Psyllid ID: psy14481

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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-------18
Protein Sequence
MLDVAPPDSPRAHQAHAEDLSNPWSGEGGVNVAMISGISFGALALVTLFGAVSFIMYRRYRWNKPQTLSDKCSNPDSSGYIDDSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQAAVKKE
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHcccHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHccccccccccccccccHHHcccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
mldvappdsprahqahaedlsnpwsgeggvNVAMISGISFGALALVTLFGAVSFIMYRRyrwnkpqtlsdkcsnpdssgyiddstlravhvqgqepltstmlAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQAAVKKE
Flexible Loop (DISEMBL)
MLDVAPPDSPRAHQAHAEDLSNPWSGEGGVNVAMISGISFGALALVTLFGAVSFIMYRRYRwnkpqtlsdkcsnpdSSGYIDDSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQakqaavkke
Low Complexity Region (SEG)
MLDVAPPDSPRAHQAHAEDLSNPWSGEGGVNVAMISGISFGALALVTLFGAVSFIMYRRYRWNKPQTLSDKCSNPDSSGYIDDSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEavavlqahqakqaavkkE
Disordered region (IsUnstruct)
**************************EGGVNVAMISGISFGALALVTLFGAVSFIMYRRYRWNK*************************************************LGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHN***************************
Disordered Region (DISOPRED)
*****************************************************************************************************************LGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVA***************
Disordered Region (DISEMBL)
******************DLSNPWSGEGGVNVAMISGISFGALALVTLFGAVSFIMYRRYRWNKPQTLSDKCSNPDSSGYIDDSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQ************
Disordered Region (DISPRO)
****APPDSPR********LSN******GVNVAMISGISFGALALVTLFGAVSFIMYRRYRWNKPQTLSDKCS*************RAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQ******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLDVAPPDSPRAHQAHAEDLSNPWSGEGGVNVAMISGISFGALALVTLFGAVSFIMYRRYRWNKPQTLSDKCSNPDSSGYIDDSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHxxxxxxxxxxxxxxxxxxxxxQAAVKKE
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	179	2.2.26 [Sep-21-2011]
P20965	633	Polyadenylate-binding pro	N/A	N/A	0.502	0.142	0.844	2e-36
Q6IP09	633	Polyadenylate-binding pro	N/A	N/A	0.502	0.142	0.844	2e-36
Q5R8F7	636	Polyadenylate-binding pro	yes	N/A	0.502	0.141	0.833	3e-36
P29341	636	Polyadenylate-binding pro	yes	N/A	0.502	0.141	0.833	3e-36
P11940	636	Polyadenylate-binding pro	yes	N/A	0.502	0.141	0.833	4e-36
P61286	636	Polyadenylate-binding pro	yes	N/A	0.502	0.141	0.833	4e-36
Q9EPH8	636	Polyadenylate-binding pro	yes	N/A	0.502	0.141	0.833	4e-36
Q13310	644	Polyadenylate-binding pro	no	N/A	0.508	0.141	0.802	1e-34
Q9H361	631	Polyadenylate-binding pro	no	N/A	0.502	0.142	0.8	3e-34
Q98SP8	629	Embryonic polyadenylate-b	N/A	N/A	0.502	0.143	0.755	1e-31

>sp|P20965|PABPA_XENLA Polyadenylate-binding protein 1-A OS=Xenopus laevis GN=pabpc1-a PE=1 SV=3

 Score =  151 bits (382), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 76/90 (84%), Positives = 84/90 (93%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AVHVQGQEPLT++MLAAA PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct: 534 AVHVQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 593

Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAAVK 177
           MLE  ESL+SKV+EAVAVLQAHQAK+AA K
Sbjct: 594 MLESPESLRSKVDEAVAVLQAHQAKEAAQK 623

Binds the poly(A) tail of mRNA. Prevents mRNA deadenylation and confers poly(A) stability. Stimulates the translation of mRNAs to which it is bound, acting, at least in part, with dazl.
Xenopus laevis (taxid: 8355)

>sp|Q6IP09|PABPB_XENLA Polyadenylate-binding protein 1-B OS=Xenopus laevis GN=pabpc1-b PE=2 SV=1

 Score =  151 bits (382), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 76/90 (84%), Positives = 84/90 (93%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AVHVQGQEPLT++MLAAA PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct: 534 AVHVQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 593

Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAAVK 177
           MLE  ESL+SKV+EAVAVLQAHQAK+AA K
Sbjct: 594 MLESPESLRSKVDEAVAVLQAHQAKEAAQK 623

Binds the poly(A) tail of mRNA. Prevents mRNA deadenylation and confers poly(A) stability. Stimulates the translation of mRNAs to which it is bound, acting, at least in part, with dazl.

Xenopus laevis (taxid: 8355)

>sp|Q5R8F7|PABP1_PONAB Polyadenylate-binding protein 1 OS=Pongo abelii GN=PABPC1 PE=2 SV=1

 Score =  150 bits (380), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 75/90 (83%), Positives = 84/90 (93%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct: 536 AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 595

Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAAVK 177
           MLE  ESL+SKV+EAVAVLQAHQAK+AA K
Sbjct: 596 MLESPESLRSKVDEAVAVLQAHQAKEAAQK 625

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Pongo abelii (taxid: 9601)

>sp|P29341|PABP1_MOUSE Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2

 Score =  150 bits (380), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 75/90 (83%), Positives = 84/90 (93%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct: 536 AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLH 595

Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAAVK 177
           MLE  ESL+SKV+EAVAVLQAHQAK+AA K
Sbjct: 596 MLESPESLRSKVDEAVAVLQAHQAKEAAQK 625

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Mus musculus (taxid: 10090)

>sp|P11940|PABP1_HUMAN Polyadenylate-binding protein 1 OS=Homo sapiens GN=PABPC1 PE=1 SV=2

 Score =  150 bits (380), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 75/90 (83%), Positives = 84/90 (93%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct: 536 AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 595

Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAAVK 177
           MLE  ESL+SKV+EAVAVLQAHQAK+AA K
Sbjct: 596 MLESPESLRSKVDEAVAVLQAHQAKEAAQK 625

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Homo sapiens (taxid: 9606)

>sp|P61286|PABP1_BOVIN Polyadenylate-binding protein 1 OS=Bos taurus GN=PABPC1 PE=2 SV=1

 Score =  150 bits (380), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 75/90 (83%), Positives = 84/90 (93%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct: 536 AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 595

Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAAVK 177
           MLE  ESL+SKV+EAVAVLQAHQAK+AA K
Sbjct: 596 MLESPESLRSKVDEAVAVLQAHQAKEAAQK 625

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Bos taurus (taxid: 9913)

>sp|Q9EPH8|PABP1_RAT Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=2 SV=1

 Score =  150 bits (380), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 75/90 (83%), Positives = 84/90 (93%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct: 536 AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLH 595

Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAAVK 177
           MLE  ESL+SKV+EAVAVLQAHQAK+AA K
Sbjct: 596 MLESPESLRSKVDEAVAVLQAHQAKEAAQK 625

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Rattus norvegicus (taxid: 10116)

>sp|Q13310|PABP4_HUMAN Polyadenylate-binding protein 4 OS=Homo sapiens GN=PABPC4 PE=1 SV=1

 Score =  145 bits (367), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 73/91 (80%), Positives = 82/91 (90%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AVHVQGQEPLT++MLAAA PQEQKQMLGERLFPLIQ M+  LAGKITGMLLEIDN+ELL+
Sbjct: 545 AVHVQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQTMHSNLAGKITGMLLEIDNSELLH 604

Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAAVKK 178
           MLE  ESL+SKV+EAVAVLQAH AK+ A +K
Sbjct: 605 MLESPESLRSKVDEAVAVLQAHHAKKEAAQK 635

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo.

Homo sapiens (taxid: 9606)

>sp|Q9H361|PABP3_HUMAN Polyadenylate-binding protein 3 OS=Homo sapiens GN=PABPC3 PE=1 SV=2

 Score =  144 bits (363), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 81/90 (90%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AVHVQGQE LT++ LA+A PQ+QKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELLY
Sbjct: 531 AVHVQGQETLTASRLASAPPQKQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLY 590

Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAAVK 177
           MLE  ESL+SKV+EAVAVLQAHQAK+A  K
Sbjct: 591 MLESPESLRSKVDEAVAVLQAHQAKEATQK 620

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism. Binds poly(A) with a slightly lower affinity as compared to PABPC1.

Homo sapiens (taxid: 9606)

>sp|Q98SP8|EPABA_XENLA Embryonic polyadenylate-binding protein A OS=Xenopus laevis GN=epabp-a PE=1 SV=2

 Score =  135 bits (341), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 68/90 (75%), Positives = 79/90 (87%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AV +QGQEPLT+++LA A PQEQKQMLGER++P+I  M+P LAGKITGMLLEIDN+ELL+
Sbjct: 533 AVLMQGQEPLTASLLAGAPPQEQKQMLGERIYPVIHEMHPTLAGKITGMLLEIDNSELLH 592

Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAAVK 177
           MLE  ESL SKVEEAVAVLQAHQAK+ A K
Sbjct: 593 MLESPESLHSKVEEAVAVLQAHQAKENAQK 622

Binds and protects the poly(A) tail of mRNA with or without an AU-rich element (ARE) and prevents mRNA deadenylation. Stimulates the translation of mRNAs to which it is bound during early development.

