities=10%  Similarity=0.128  Sum_probs=37.6

Q ss_pred             EEEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         18 VVMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        18 iV~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      .++|+|+-.. ..|. ||.-++ ++-+=|+|+|.+.....    ..+++||.|...+..
T Consensus         3 r~~G~Vk~f~~~kGfGFI~~d~-g~~diFvH~s~l~~~~~----~~L~~G~~V~f~~~~   56 (69)
T d1mjca_           3 KMTGIVKWFNADKGFGFITPDD-GSKDVFVHFSAIQNDGY----KSLDEGQKVSFTIES   56 (69)
T ss_dssp             CEEEEEEEEETTTTEEEEEETT-SCCCEEEEGGGBCCTTT----CCCCTTCEEEEEEEC
T ss_pred             CEEEEEEEEeCCCCEEEEEEcC-CCccEEEEhHHhcccCC----CcCCCCCEEEEEEEe
Confidence            3789998873 4455 666554 14689999999975433    458899999998764

>d1h95a_ b.40.4.5 (A:) Y-box protein 1 cold shock domain (YB1-CSD) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Y-box protein 1 cold shock domain (YB1-CSD)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.45  E-value=0.47  Score=30.26  Aligned_cols=60  Identities=13%  Similarity=0.149  Sum_probs=41.7

Q ss_pred             CCCEEEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072         15 VEDVVMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV   75 (174)
Q Consensus        15 ~GdiV~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V   75 (174)
                      .-..+.|+|+-.. ..|. ||.-.+- +-+=|+|.|.|...-.......|..||.|...+..-
T Consensus         5 ~~~r~~G~VKwfn~~KGfGFI~~ddg-~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~~   66 (79)
T d1h95a_           5 IATKVLGTVKWFNVRNGYGFINRNDT-KEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEG   66 (79)
T ss_dssp             CEEEEEEEEEEEETTTTEEEEEEGGG-TEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEEC
T ss_pred             hcCcccEEEEEEcCCCCeEEEEECCC-CccEEEEhhHcccCCCcceeeecCCCCEEEEEEEeC
Confidence            3456899999873 3455 6665441 478999999997543333335688999999988763

>d1yeza1 b.40.4.12 (A:1-68) Hypothetical protein MM1357 {Methanosarcina mazei [TaxId: 2209]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: TRAM domain
domain: Hypothetical protein MM1357
species: Methanosarcina mazei [TaxId: 2209]

Probab=89.26  E-value=0.87  Score=27.99  Aligned_cols=49  Identities=27%  Similarity=0.222  Sum_probs=36.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      ++|+.+..+|.++...|-=|.-.+  ++-=|++             ..+ +|+.|.++|.++...
T Consensus        12 ~~g~~~~l~I~~l~~~G~Gi~~~~--g~vvfV~-------------gal-pGe~v~v~i~k~kk~   60 (68)
T d1yeza1          12 EEGEVYDVTIQDIARQGDGIARIE--GFVIFVP-------------GTK-VGDEVRIKVERVLPK   60 (68)
T ss_dssp             CTTEEEEEECCEEETTTEEEEEET--TEEEEEE-------------SCC-TTCEEEEEEEEECSS
T ss_pred             CCCCEEEEEEEECCCCCcEEEEEC--CEEEEeC-------------CCC-CCCEEEEEEEEEeCC
Confidence            589999999999977666444323  4555555             333 899999999998654

>d1wfqa_ b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Cold shock domain protein E1 (UNR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.73  E-value=0.79  Score=29.76  Aligned_cols=55  Identities=9%  Similarity=0.001  Sum_probs=41.2

Q ss_pred             CCCEEEEEEEEEecceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEe
Q psy18072         15 VEDVVMVTVISIAEMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD   76 (174)
Q Consensus        15 ~GdiV~G~V~~i~~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd   76 (174)
                      .+...+|+|....+ |. ||...+. .-+=|+|+|.+...     ...+++||.|...|..-.
T Consensus        15 ~~~r~~G~I~~~~~-gfGFI~~~~~-~~dvF~H~s~~~~~-----~~~l~~G~~VeF~v~~~~   70 (89)
T d1wfqa_          15 AALRETGVIEKLLT-SYGFIQCSER-QARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDR   70 (89)
T ss_dssp             CCCEEEEEEEEECS-SEEEEEETTT-TEEEEEETTTCSSC-----TTTCCTTCCEEEEEEECS
T ss_pred             ccceEEEEEEEecC-ccceEEeCCC-CceEEEEeehhhcc-----CCcccCCCEEEEEEEECC
Confidence            57788999999954 44 6666552 46899999998532     256999999999987643

>d1yvca1 b.40.4.12 (A:1-69) Hypothetical protein MMP0076 {Methanococcus maripaludis [TaxId: 39152]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: TRAM domain
domain: Hypothetical protein MMP0076
species: Methanococcus maripaludis [TaxId: 39152]

Probab=87.55  E-value=1.1  Score=27.70  Aligned_cols=49  Identities=16%  Similarity=0.144  Sum_probs=34.9

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072         14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus        14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      ++|+.+..+|.++...|-=|.-.+  +.-=||+             ..+ +|+.|.++|.++...
T Consensus        14 k~g~~~~v~I~~l~~~G~Giar~~--g~vvfV~-------------~al-PGe~V~v~I~k~kk~   62 (69)
T d1yvca1          14 EAGKEYEVTIEDMGKGGDGIARID--GFVVFVP-------------NAE-KGSVINVKVTAVKEK   62 (69)
T ss_dssp             CTTCEEEEECCEECTTSCEEEEET--TEEEEET-------------TCC-TTCEEEEEEEEECSS
T ss_pred             CCCCEEEEEEEECCCCCcEEEEEC--CEEEEeC-------------CCC-CCCEEEEEEEEecCC
Confidence            589999999999877665443323  4444444             334 999999999998653