Xenopus laevis (taxid: 8355)

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	179
91095037	607	PREDICTED: similar to poly A binding pro	0.519	0.153	0.903	1e-41
332374002	634	unknown [Dendroctonus ponderosae]	0.513	0.145	0.902	1e-40
328782034	601	PREDICTED: polyadenylate-binding protein	0.905	0.269	0.561	6e-39
380019828	630	PREDICTED: polyadenylate-binding protein	0.905	0.257	0.561	8e-39
383862671	601	PREDICTED: polyadenylate-binding protein	0.905	0.269	0.556	2e-38
383862667	630	PREDICTED: polyadenylate-binding protein	0.905	0.257	0.556	2e-38
350408508	601	PREDICTED: polyadenylate-binding protein	0.837	0.249	0.590	7e-38
350408504	630	PREDICTED: polyadenylate-binding protein	0.837	0.238	0.590	7e-38
383862669	612	PREDICTED: polyadenylate-binding protein	0.519	0.151	0.861	1e-37
340719920	609	PREDICTED: polyadenylate-binding protein	0.519	0.152	0.861	1e-37

>gi|91095037|ref|XP_975975.1| PREDICTED: similar to poly A binding protein isoform 4 [Tribolium castaneum] gi|270014772|gb|EFA11220.1| hypothetical protein TcasGA2_TC005185 [Tribolium castaneum]

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 84/93 (90%), Positives = 92/93 (98%)

Query: 87  RAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELL 146
           +AVH+QGQEPLT+TMLAAA PQEQKQMLGERLFPLIQRMYP+LAGKITGMLLEIDN+ELL
Sbjct: 515 QAVHIQGQEPLTATMLAAAPPQEQKQMLGERLFPLIQRMYPDLAGKITGMLLEIDNSELL 574

Query: 147 YMLEHNESLKSKVEEAVAVLQAHQAKQAAVKKE 179
           +MLEHNESLK+KVEEAVAVLQAHQAKQAA+KKE
Sbjct: 575 HMLEHNESLKAKVEEAVAVLQAHQAKQAAIKKE 607

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332374002|gb|AEE62142.1| unknown [Dendroctonus ponderosae]

 Score =  171 bits (433), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 83/92 (90%), Positives = 90/92 (97%)

Query: 87  RAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELL 146
           +AVH+QGQEPLT+TMLAAAQPQEQKQMLGERLFPLIQRMY +LAGKITGMLLEIDN ELL
Sbjct: 543 QAVHIQGQEPLTATMLAAAQPQEQKQMLGERLFPLIQRMYADLAGKITGMLLEIDNTELL 602

Query: 147 YMLEHNESLKSKVEEAVAVLQAHQAKQAAVKK 178
           +MLEHNESLK+KVEEAVAVLQAHQAKQAA+KK
Sbjct: 603 HMLEHNESLKNKVEEAVAVLQAHQAKQAAIKK 634

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328782034|ref|XP_396057.4| PREDICTED: polyadenylate-binding protein 1-like isoform 1 [Apis mellifera]

 Score =  165 bits (418), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 100/178 (56%), Positives = 117/178 (65%), Gaps = 16/178 (8%)

Query: 9   SPRAHQAHAEDLSN-----PWSGEGGVNVAMISGISFGALAL-VTLFGAVSFIMYRRYRW 62
           +PRA  A A  + N     P +G+  V  A +   S    A+ V+     S   Y     
Sbjct: 433 APRAPTAQAGTMRNTLSARPITGQQAVGGANMQNRSMAGPAVGVSAQSRPSNYKYTSNMR 492

Query: 63  NKPQTLSDKCSNPDSSGYIDDSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLI 122
           N PQ ++     P           +AVH+QGQEPLT++MLAAA PQEQKQMLGERLFPLI
Sbjct: 493 NPPQAMAIPAPTP---------VQQAVHIQGQEPLTASMLAAAPPQEQKQMLGERLFPLI 543

Query: 123 QRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQA-AVKKE 179
           Q MYP+L GKITGMLLEIDN+ELL+MLEHNESLK+KVEEAVAVLQAHQAKQA A KKE
Sbjct: 544 QCMYPQLTGKITGMLLEIDNSELLHMLEHNESLKAKVEEAVAVLQAHQAKQAVASKKE 601

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380019828|ref|XP_003693803.1| PREDICTED: polyadenylate-binding protein 1-like [Apis florea]

 Score =  165 bits (417), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 100/178 (56%), Positives = 117/178 (65%), Gaps = 16/178 (8%)

Query: 9   SPRAHQAHAEDLSN-----PWSGEGGVNVAMISGISFGALAL-VTLFGAVSFIMYRRYRW 62
           +PRA  A A  + N     P +G+  V  A +   S    A+ V+     S   Y     
Sbjct: 462 APRAPTAQAGTMRNTLSARPITGQQAVGGANMQNRSMAGPAVGVSAQSRPSNYKYTSNMR 521

Query: 63  NKPQTLSDKCSNPDSSGYIDDSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLI 122
           N PQ ++     P           +AVH+QGQEPLT++MLAAA PQEQKQMLGERLFPLI
Sbjct: 522 NPPQAMAIPAPTP---------VQQAVHIQGQEPLTASMLAAAPPQEQKQMLGERLFPLI 572

Query: 123 QRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQA-AVKKE 179
           Q MYP+L GKITGMLLEIDN+ELL+MLEHNESLK+KVEEAVAVLQAHQAKQA A KKE
Sbjct: 573 QCMYPQLTGKITGMLLEIDNSELLHMLEHNESLKAKVEEAVAVLQAHQAKQAVASKKE 630

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383862671|ref|XP_003706807.1| PREDICTED: polyadenylate-binding protein 1-like isoform 3 [Megachile rotundata]

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 99/178 (55%), Positives = 117/178 (65%), Gaps = 16/178 (8%)

Query: 9   SPRAHQAHAEDL-----SNPWSGEGGVNVAMISGISFGALAL-VTLFGAVSFIMYRRYRW 62
           +PRA  A A  +     + P +G+  V  A +   S    A+ V+     S   Y     
Sbjct: 433 TPRAPTAQAGTMRSTLSARPITGQQAVGGANMQSRSMAGPAVGVSAQSRPSNYKYTSNMR 492

Query: 63  NKPQTLSDKCSNPDSSGYIDDSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLI 122
           N PQ ++     P           +AVH+QGQEPLT++MLAAA PQEQKQMLGERLFPLI
Sbjct: 493 NPPQAMAIPAPTP---------VQQAVHIQGQEPLTASMLAAAPPQEQKQMLGERLFPLI 543

Query: 123 QRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQA-AVKKE 179
           Q MYP+L GKITGMLLEIDN+ELL+MLEHNESLK+KVEEAVAVLQAHQAKQA A KKE
Sbjct: 544 QCMYPQLTGKITGMLLEIDNSELLHMLEHNESLKAKVEEAVAVLQAHQAKQAVASKKE 601

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383862667|ref|XP_003706805.1| PREDICTED: polyadenylate-binding protein 1-like isoform 1 [Megachile rotundata]

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 99/178 (55%), Positives = 117/178 (65%), Gaps = 16/178 (8%)

Query: 9   SPRAHQAHAEDL-----SNPWSGEGGVNVAMISGISFGALAL-VTLFGAVSFIMYRRYRW 62
           +PRA  A A  +     + P +G+  V  A +   S    A+ V+     S   Y     
Sbjct: 462 TPRAPTAQAGTMRSTLSARPITGQQAVGGANMQSRSMAGPAVGVSAQSRPSNYKYTSNMR 521

Query: 63  NKPQTLSDKCSNPDSSGYIDDSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLI 122
           N PQ ++     P           +AVH+QGQEPLT++MLAAA PQEQKQMLGERLFPLI
Sbjct: 522 NPPQAMAIPAPTP---------VQQAVHIQGQEPLTASMLAAAPPQEQKQMLGERLFPLI 572

Query: 123 QRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQA-AVKKE 179
           Q MYP+L GKITGMLLEIDN+ELL+MLEHNESLK+KVEEAVAVLQAHQAKQA A KKE
Sbjct: 573 QCMYPQLTGKITGMLLEIDNSELLHMLEHNESLKAKVEEAVAVLQAHQAKQAVASKKE 630

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350408508|ref|XP_003488428.1| PREDICTED: polyadenylate-binding protein 1-like isoform 3 [Bombus impatiens]

 Score =  162 bits (409), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 95/161 (59%), Positives = 110/161 (68%), Gaps = 11/161 (6%)

Query: 21  SNPWSGEGGVNVAMISGISFGALAL-VTLFGAVSFIMYRRYRWNKPQTLSDKCSNPDSSG 79
           + P +G+  V  A +   S    A+ VT     S   Y     N PQ ++     P    
Sbjct: 450 ARPITGQQTVGGANMQNRSMAGPAVGVTAQSRPSNYKYTSNMRNPPQAMAIPAPTP---- 505

Query: 80  YIDDSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLE 139
                  +AVH+QGQEPLT++MLAAA PQEQKQMLGERLFPLIQ MYP+L GKITGMLLE
Sbjct: 506 -----VQQAVHIQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQCMYPQLTGKITGMLLE 560

Query: 140 IDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQA-AVKKE 179
           IDN+ELL+MLEHNESLK+KVEEAVAVLQAHQAKQA A KKE
Sbjct: 561 IDNSELLHMLEHNESLKAKVEEAVAVLQAHQAKQAVASKKE 601

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350408504|ref|XP_003488426.1| PREDICTED: polyadenylate-binding protein 1-like isoform 1 [Bombus impatiens]

 Score =  162 bits (409), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 95/161 (59%), Positives = 110/161 (68%), Gaps = 11/161 (6%)

Query: 21  SNPWSGEGGVNVAMISGISFGALAL-VTLFGAVSFIMYRRYRWNKPQTLSDKCSNPDSSG 79
           + P +G+  V  A +   S    A+ VT     S   Y     N PQ ++     P    
Sbjct: 479 ARPITGQQTVGGANMQNRSMAGPAVGVTAQSRPSNYKYTSNMRNPPQAMAIPAPTP---- 534

Query: 80  YIDDSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLE 139
                  +AVH+QGQEPLT++MLAAA PQEQKQMLGERLFPLIQ MYP+L GKITGMLLE
Sbjct: 535 -----VQQAVHIQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQCMYPQLTGKITGMLLE 589

Query: 140 IDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQA-AVKKE 179
           IDN+ELL+MLEHNESLK+KVEEAVAVLQAHQAKQA A KKE
Sbjct: 590 IDNSELLHMLEHNESLKAKVEEAVAVLQAHQAKQAVASKKE 630

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383862669|ref|XP_003706806.1| PREDICTED: polyadenylate-binding protein 1-like isoform 2 [Megachile rotundata]

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 81/94 (86%), Positives = 89/94 (94%), Gaps = 1/94 (1%)

Query: 87  RAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELL 146
           +AVH+QGQEPLT++MLAAA PQEQKQMLGERLFPLIQ MYP+L GKITGMLLEIDN+ELL
Sbjct: 519 QAVHIQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQCMYPQLTGKITGMLLEIDNSELL 578

Query: 147 YMLEHNESLKSKVEEAVAVLQAHQAKQA-AVKKE 179
           +MLEHNESLK+KVEEAVAVLQAHQAKQA A KKE
Sbjct: 579 HMLEHNESLKAKVEEAVAVLQAHQAKQAVASKKE 612

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340719920|ref|XP_003398392.1| PREDICTED: polyadenylate-binding protein 1-like isoform 2 [Bombus terrestris]

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 81/94 (86%), Positives = 89/94 (94%), Gaps = 1/94 (1%)

Query: 87  RAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELL 146
           +AVH+QGQEPLT++MLAAA PQEQKQMLGERLFPLIQ MYP+L GKITGMLLEIDN+ELL
Sbjct: 516 QAVHIQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQCMYPQLTGKITGMLLEIDNSELL 575

Query: 147 YMLEHNESLKSKVEEAVAVLQAHQAKQA-AVKKE 179
           +MLEHNESLK+KVEEAVAVLQAHQAKQA A KKE
Sbjct: 576 HMLEHNESLKAKVEEAVAVLQAHQAKQAVASKKE 609

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	179
ZFIN|ZDB-GENE-030131-9663	637	pabpc4 "poly(A) binding protei	0.413	0.116	0.851	1.9e-27
UNIPROTKB|H0YAS6	169	PABPC1 "Polyadenylate-binding	0.413	0.437	0.824	3.5e-27
UNIPROTKB|H0YB75	183	PABPC1 "Polyadenylate-binding	0.413	0.404	0.824	3.5e-27
UNIPROTKB|E1C903	630	PABPC4 "Uncharacterized protei	0.413	0.117	0.851	4e-27
UNIPROTKB|F1NH82	469	F1NH82 "Uncharacterized protei	0.413	0.157	0.824	5.8e-27
ZFIN|ZDB-GENE-030131-3238	634	pabpc1a "poly A binding protei	0.413	0.116	0.837	6.7e-27
ZFIN|ZDB-GENE-050308-1	634	pabpc1b "poly A binding protei	0.413	0.116	0.837	6.7e-27
UNIPROTKB|H0Y6X6	195	PABPC4 "Polyadenylate-binding	0.413	0.379	0.824	9.4e-27
RGD|1305015	415	Pabpc4 "poly(A) binding protei	0.413	0.178	0.824	9.4e-27
UNIPROTKB|P20965	633	pabpc1-a "Polyadenylate-bindin	0.413	0.116	0.837	1.1e-26

ZFIN|ZDB-GENE-030131-9663 pabpc4 "poly(A) binding protein, cytoplasmic 4 (inducible form)" [Danio rerio (taxid:7955)]

 Score = 315 (115.9 bits), Expect = 1.9e-27, P = 1.9e-27
 Identities = 63/74 (85%), Positives = 70/74 (94%)

Query:    88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
             AVHVQGQEPLT++MLAAA PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct:   535 AVHVQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLH 594

Query:   148 MLEHNESLKSKVEE 161
             MLE +ESL+SKVEE
Sbjct:   595 MLESHESLRSKVEE 608

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|H0YAS6 PABPC1 "Polyadenylate-binding protein 1" [Homo sapiens (taxid:9606)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 61/74 (82%), Positives = 69/74 (93%)

Query:    88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
             AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct:    69 AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 128

Query:   148 MLEHNESLKSKVEE 161
             MLE  ESL+SKV+E
Sbjct:   129 MLESPESLRSKVDE 142

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|H0YB75 PABPC1 "Polyadenylate-binding protein 1" [Homo sapiens (taxid:9606)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 61/74 (82%), Positives = 69/74 (93%)

Query:    88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
             AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct:    83 AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 142

Query:   148 MLEHNESLKSKVEE 161
             MLE  ESL+SKV+E
Sbjct:   143 MLESPESLRSKVDE 156

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|E1C903 PABPC4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 312 (114.9 bits), Expect = 4.0e-27, P = 4.0e-27
 Identities = 63/74 (85%), Positives = 69/74 (93%)

Query:    88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
             AVHVQGQEPLT++MLAAA PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct:   532 AVHVQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLH 591

Query:   148 MLEHNESLKSKVEE 161
             MLE  ESL+SKVEE
Sbjct:   592 MLESPESLRSKVEE 605

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0008266 "poly(U) RNA binding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

UNIPROTKB|F1NH82 F1NH82 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 305 (112.4 bits), Expect = 5.8e-27, P = 5.8e-27
 Identities = 61/74 (82%), Positives = 69/74 (93%)

Query:    88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
             AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct:   369 AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQSMHPTLAGKITGMLLEIDNSELLH 428

Query:   148 MLEHNESLKSKVEE 161
             MLE  ESL+SKV+E
Sbjct:   429 MLESPESLRSKVDE 442

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

ZFIN|ZDB-GENE-030131-3238 pabpc1a "poly A binding protein, cytoplasmic 1 a" [Danio rerio (taxid:7955)]

 Score = 310 (114.2 bits), Expect = 6.7e-27, P = 6.7e-27
 Identities = 62/74 (83%), Positives = 69/74 (93%)

Query:    88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
             AVHVQGQEPLT++MLAAA PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct:   535 AVHVQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQNMHPSLAGKITGMLLEIDNSELLH 594

Query:   148 MLEHNESLKSKVEE 161
             MLE  ESL+SKV+E
Sbjct:   595 MLESPESLRSKVDE 608

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0007507 "heart development" evidence=IMP

ZFIN|ZDB-GENE-050308-1 pabpc1b "poly A binding protein, cytoplasmic 1 b" [Danio rerio (taxid:7955)]

 Score = 310 (114.2 bits), Expect = 6.7e-27, P = 6.7e-27
 Identities = 62/74 (83%), Positives = 69/74 (93%)

Query:    88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
             AVHVQGQEPLT++MLAAA PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct:   534 AVHVQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQNMHPSLAGKITGMLLEIDNSELLH 593

Query:   148 MLEHNESLKSKVEE 161
             MLE  ESL+SKV+E
Sbjct:   594 MLESPESLRSKVDE 607

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|H0Y6X6 PABPC4 "Polyadenylate-binding protein 4" [Homo sapiens (taxid:9606)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 61/74 (82%), Positives = 68/74 (91%)

Query:    88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
             AVHVQGQEPLT++MLAAA PQEQKQMLGERLFPLIQ M+  LAGKITGMLLEIDN+ELL+
Sbjct:   100 AVHVQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQTMHSNLAGKITGMLLEIDNSELLH 159

Query:   148 MLEHNESLKSKVEE 161
             MLE  ESL+SKV+E
Sbjct:   160 MLESPESLRSKVDE 173

GO:0003723 "RNA binding" evidence=IEA

RGD|1305015 Pabpc4 "poly(A) binding protein, cytoplasmic 4" [Rattus norvegicus (taxid:10116)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 61/74 (82%), Positives = 68/74 (91%)

Query:    88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
             AVHVQGQEPLT++MLAAA PQEQKQMLGERLFPLIQ M+  LAGKITGMLLEIDN+ELL+
Sbjct:   316 AVHVQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQTMHSNLAGKITGMLLEIDNSELLH 375

Query:   148 MLEHNESLKSKVEE 161
             MLE  ESL+SKV+E
Sbjct:   376 MLESPESLRSKVDE 389

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0008143 "poly(A) RNA binding" evidence=ISO

GO:0008266 "poly(U) RNA binding" evidence=ISO

GO:0010494 "cytoplasmic stress granule" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO

GO:0017130 "poly(C) RNA binding" evidence=ISO

UNIPROTKB|P20965 pabpc1-a "Polyadenylate-binding protein 1-A" [Xenopus laevis (taxid:8355)]

 Score = 308 (113.5 bits), Expect = 1.1e-26, P = 1.1e-26
 Identities = 62/74 (83%), Positives = 69/74 (93%)

Query:    88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
             AVHVQGQEPLT++MLAAA PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct:   534 AVHVQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 593

Query:   148 MLEHNESLKSKVEE 161
             MLE  ESL+SKV+E
Sbjct:   594 MLESPESLRSKVDE 607

GO:0005515 "protein binding" evidence=IPI

GO:0005844 "polysome" evidence=IDA

GO:0008143 "poly(A) RNA binding" evidence=IDA

GO:0031370 "eukaryotic initiation factor 4G binding" evidence=IPI

GO:0043621 "protein self-association" evidence=IPI

GO:0048255 "mRNA stabilization" evidence=IDA

GO:0060212 "negative regulation of nuclear-transcribed mRNA poly(A) tail shortening" evidence=IDA