>d1fr3a_ b.40.6.1 (A:) Molybdate/tungstate binding protein MOP {Sporomusa ovata [TaxId: 2378]}

class: All beta proteins
fold: OB-fold
superfamily: MOP-like
family: Molybdate/tungstate binding protein MOP
domain: Molybdate/tungstate binding protein MOP
species: Sporomusa ovata [TaxId: 2378]

Probab=86.30  E-value=0.42  Score=29.22  Aligned_cols=55  Identities=13%  Similarity=0.232  Sum_probs=36.3

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      -..+.|+|.+|.+.|..+.+.=  ...|.--.+.++..-...+.  +++|+.|.|.+..
T Consensus         6 rN~l~g~V~~I~~~~~~~~V~l--~~~g~~l~a~IT~~s~~~L~--L~~G~~V~a~iKa   60 (67)
T d1fr3a_           6 RNKLEATVKEIVKGTVMAKIVM--DYKGTELVAAITIDSVADLD--LVPGDKVTALVKA   60 (67)
T ss_dssp             CEEEEEEEEEEEECSSEEEEEE--EETTEEEEEEEEHHHHHHHT--CCTTCEEEEEECG
T ss_pred             ccEEEEEEEEEEECCCeEEEEE--EECCcEEEEEcCHHHHHhcC--CCCCCEEEEEEEh
Confidence            4578999999987776654432  22233344556665555544  9999999998753

>d1g6pa_ b.40.4.5 (A:) Major cold shock protein {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Thermotoga maritima [TaxId: 2336]

Probab=86.24  E-value=0.2  Score=30.99  Aligned_cols=49  Identities=12%  Similarity=0.118  Sum_probs=35.0

Q ss_pred             EEEEEEE-ecceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072         20 MVTVISI-AEMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR   74 (174)
Q Consensus        20 ~G~V~~i-~~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~   74 (174)
                      +|+|... ...|. ||.-..  +-+=|+|.|.+...-.    ..+++|+.|...+..
T Consensus         2 ~G~Vk~f~~~kGfGFI~~~~--g~diFvH~s~l~~~g~----~~l~~G~~V~f~~~~   52 (66)
T d1g6pa_           2 RGKVKWFDSKKGYGFITKDE--GGDVFVHWSAIEMEGF----KTLKEGQVVEFEIQE   52 (66)
T ss_dssp             CEEEEEEETTTTEEEEEETT--SCBCBBCSSSSCCSSC----CCCCSSSEEEEEEEC
T ss_pred             eEEEEEEeCCCCeeEEEecC--CceEEEEhHHhcccCC----CcCCCCCEEEEEEEE
Confidence            5888887 34455 565565  5588999999864332    458899999998754

>d1e1oa1 b.40.4.1 (A:11-153) Lysyl-tRNA synthetase (LysRS) {Escherichia coli, gene lysU [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Lysyl-tRNA synthetase (LysRS)
species: Escherichia coli, gene lysU [TaxId: 562]

Probab=83.68  E-value=1.6  Score=30.51  Aligned_cols=53  Identities=15%  Similarity=0.118  Sum_probs=41.4

Q ss_pred             EEEEEEEEEecc--eEEEEECCCC-CeEEEEEceecchhhhhccccccCCCCEEEE
Q psy18072         18 VVMVTVISIAEM--GAYVHLLEYN-NIEGMILLSELSRRRIRSINKLIRVGKTEPV   70 (174)
Q Consensus        18 iV~G~V~~i~~~--GafV~L~~~~-~~~GlI~iSels~~~v~~~~~~l~vGd~V~v   70 (174)
                      .+-|+|..+..+  .+|+.|.+.. .++-++....+....+....+.+.+||.|-|
T Consensus        58 ~vaGRI~~~R~~Gk~~F~~i~D~~g~iQi~~~~~~~~~~~~~~~~k~ld~GDiIgv  113 (143)
T d1e1oa1          58 SVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGA  113 (143)
T ss_dssp             EEEEEEEEEEEETTEEEEEEEETTEEEEEEEETTTSSTTHHHHTGGGCCTTCEEEE
T ss_pred             EEEEEEEEEcccCCeeEEEEEeCCceEEEEEccccchhhhHHHHHhcCCcccEEEe
Confidence            488999998654  6799997643 5788888888877666666688999999966

>d1uwva1 b.40.4.12 (A:15-74) rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: TRAM domain
domain: rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.39  E-value=3.9  Score=24.03  Aligned_cols=45  Identities=20%  Similarity=0.209  Sum_probs=31.2

Q ss_pred             EEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072         18 VVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE   78 (174)
Q Consensus        18 iV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~   78 (174)
                      +++.+|.++...|.-|.-.+  +.--|++             ..+ +|+.|.|+|.+..+.
T Consensus         2 ~i~v~I~~l~~~G~Gv~r~~--g~vvfV~-------------~al-PGE~V~v~i~~~~~~   46 (60)
T d1uwva1           2 IITVSVNDLDSFGQGVARHN--GKTLFIP-------------GLL-PQENAEVTVTEDKKQ   46 (60)
T ss_dssp             CEEEEEEEECTTSEEEEEET--TEEEEEE-------------TCC-TTCEEEEEEEEECSS
T ss_pred             EEEEEEEECCCCCcEEEEEC--CEEEEEC-------------CCC-CCCEEEEEEEEecCC
Confidence            56778888877776555433  4444544             344 899999999998754