---

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)
P11940	PABP1_HUMAN	No assigned EC number	0.8333	0.5027	0.1415	yes	N/A
Q4WK03	PABP_ASPFU	No assigned EC number	0.5890	0.4078	0.0969	yes	N/A
Q5R8F7	PABP1_PONAB	No assigned EC number	0.8333	0.5027	0.1415	yes	N/A
P61286	PABP1_BOVIN	No assigned EC number	0.8333	0.5027	0.1415	yes	N/A
Q5B630	PABP_EMENI	No assigned EC number	0.6164	0.4078	0.0997	yes	N/A
Q9EPH8	PABP1_RAT	No assigned EC number	0.8333	0.5027	0.1415	yes	N/A
P29341	PABP1_MOUSE	No assigned EC number	0.8333	0.5027	0.1415	yes	N/A
P21187	PABP_DROME	No assigned EC number	0.6136	0.4804	0.1356	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	179
pfam00658	72	pfam00658, PABP, Poly-adenylate binding protein, u	2e-39
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-33
smart00517	64	smart00517, PolyA, C-terminal domain of Poly(A)-bi	1e-29

>gnl|CDD|201378 pfam00658, PABP, Poly-adenylate binding protein, unique domain

 Score =  128 bits (324), Expect = 2e-39
 Identities = 55/72 (76%), Positives = 68/72 (94%)

Query: 95  EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 154
           EPLT++ LAAA PQEQKQMLGERL+PLIQ M+PELAGKITGMLLE+DN+ELL++LE +E+
Sbjct: 1   EPLTASALAAAPPQEQKQMLGERLYPLIQAMHPELAGKITGMLLEMDNSELLHLLESDEA 60

Query: 155 LKSKVEEAVAVL 166
           LK+KV+EA+AVL
Sbjct: 61  LKAKVDEALAVL 72

The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family. Length = 72

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score =  124 bits (312), Expect = 1e-33
 Identities = 46/81 (56%), Positives = 60/81 (74%)

Query: 87  RAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELL 146
                 GQ    + +LA+A PQ QKQ+LGERLFPL++ + P LA KITGMLLE+DN+ELL
Sbjct: 482 STASQGGQNKKLAQVLASATPQMQKQVLGERLFPLVEAIEPALAAKITGMLLEMDNSELL 541

Query: 147 YMLEHNESLKSKVEEAVAVLQ 167
           ++LE  E LKSKV+EA+ VL+
Sbjct: 542 HLLESPELLKSKVDEALEVLK 562

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|197769 smart00517, PolyA, C-terminal domain of Poly(A)-binding protein

 Score =  103 bits (258), Expect = 1e-29
 Identities = 42/63 (66%), Positives = 55/63 (87%)

Query: 107 PQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVL 166
           PQEQKQ LGERL+P +Q + PELAGKITGMLLE+DN+ELL++LE  E L++KV+EA+ VL
Sbjct: 2   PQEQKQALGERLYPKVQALEPELAGKITGMLLEMDNSELLHLLESPELLRAKVDEALEVL 61

Query: 167 QAH 169
           ++H
Sbjct: 62  KSH 64

Present also in Drosophila hyperplastics discs protein. Involved in homodimerisation (either directly or indirectly). Length = 64

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	179
smart00517	64	PolyA C-terminal domain of Poly(A)-binding protein	99.97
PF00658	72	PABP: Poly-adenylate binding protein, unique domai	99.96
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.95
KOG0943|consensus	3015		97.51
PTZ00382	96	Variant-specific surface protein (VSP); Provisiona	95.43
PF03302	397	VSP: Giardia variant-specific surface protein; Int	93.18
PF05808	162	Podoplanin: Podoplanin; InterPro: IPR008783 This f	91.75
PF08693	40	SKG6: Transmembrane alpha-helix domain; InterPro:	87.34
PF01034	64	Syndecan: Syndecan domain; InterPro: IPR001050 The	84.1
PF12301	169	CD99L2: CD99 antigen like protein 2; InterPro: IPR	82.52

>smart00517 PolyA C-terminal domain of Poly(A)-binding protein

Probab=99.97  E-value=3.8e-31  Score=187.71  Aligned_cols=64  Identities=67%  Similarity=0.994  Sum_probs=62.3

Q ss_pred             ChHHHHHHhhhhhhhhHhhhCCCCCCCceeeccCCChHHHHHhhcChHHHHHHHHHHHHHHHHH
Q psy14481        106 QPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH  169 (179)
Q Consensus       106 ~peeQKq~LGErLyplV~~l~p~~AgKITGMLLEmd~sELL~mLes~e~L~~KV~EA~~vL~~~  169 (179)
                      +|++|||+|||+|||+|++++|++||||||||||||++|+++||+|+++|++||+||++||++|
T Consensus         1 ~p~~qkq~LGE~Lyp~V~~~~p~~A~KITGMLLEmd~~ell~lle~~~~L~~kv~EA~~vl~~~   64 (64)
T smart00517        1 PPQEQKQALGERLYPKVQALEPELAGKITGMLLEMDNSELLHLLESPELLRSKVDEALEVLKSH   64 (64)
T ss_pred             CHHHHHHHHhHHHhHHHHhhCcccCCcCeeeeeCCCHHHHHHHhcCHHHHHHHHHHHHHHHHhC
Confidence            5899999999999999999999999999999999999999999999999999999999999874

Present also in Drosophila hyperplastics discs protein. Involved in homodimerisation (either directly or indirectly)

>PF00658 PABP: Poly-adenylate binding protein, unique domain; InterPro: IPR002004 The polyadenylate-binding protein (PABP) has a conserved C-terminal domain (PABC), which is also found in the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains (IPR000569 from INTERPRO) []

Probab=99.96  E-value=6.3e-30  Score=184.24  Aligned_cols=72  Identities=67%  Similarity=1.054  Sum_probs=70.6

Q ss_pred             CCCChhHhhcCChHHHHHHhhhhhhhhHhhhCCCCCCCceeeccCCChHHHHHhhcChHHHHHHHHHHHHHH
Q psy14481         95 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVL  166 (179)
Q Consensus        95 epl~~s~La~a~peeQKq~LGErLyplV~~l~p~~AgKITGMLLEmd~sELL~mLes~e~L~~KV~EA~~vL  166 (179)
                      +|+++++|+++++++||++|||+|||+|+.++|++||||||||||||++||++||+|++.|+.||+||++||
T Consensus         1 ~~~~~~~la~~~~~~qk~~LGe~Ly~~V~~~~p~~A~KITGMLLe~~~~ell~ll~~~~~L~~kv~eA~~vL   72 (72)
T PF00658_consen    1 EPLTASALASASPEQQKQILGERLYPLVQAIYPELAGKITGMLLEMDNSELLHLLEDPELLREKVQEAIEVL   72 (72)
T ss_dssp             SSTSHHHHHTSCHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTSCHHHHHHHHHTHHHHHHHHHHHHHHH
T ss_pred             CcchHHHHhcCCHHHHHHHHhccccHHHHHhCcchhHHHHHHHhcCCHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence            578999999999999999999999999999999999999999999999999999999999999999999987

PABP recognises the 3' mRNA poly(A) tail and plays an essential role in eukaryotic translation initiation and mRNA stabilisation/degradation. PABC domains of PABP are peptide-binding domains that mediate PABP homo-oligomerisation and protein-protein interactions. In mammals, the PABC domain of PABP functions to recruit several different translation factors to the mRNA poly(A) tail [].; GO: 0003723 RNA binding; PDB: 3KUR_E 1JH4_A 2RQH_B 3KUI_A 3KUS_A 3KUJ_A 3KTR_A 2X04_A 3PTH_A 1JGN_A ....

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.95  E-value=9.2e-29  Score=225.54  Aligned_cols=80  Identities=58%  Similarity=0.813  Sum_probs=77.0

Q ss_pred             ccccCCCCCCChhHhhcCChHHHHHHhhhhhhhhHhhhCCCCCCCceeeccCCChHHHHHhhcChHHHHHHHHHHHHHHH
Q psy14481         88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQ  167 (179)
Q Consensus        88 ~~~~~g~epl~~s~La~a~peeQKq~LGErLyplV~~l~p~~AgKITGMLLEmd~sELL~mLes~e~L~~KV~EA~~vL~  167 (179)
                      +++.+|++++++++|++++|++||+||||+|||+|++++|++||||||||||||++|||+||||+|+|++||+||++||+
T Consensus       483 ~~~~~~~~~~~~~~la~~~p~~q~~~lg~~~~~~~~~~~~~~~~~~tgm~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (562)
T TIGR01628       483 TASQGGQNKKLAQVLASATPQMQKQVLGERLFPLVEAIEPALAAKITGMLLEMDNSELLHLLESPELLKSKVDEALEVLK  562 (562)
T ss_pred             CccccccchhHHHHHhhCCHHHHHHHHHHHhHHHHHhhChhhcCcceEEEecCCHHHHHHHhcCHHHHHHHHHHHHHHhC
Confidence            46677889999999999999999999999999999999999999999999999999999999999999999999999984

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0943|consensus

Probab=97.51  E-value=4.4e-05  Score=79.06  Aligned_cols=66  Identities=30%  Similarity=0.459  Sum_probs=61.2

Q ss_pred             HHHHHHhhhhhhhhHhhhCCCCCCCceeeccCCChHHHHHhhcChHHHHHHHHHHH--HHHHHHHHhH
Q psy14481        108 QEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAV--AVLQAHQAKQ  173 (179)
Q Consensus       108 eeQKq~LGErLyplV~~l~p~~AgKITGMLLEmd~sELL~mLes~e~L~~KV~EA~--~vL~~~q~~~  173 (179)
                      .-.+|.|||+||+.++.+.|..|.||||||||.....++..|..++.|+..|++|+  +++..|.++-
T Consensus      2605 sAe~Q~la~l~wgqhe~~l~a~~s~~sGfL~dek~~g~llgi~ce~p~eafVdaa~ndd~i~~H~qei 2672 (3015)
T KOG0943|consen 2605 SAERQALAELLWGQHEAMLPAFASKISGFLLDEKPAGLLLGIACEDPLEAFVDAAMNDDLIIAHGQEI 2672 (3015)
T ss_pred             hhhhccchhhcchhhhhHHHHHHHhhhhhhhccchHHHHHHHhhcCcHHHHHHHhcchHHHHHHHHHh
Confidence            34688999999999999999999999999999999999999999999999999999  8888887653

>PTZ00382 Variant-specific surface protein (VSP); Provisional

Probab=95.43  E-value=0.0092  Score=45.12  Aligned_cols=33  Identities=27%  Similarity=0.460  Sum_probs=23.0

Q ss_pred             CCCceeeeeechhhhHHHHHHhh-hcceeeeeec
Q psy14481         27 EGGVNVAMISGISFGALALVTLF-GAVSFIMYRR   59 (179)
Q Consensus        27 ~~~~~~~~i~g~~~~~~~i~~~~-~~~~~~~yrr   59 (179)
                      .++++.|+|+||..|+++++..+ |.+-+++++|
T Consensus        60 ~~~ls~gaiagi~vg~~~~v~~lv~~l~w~f~~r   93 (96)
T PTZ00382         60 RSGLSTGAIAGISVAVVAVVGGLVGFLCWWFVCR   93 (96)
T ss_pred             CCCcccccEEEEEeehhhHHHHHHHHHhheeEEe
Confidence            36788999999999988777554 4444444434

>PF03302 VSP: Giardia variant-specific surface protein; InterPro: IPR005127 During infection, the intestinal protozoan parasite Giardia lamblia virus undergoes continuous antigenic variation which is determined by diversification of the parasite's major surface antigen, named VSP (variant surface protein)

Probab=93.18  E-value=0.044  Score=50.21  Aligned_cols=34  Identities=26%  Similarity=0.503  Sum_probs=26.9

Q ss_pred             CCCCceeeeeechhhhHHHHHH-hhhcceeeeeec
Q psy14481         26 GEGGVNVAMISGISFGALALVT-LFGAVSFIMYRR   59 (179)
Q Consensus        26 ~~~~~~~~~i~g~~~~~~~i~~-~~~~~~~~~yrr   59 (179)
                      ..+||..|+|+||+.|++|+|. ++|.|-|+|.-|
T Consensus       360 n~s~LstgaIaGIsvavvvvVgglvGfLcWwf~cr  394 (397)
T PF03302_consen  360 NKSGLSTGAIAGISVAVVVVVGGLVGFLCWWFICR  394 (397)
T ss_pred             ccccccccceeeeeehhHHHHHHHHHHHhhheeec
Confidence            4578999999999999887666 777777776554

>PF05808 Podoplanin: Podoplanin; InterPro: IPR008783 This family consists of several mammalian podoplanin-like proteins which are thought to control specifically the unique shape of podocytes []

Probab=91.75  E-value=0.05  Score=45.32  Aligned_cols=37  Identities=19%  Similarity=0.445  Sum_probs=0.0

Q ss_pred             CCCCCCCceeeeeechhhhHHHHHHhhhcceeeeeec
Q psy14481         23 PWSGEGGVNVAMISGISFGALALVTLFGAVSFIMYRR   59 (179)
Q Consensus        23 ~~~~~~~~~~~~i~g~~~~~~~i~~~~~~~~~~~yrr   59 (179)
                      ++...+|+..+.+.||..|.++-++++|++-|++.||
T Consensus       119 tt~ek~GL~T~tLVGIIVGVLlaIG~igGIIivvvRK  155 (162)
T PF05808_consen  119 TTVEKDGLSTVTLVGIIVGVLLAIGFIGGIIIVVVRK  155 (162)
T ss_dssp             -------------------------------------
T ss_pred             cccccCCcceeeeeeehhhHHHHHHHHhheeeEEeeh
Confidence            3456789999999999999999999999999999998

; GO: 0016021 integral to membrane; PDB: 3IET_X.

>PF08693 SKG6: Transmembrane alpha-helix domain; InterPro: IPR014805 SKG6 and AXL2 are membrane proteins that show polarised intracellular localisation [, ]

Probab=87.34  E-value=0.68  Score=30.54  Aligned_cols=30  Identities=30%  Similarity=0.561  Sum_probs=23.8

Q ss_pred             eeeeechhhhHHHHHHhhhcceeeeeeccc
Q psy14481         32 VAMISGISFGALALVTLFGAVSFIMYRRYR   61 (179)
Q Consensus        32 ~~~i~g~~~~~~~i~~~~~~~~~~~yrr~~   61 (179)
                      ++.--|......+|+..++.+.|++|||+.
T Consensus        11 vaIa~~VvVPV~vI~~vl~~~l~~~~rR~k   40 (40)
T PF08693_consen   11 VAIAVGVVVPVGVIIIVLGAFLFFWYRRKK   40 (40)
T ss_pred             EEEEEEEEechHHHHHHHHHHhheEEeccC
Confidence            344457788888999999999999999863

This entry represents the highly conserved transmembrane alpha-helical domain found in these proteins [, ]. The full-length AXL2 protein has a negative regulatory function in cytokinesis [].

>PF01034 Syndecan: Syndecan domain; InterPro: IPR001050 The syndecans are transmembrane proteoglycans which are involved in the organisation of cytoskeleton and/or actin microfilaments, and have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions [, ]

Probab=84.10  E-value=0.33  Score=34.99  Aligned_cols=32  Identities=25%  Similarity=0.366  Sum_probs=0.4

Q ss_pred             CCCceeeeeechhhhHHHHHHhhhcceeeeeeccc
Q psy14481         27 EGGVNVAMISGISFGALALVTLFGAVSFIMYRRYR   61 (179)
Q Consensus        27 ~~~~~~~~i~g~~~~~~~i~~~~~~~~~~~yrr~~   61 (179)
                      ..++-+|+|+|+..|.   ++++..+.|++||-|.
T Consensus         7 ~~~vlaavIaG~Vvgl---l~ailLIlf~iyR~rk   38 (64)
T PF01034_consen    7 RSEVLAAVIAGGVVGL---LFAILLILFLIYRMRK   38 (64)
T ss_dssp             ---------------------------------S-
T ss_pred             cchHHHHHHHHHHHHH---HHHHHHHHHHHHHHHh
Confidence            3444488888876544   4444556788888543

Structurally, these proteins consist of four separate domains: A signal sequence; An extracellular domain (ectodomain) of variable length whose sequence is not evolutionary conserved in the various forms of syndecans. The ectodomain contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A transmembrane region; A highly conserved cytoplasmic domain of about 30 to 35 residues, which could interact with cytoskeletal proteins. The proteins known to belong to this family are: Syndecan 1. Syndecan 2 or fibroglycan. Syndecan 3 or neuroglycan or N-syndecan. Syndecan 4 or amphiglycan or ryudocan. Drosophila syndecan. Caenorhabditis elegans probable syndecan (F57C7.3). Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion [, ].; GO: 0008092 cytoskeletal protein binding, 0016020 membrane; PDB: 1EJQ_B 1EJP_B 1YBO_C 1OBY_Q.

>PF12301 CD99L2: CD99 antigen like protein 2; InterPro: IPR022078 This family of proteins is found in eukaryotes

Probab=82.52  E-value=0.51  Score=39.34  Aligned_cols=35  Identities=34%  Similarity=0.648  Sum_probs=23.4

Q ss_pred             CCCCceeeeeechhhhHHHHHHhhhcc-eeeeeecccC
Q psy14481         26 GEGGVNVAMISGISFGALALVTLFGAV-SFIMYRRYRW   62 (179)
Q Consensus        26 ~~~~~~~~~i~g~~~~~~~i~~~~~~~-~~~~yrr~~~   62 (179)
                      ..+....+.|+||.  +.|.++++|++ |||-|.||.|
T Consensus       108 ~~~~~~~g~IaGIv--sav~valvGAvsSyiaYqkKKl  143 (169)
T PF12301_consen  108 QDGEAEAGTIAGIV--SAVVVALVGAVSSYIAYQKKKL  143 (169)
T ss_pred             cccCcccchhhhHH--HHHHHHHHHHHHHHHHHHhhcc
Confidence            34556678889987  44455566654 5666988877

Proteins in this family are typically between 165 and 237 amino acids in length. CD99L2 and CD99 are involved in trans-endothelial migration of neutrophils in vitro and in the recruitment of neutrophils into inflamed peritoneum.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	179
1g9l_A	144	Solution Structure Of The Pabc Domain Of Human Poly		7e-30
2rqg_B	83	Structure Of Gspt1ERF3A-Pabc Length = 83		2e-26
3pth_A	82	The Pabc1 Mlle Domain Bound To The Variant Pam2 Mot		6e-25
1jgn_A	98	Solution Structure Of The C-Terminal Pabc Domain Of		7e-25
3kus_A	88	Crystal Structure Of The Mlle Domain Of Poly(A)-Bin		1e-24
3kur_A	79	Crystal Structure Of The Mlle Domain Of Poly(A)-Bin		2e-24
2x04_A	80	Crystal Structure Of The Pabc-Tnrc6c Complex Length		1e-23
4ive_A	98	Crystal Structure Of A Polyadenylate-binding Protei		1e-22
2dyd_A	85	Solution Structure Of The Pabc Domain From Triticum		1e-10
1nmr_A	85	Solution Structure Of C-Terminal Domain From Trypan		2e-10
3ntw_A	65	Structure Of The Mlle Domain Of Edd In Complex With		8e-08
1i2t_A	61	X-Ray Structure Of The Human Hyperplastic Discs Pro		2e-07

>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A) Binding Protein Length = 144

Iteration: 1
 Score =  126 bits (316), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 61/74 (82%), Positives = 69/74 (93%)
Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct: 44  AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 103
Query: 148 MLEHNESLKSKVEE 161
           MLE  ESL+SKV+E
Sbjct: 104 MLESPESLRSKVDE 117

>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc Length = 83

Iteration: 1
 Score =  114 bits (286), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/69 (81%), Positives = 64/69 (92%)
Query: 93  GQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHN 152
           GQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  
Sbjct: 1   GQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESP 60
Query: 153 ESLKSKVEE 161
           ESL+SKV+E
Sbjct: 61  ESLRSKVDE 69

>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of Larp4b Length = 82

Iteration: 1
 Score =  110 bits (274), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 54/67 (80%), Positives = 62/67 (92%)
Query: 95  EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 154
           EPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ES
Sbjct: 4   EPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPES 63
Query: 155 LKSKVEE 161
           L+SKV+E
Sbjct: 64  LRSKVDE 70

>pdb|1JGN|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human Poly(A)-Binding Protein In Complex With The Peptide From Paip2 Length = 98

Iteration: 1
 Score =  109 bits (273), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 53/66 (80%), Positives = 61/66 (92%)
Query: 96  PLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESL 155
           PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL
Sbjct: 6   PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESL 65
Query: 156 KSKVEE 161
           +SKV+E
Sbjct: 66  RSKVDE 71

>pdb|3KUS|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding Protein In Complex With The Binding Region Of Paip2 Length = 88

Iteration: 1
 Score =  108 bits (271), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 53/66 (80%), Positives = 61/66 (92%)
Query: 96  PLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESL 155
           PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL
Sbjct: 6   PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESL 65
Query: 156 KSKVEE 161
           +SKV+E
Sbjct: 66  RSKVDE 71

>pdb|3KUR|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding Protein Length = 79

Iteration: 1
 Score =  108 bits (269), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 53/66 (80%), Positives = 61/66 (92%)
Query: 96  PLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESL 155
           PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL
Sbjct: 6   PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESL 65
Query: 156 KSKVEE 161
           +SKV+E
Sbjct: 66  RSKVDE 71

>pdb|2X04|A Chain A, Crystal Structure Of The Pabc-Tnrc6c Complex Length = 80

Iteration: 1
 Score =  105 bits (263), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 52/65 (80%), Positives = 60/65 (92%)
Query: 97  LTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLK 156
           LT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL+
Sbjct: 6   LTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLR 65
Query: 157 SKVEE 161
           SKV+E
Sbjct: 66  SKVDE 70

>pdb|4IVE|A Chain A, Crystal Structure Of A Polyadenylate-binding Protein 3 (pabpc3) From Homo Sapiens At 2.30 A Resolution Length = 98

Iteration: 1
 Score =  102 bits (254), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/70 (72%), Positives = 59/70 (84%)
Query: 92  QGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEH 151
           QGQE LT++ LA+A PQ+QKQ LGERLFPLIQ  +P LAGKITG LLEIDN+ELLY LE 
Sbjct: 2   QGQETLTASRLASAPPQKQKQXLGERLFPLIQAXHPTLAGKITGXLLEIDNSELLYXLES 61
Query: 152 NESLKSKVEE 161
            ESL+SKV+E
Sbjct: 62  PESLRSKVDE 71

>pdb|2DYD|A Chain A, Solution Structure Of The Pabc Domain From Triticum Aevestium Poly(A)-Binding Protein Length = 85

Iteration: 1
 Score = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/63 (46%), Positives = 47/63 (74%)
Query: 99  STMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSK 158
           ++ LA + P+ Q+ MLGE L+PL+ ++  + A K+TGMLLE+D  E+L++LE  ++LK+K
Sbjct: 11  ASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPDALKAK 70
Query: 159 VEE 161
           V E
Sbjct: 71  VAE 73

>pdb|1NMR|A Chain A, Solution Structure Of C-Terminal Domain From Trypanosoma Cruzi Poly(A)-Binding Protein Length = 85

Iteration: 1
 Score = 61.6 bits (148), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/70 (48%), Positives = 47/70 (67%), Gaps = 2/70 (2%)
Query: 92  QGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEH 151
           QGQ    ST+LA   P++QK +LGERL+  I  + P  A K+TGMLLE+DN E+L +L+ 
Sbjct: 7   QGQN--LSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDT 64
Query: 152 NESLKSKVEE 161
              L +KV+E
Sbjct: 65  PGLLDAKVQE 74

>pdb|3NTW|A Chain A, Structure Of The Mlle Domain Of Edd In Complex With A Pam2 Peptide From Paip1 Length = 65

Iteration: 1
 Score = 53.1 bits (126), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 28/52 (53%), Positives = 38/52 (73%)
Query: 110 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 161
            +Q LGERL+P +Q M P  A KITGMLLE+  A+LL +L   +SL+++VEE
Sbjct: 6   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVEE 57

>pdb|1I2T|A Chain A, X-Ray Structure Of The Human Hyperplastic Discs Protein: An Ortholog Of The C-Terminal Domain Of Poly(A)-Binding Protein Length = 61

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/52 (51%), Positives = 38/52 (73%)
Query: 110 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 161
            +Q LGERL+P +Q M P  A KITGMLLE+  A+LL +L   +SL+++V+E
Sbjct: 1   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDE 52

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	179
1ifw_A	92	Polyadenylate-binding protein, cytoplasmic and nuc	1e-37
1nmr_A	85	Poly(A)-binding protein; all helical domain, pepti	5e-36
2dyd_A	85	Poly(A)-binding protein; alpha helical protein, RN	3e-34
1i2t_A	61	HYD protein; four alpha-helical domain, ligase; 1.	9e-31
3kuj_A	88	Polyadenylate-binding protein 1; protein-protein c	2e-30
1g9l_A	144	Polyadenylate-binding protein 1; all-helical domai	1e-29

>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical domain, RNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.144.1.1 Length = 92

 Score =  124 bits (312), Expect = 1e-37
 Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 2/88 (2%)

Query: 94  QEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMY--PELAGKITGMLLEIDNAELLYMLEH 151
             P  +        Q+Q+Q LGE+L+  +       E AGKITGM+L++   E+  +LE 
Sbjct: 4   GSPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLES 63

Query: 152 NESLKSKVEEAVAVLQAHQAKQAAVKKE 179
           +E  +   +EA A  ++ + +Q    ++
Sbjct: 64  DELFEQHYKEASAAYESFKKEQEQQTEQ 91

>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1 Length = 85

 Score =  119 bits (300), Expect = 5e-36
 Identities = 36/84 (42%), Positives = 51/84 (60%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
              +  Q    ST+LA   P++QK +LGERL+  I  + P  A K+TGMLLE+DN E+L 
Sbjct: 1   GSSLASQGQNLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILN 60

Query: 148 MLEHNESLKSKVEEAVAVLQAHQA 171
           +L+    L +KV+EA+ VL  H  
Sbjct: 61  LLDTPGLLDAKVQEALEVLNRHMN 84

>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding protein; NMR {Triticum aestivum} Length = 85

 Score =  115 bits (289), Expect = 3e-34
 Identities = 33/82 (40%), Positives = 55/82 (67%)

Query: 91  VQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLE 150
           +       ++ LA + P+ Q+ MLGE L+PL+ ++  + A K+TGMLLE+D  E+L++LE
Sbjct: 3   LGSPIGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLE 62

Query: 151 HNESLKSKVEEAVAVLQAHQAK 172
             ++LK+KV EA+ VL++ Q  
Sbjct: 63  SPDALKAKVAEAMEVLRSAQQH 84

>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo sapiens} SCOP: a.144.1.1 PDB: 3ntw_A Length = 61

 Score =  105 bits (264), Expect = 9e-31
 Identities = 30/60 (50%), Positives = 44/60 (73%)

Query: 110 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH 169
            +Q LGERL+P +Q M P  A KITGMLLE+  A+LL +L   +SL+++V+EA+ ++ AH
Sbjct: 1   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAH 60

>3kuj_A Polyadenylate-binding protein 1; protein-protein complex, methylation, mRNA processing, mRNA nucleus, phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A 3pkn_A 2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A Length = 88

 Score =  105 bits (263), Expect = 2e-30
 Identities = 66/83 (79%), Positives = 75/83 (90%)

Query: 93  GQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHN 152
              PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  
Sbjct: 3   LGSPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESP 62

Query: 153 ESLKSKVEEAVAVLQAHQAKQAA 175
           ESL+SKV+EAVAVLQAHQAK+AA
Sbjct: 63  ESLRSKVDEAVAVLQAHQAKEAA 85

>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A 1jh4_A Length = 144

 Score =  105 bits (262), Expect = 1e-29
 Identities = 74/88 (84%), Positives = 83/88 (94%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct: 44  AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 103

Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAA 175
           MLE  ESL+SKV+EAVAVLQAHQAK+AA
Sbjct: 104 MLESPESLRSKVDEAVAVLQAHQAKEAA 131

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	179
1g9l_A	144	Polyadenylate-binding protein 1; all-helical domai	100.0
1nmr_A	85	Poly(A)-binding protein; all helical domain, pepti	100.0
3kuj_A	88	Polyadenylate-binding protein 1; protein-protein c	100.0
1ifw_A	92	Polyadenylate-binding protein, cytoplasmic and nuc	100.0
2dyd_A	85	Poly(A)-binding protein; alpha helical protein, RN	99.97
1i2t_A	61	HYD protein; four alpha-helical domain, ligase; 1.	99.96
2k1k_A	38	Ephrin type-A receptor 1; EPHA1, receptor tyrosine	97.01
2k9y_A	41	Ephrin type-A receptor 2; receptor tyrosine kinase	90.62
2ks1_B	44	Epidermal growth factor receptor; ERBB1, ERBB2, tr	89.53
2l2t_A	44	Receptor tyrosine-protein kinase ERBB-4; transmemb	89.37

>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A 1jh4_A

Probab=100.00  E-value=4.8e-36  Score=239.80  Aligned_cols=109  Identities=69%  Similarity=0.884  Sum_probs=96.4

Q ss_pred             cccccCCCCCCCCCC-CC--CccccccccCCCCCCChhHhhcCChHHHHHHhhhhhhhhHhhhCCCCCCCceeeccCCCh
Q psy14481         66 QTLSDKCSNPDSSGY-ID--DSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDN  142 (179)
Q Consensus        66 q~YS~~vRNP~s~~~-iq--DSt~~~~~~~g~epl~~s~La~a~peeQKq~LGErLyplV~~l~p~~AgKITGMLLEmd~  142 (179)
                      .+|+.+++||+.+.. .+  ...+++++++|++|+++++|+++++++||+||||+|||+|+.++|++||||||||||||+
T Consensus        19 ~~y~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~pl~as~La~a~p~eQkq~LGE~LyplV~~~~p~~A~KITGMLLEmd~   98 (144)
T 1g9l_A           19 YKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDN   98 (144)
T ss_dssp             CCCCCTTSCCCCCCCCCSCCCCSSCSCCCCSCCCCSHHHHTTCTTTTTTTTTTSSSHHHHHHHTTSCCSSHHHHTTTSSS
T ss_pred             cCCCCCCCCCCCcccccccccCCCCCCCCCCcchhhHHHHHcCCHHHHHHHHHHHHHHHHHHhCccccchhhhhhccCCH
Confidence            467889999952111 11  223477899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhcChHHHHHHHHHHHHHHHHHHHhHH
Q psy14481        143 AELLYMLEHNESLKSKVEEAVAVLQAHQAKQA  174 (179)
Q Consensus       143 sELL~mLes~e~L~~KV~EA~~vL~~~q~~~~  174 (179)
                      +|||+||+|+|+|++||+||++||++|++++.
T Consensus        99 ~ElL~LLes~e~L~~kV~EA~~vL~~~~~~~~  130 (144)
T 1g9l_A           99 SELLHMLESPESLRSKVDEAVAVLQAHQAKEA  130 (144)
T ss_dssp             HHHHHHHHCTTHHHHHHHHHHHHHHTTSSSTT
T ss_pred             HHHHHHHcCHHHHHHHHHHHHHHHHHHHhccc
Confidence            99999999999999999999999999997654

>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1

Probab=100.00  E-value=8.3e-36  Score=220.56  Aligned_cols=82  Identities=44%  Similarity=0.643  Sum_probs=79.1

Q ss_pred             ccCCCCCCChhHhhcCChHHHHHHhhhhhhhhHhhhCCCCCCCceeeccCCChHHHHHhhcChHHHHHHHHHHHHHHHHH
Q psy14481         90 HVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH  169 (179)
Q Consensus        90 ~~~g~epl~~s~La~a~peeQKq~LGErLyplV~~l~p~~AgKITGMLLEmd~sELL~mLes~e~L~~KV~EA~~vL~~~  169 (179)
                      .++|++|+++++|++++|++|||+|||+|||+|++++|++||||||||||||++||++||+|+++|++||+||++||++|
T Consensus         3 ~~~~~~~l~~s~La~a~p~~Qkq~LGE~LyplV~~~~p~~AgKITGMLLEmd~~ElL~Lle~~e~L~~kV~EA~~vL~~~   82 (85)
T 1nmr_A            3 SLASQGQNLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDAKVQEALEVLNRH   82 (85)
T ss_dssp             CCCCCCCTTHHHHTTCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHCSCTHHHHHHTTCCTHHHHHHHHHHHHHHTTCC
T ss_pred             CccCCCccCHHHHHcCChHHHHHHHHHHHHHHHHHhCccccchhhHhHhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHh
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             HH
Q psy14481        170 QA  171 (179)
Q Consensus       170 q~  171 (179)
                      ++
T Consensus        83 ~~   84 (85)
T 1nmr_A           83 MN   84 (85)
T ss_dssp             CC
T ss_pred             hc
Confidence            53

>3kuj_A Polyadenylate-binding protein 1; protein-protein complex, methylation, mRNA processing, mRNA nucleus, phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A 3pkn_A 2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A

Probab=100.00  E-value=1.2e-34  Score=215.45  Aligned_cols=83  Identities=81%  Similarity=1.062  Sum_probs=76.4

Q ss_pred             CCCChhHhhcCChHHHHHHhhhhhhhhHhhhCCCCCCCceeeccCCChHHHHHhhcChHHHHHHHHHHHHHHHHHHHhHH
Q psy14481         95 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQA  174 (179)
Q Consensus        95 epl~~s~La~a~peeQKq~LGErLyplV~~l~p~~AgKITGMLLEmd~sELL~mLes~e~L~~KV~EA~~vL~~~q~~~~  174 (179)
                      +|+++++|++++|++|||+|||+|||+|++++|++||||||||||||++|+++||+|+++|++||+||++||++|+.++.
T Consensus         5 ~~l~~s~la~a~p~~Qkq~LGE~Lyp~V~~~~p~~A~KITGMLLEmd~~Ell~lle~~e~L~~kV~EA~~vL~~~~~~~~   84 (88)
T 3kuj_A            5 SPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA   84 (88)
T ss_dssp             -CCCHHHHHTSCHHHHHHHHHHHHHHHHHHHCTTTHHHHHHHHTTSCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             ccchHHHHHcCCHHHHHHHHHHHhHHHHHhhCCCccchhhhHhhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHhhhc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             hhh
Q psy14481        175 AVK  177 (179)
Q Consensus       175 ~~~  177 (179)
                      ++|
T Consensus        85 ~~~   87 (88)
T 3kuj_A           85 AQK   87 (88)
T ss_dssp             ---
T ss_pred             cCC
Confidence            665

>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical domain, RNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.144.1.1

Probab=100.00  E-value=1.4e-34  Score=216.65  Aligned_cols=82  Identities=30%  Similarity=0.440  Sum_probs=78.1

Q ss_pred             CCCChhHhhcCChHHHHHHhhhhhhhhHhh--hCCCCCCCceeeccCCChHHHHHhhcChHHHHHHHHHHHHHHHHHHHh
Q psy14481         95 EPLTSTMLAAAQPQEQKQMLGERLFPLIQR--MYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAK  172 (179)
Q Consensus        95 epl~~s~La~a~peeQKq~LGErLyplV~~--l~p~~AgKITGMLLEmd~sELL~mLes~e~L~~KV~EA~~vL~~~q~~  172 (179)
                      .|+++++|++++|++||+||||+|||+|+.  ++|++||||||||||||++||++||+|+++|++||+||++||++|++.
T Consensus         5 ~p~~a~~la~~~p~~Qkq~LGE~LyplV~~~~~~pelAgKITGMLLEmd~~ElL~LLes~e~L~~kV~EA~~vL~~~~~~   84 (92)
T 1ifw_A            5 SPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAAYESFKKE   84 (92)
T ss_dssp             CSSCCSSCCSCSCHHHHHHHHHHHHHHHGGGCCCHHHHHHHHHHHTTSCHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CccchHHHhcCChHHHHHHHHHHHHHHHHHhhcCccccchhhHhHhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHh
Confidence            688999999999999999999999999999  999999999999999999999999999999999999999999999975


Q ss_pred             HHhh
Q psy14481        173 QAAV  176 (179)
Q Consensus       173 ~~~~  176 (179)
                      +.+|
T Consensus        85 ~~~~   88 (92)
T 1ifw_A           85 QEQQ   88 (92)
T ss_dssp             CTTS
T ss_pred             hhhh
Confidence            5443

>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding protein; NMR {Triticum aestivum}

Probab=99.97  E-value=8.8e-34  Score=209.71  Aligned_cols=77  Identities=43%  Similarity=0.698  Sum_probs=73.9

Q ss_pred             CCChhHhhcCChHHHHHHhhhhhhhhHhhhCCCCCCCceeeccCCChHHHHHhhcChHHHHHHHHHHHHHHHHHHHh
Q psy14481         96 PLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAK  172 (179)
Q Consensus        96 pl~~s~La~a~peeQKq~LGErLyplV~~l~p~~AgKITGMLLEmd~sELL~mLes~e~L~~KV~EA~~vL~~~q~~  172 (179)
                      ++++++|++++|++||++|||+|||+|++++|++||||||||||||++||++||+|+|+|++||+||++||++|+++
T Consensus         8 ~~~as~La~~~p~~Qkq~LGE~LyplV~~~~p~~AgKITGMLLEmd~~Ell~Lles~e~L~~kv~EA~~vL~~~~~~   84 (85)
T 2dyd_A            8 GALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPDALKAKVAEAMEVLRSAQQH   84 (85)
T ss_dssp             TTSCHHHHCCCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHCHHHHHHHTTCSHHHHHHHHHHHHHHTSCSSC
T ss_pred             hhhHHHHHcCCHHHHHHHHHHHHHHHHHHhCccccchhhhhhhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHhhc
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999988753

>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo sapiens} SCOP: a.144.1.1 PDB: 3ntw_A

Probab=99.96  E-value=2.7e-30  Score=180.72  Aligned_cols=61  Identities=49%  Similarity=0.835  Sum_probs=59.6

Q ss_pred             HHHHhhhhhhhhHhhhCCCCCCCceeeccCCChHHHHHhhcChHHHHHHHHHHHHHHHHHH
Q psy14481        110 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQ  170 (179)
Q Consensus       110 QKq~LGErLyplV~~l~p~~AgKITGMLLEmd~sELL~mLes~e~L~~KV~EA~~vL~~~q  170 (179)
                      |||+|||+|||+|++++|++||||||||||||++|+++||+|+++|++||+||++||++|+
T Consensus         1 qkq~LGe~Lyp~V~~~~p~~A~KITGMLLE~d~~ell~ll~~~e~L~~kv~EA~~vl~~~~   61 (61)
T 1i2t_A            1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAHG   61 (61)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGHHHHHHHHTTSCHHHHHHHHHCHHHHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHHhCcccccchhhhhccCCHHHHHHHHcCHHHHHHHHHHHHHHHHHcC
Confidence            7999999999999999999999999999999999999999999999999999999999874

>2k1k_A Ephrin type-A receptor 1; EPHA1, receptor tyrosine kinase, dimeric transmembrane domain, ATP-binding, glycoprotein, nucleotide-binding; NMR {Homo sapiens} PDB: 2k1l_A

Probab=97.01  E-value=9e-05  Score=46.99  Aligned_cols=35  Identities=23%  Similarity=0.231  Sum_probs=30.7

Q ss_pred             CCCCceeeeeechhhhHHHHHHhhhcceeeeeecc
Q psy14481         26 GEGGVNVAMISGISFGALALVTLFGAVSFIMYRRY   60 (179)
Q Consensus        26 ~~~~~~~~~i~g~~~~~~~i~~~~~~~~~~~yrr~   60 (179)
                      +.++++.|+|+||..|+++-+.++.++.|++||||
T Consensus         4 ~~~~ls~GaIAGiVvG~v~gv~li~~l~~~~~rrr   38 (38)
T 2k1k_A            4 VSRGLTGGEIVAVIFGLLLGAALLLGILVFRSRRA   38 (38)
T ss_dssp             SSTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCceeeeehHHHHHHHHHHHHHHHHeecC
Confidence            34678889999999999999999999999999886

>2k9y_A Ephrin type-A receptor 2; receptor tyrosine kinase, membrane protein, dimeric transmembrane domain, ephrin receptor, ATP-binding, glycoprotein; NMR {Homo sapiens}

Probab=90.62  E-value=0.064  Score=33.21  Aligned_cols=32  Identities=22%  Similarity=0.315  Sum_probs=20.3

Q ss_pred             CceeeeeechhhhHHHHHHhhhcceeeeeecc
Q psy14481         29 GVNVAMISGISFGALALVTLFGAVSFIMYRRY   60 (179)
Q Consensus        29 ~~~~~~i~g~~~~~~~i~~~~~~~~~~~yrr~   60 (179)
                      +.+.++|.|...++++++.++..+.+++.|||
T Consensus         9 ~~~~~~I~~~vv~Gv~ll~~iv~~~~~~~rRr   40 (41)
T 2k9y_A            9 GSGNLAVIGGVAVGVVLLLVLAGVGFFIHRRR   40 (41)
T ss_dssp             CCSSTHHHHHHHHHHHHHHHHHHHHHSSSSSC
T ss_pred             CCceEEEEeehhHHHHHHHHHHHHheeEeeec
Confidence            34567788888888888774444445544543

>2ks1_B Epidermal growth factor receptor; ERBB1, ERBB2, transmembrane, heterodimer, complex, tyrosine receptor, bicelles, transferase; NMR {Homo sapiens}

Probab=89.53  E-value=0.065  Score=34.84  Aligned_cols=32  Identities=22%  Similarity=0.198  Sum_probs=22.9

Q ss_pred             eeeeeechhhhHHHHHHhhhcceeeeeecccC
Q psy14481         31 NVAMISGISFGALALVTLFGAVSFIMYRRYRW   62 (179)
Q Consensus        31 ~~~~i~g~~~~~~~i~~~~~~~~~~~yrr~~~   62 (179)
                      ++++|+|-..|+++++.+++.+.|++.|||+-
T Consensus         9 ~~~~IA~gVVgGv~~~~ii~~~~~~~~RRr~~   40 (44)
T 2ks1_B            9 KIPSIATGMVGALLLLLVVALGIGLFMRRRHI   40 (44)
T ss_dssp             CSSSSTHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             CcceEEeehhHHHHHHHHHHHHHHHHhhhhHh
Confidence            46677888888888888877666666666544

>2l2t_A Receptor tyrosine-protein kinase ERBB-4; transmembrane dimer, membrane domain, membrane protei; NMR {Homo sapiens}

Probab=89.37  E-value=0.059  Score=35.16  Aligned_cols=34  Identities=18%  Similarity=0.265  Sum_probs=25.5

Q ss_pred             CceeeeeechhhhHHHHHHhhhcceeeeeecccC
Q psy14481         29 GVNVAMISGISFGALALVTLFGAVSFIMYRRYRW   62 (179)
Q Consensus        29 ~~~~~~i~g~~~~~~~i~~~~~~~~~~~yrr~~~   62 (179)
                      +-++++|+|-..|+++++.+++.+.|++.|||+-
T Consensus         6 ~s~~~aIA~gVVgGv~~v~ii~~~~~~~~RRRr~   39 (44)
T 2l2t_A            6 HARTPLIAAGVIGGLFILVIVGLTFAVYVRRKSI   39 (44)
T ss_dssp             SCSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCS
T ss_pred             CCCcceEEEeehHHHHHHHHHHHHHHHHhhhhhh
Confidence            4567788998898888888888776666666554

---

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	179
d1g9la_	144	a.144.1.1 (A:) poly(A) binding protein {Human (Hom	1e-42
d1nmra_	85	a.144.1.1 (A:) poly(A) binding protein {Protozoan	4e-40
d1ifwa_	92	a.144.1.1 (A:) poly(A) binding protein {Baker's ye	6e-35
d1i2ta_	61	a.144.1.1 (A:) hyperplastic discs protein {Human (	3e-32

>d1g9la_ a.144.1.1 (A:) poly(A) binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 144

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  137 bits (346), Expect = 1e-42
 Identities = 75/92 (81%), Positives = 84/92 (91%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct: 44  AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 103

Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAAVKKE 179
           MLE  ESL+SKV+EAVAVLQAHQAK+AA K  
Sbjct: 104 MLESPESLRSKVDEAVAVLQAHQAKEAAQKAV 135

>d1nmra_ a.144.1.1 (A:) poly(A) binding protein {Protozoan (Trypanosoma cruzi) [TaxId: 5693]} Length = 85

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Protozoan (Trypanosoma cruzi) [TaxId: 5693]

 Score =  128 bits (324), Expect = 4e-40
 Identities = 38/83 (45%), Positives = 54/83 (65%), Gaps = 2/83 (2%)

Query: 88  AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
           ++  QGQ    ST+LA   P++QK +LGERL+  I  + P  A K+TGMLLE+DN E+L 
Sbjct: 3   SLASQGQN--LSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILN 60

Query: 148 MLEHNESLKSKVEEAVAVLQAHQ 170
           +L+    L +KV+EA+ VL  H 
Sbjct: 61  LLDTPGLLDAKVQEALEVLNRHM 83

>d1ifwa_ a.144.1.1 (A:) poly(A) binding protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 92

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  116 bits (291), Expect = 6e-35
 Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 2/86 (2%)

Query: 96  PLTSTMLAAAQPQEQKQMLGERLFPLIQRMY--PELAGKITGMLLEIDNAELLYMLEHNE 153
           P  +        Q+Q+Q LGE+L+  +       E AGKITGM+L++   E+  +LE +E
Sbjct: 6   PRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDE 65

Query: 154 SLKSKVEEAVAVLQAHQAKQAAVKKE 179
             +   +EA A  ++ + +Q    ++
Sbjct: 66  LFEQHYKEASAAYESFKKEQEQQTEQ 91

>d1i2ta_ a.144.1.1 (A:) hyperplastic discs protein {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: hyperplastic discs protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  108 bits (271), Expect = 3e-32
 Identities = 30/60 (50%), Positives = 44/60 (73%)

Query: 110 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH 169
            +Q LGERL+P +Q M P  A KITGMLLE+  A+LL +L   +SL+++V+EA+ ++ AH
Sbjct: 1   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAH 60

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	179
d1g9la_	144	poly(A) binding protein {Human (Homo sapiens) [Tax	100.0
d1nmra_	85	poly(A) binding protein {Protozoan (Trypanosoma cr	99.97
d1ifwa_	92	poly(A) binding protein {Baker's yeast (Saccharomy	99.96
d1i2ta_	61	hyperplastic discs protein {Human (Homo sapiens) [	99.95

>d1g9la_ a.144.1.1 (A:) poly(A) binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.2e-38  Score=252.88  Aligned_cols=115  Identities=69%  Similarity=0.886  Sum_probs=102.7

Q ss_pred             CCc-ccccCCCCCCCCCCCC---CccccccccCCCCCCChhHhhcCChHHHHHHhhhhhhhhHhhhCCCCCCCceeeccC
Q psy14481         64 KPQ-TLSDKCSNPDSSGYID---DSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLE  139 (179)
Q Consensus        64 ~pq-~YS~~vRNP~s~~~iq---DSt~~~~~~~g~epl~~s~La~a~peeQKq~LGErLyplV~~l~p~~AgKITGMLLE  139 (179)
                      -|+ .|++++|||..++..+   ...+++++++|++++|+++|++++++|||++|||+|||+|++++|++|+||||||||
T Consensus        16 ~P~~ky~~~~rnp~~~~~~~p~~~~~~p~~~~~~q~pltas~la~a~p~eQkq~LGE~Lyp~I~~~~p~~A~KITGMLLE   95 (144)
T d1g9la_          16 VPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLE   95 (144)
T ss_dssp             CCCCCCCCTTSCCCCCCCCCSCCCCSSCSCCCCSCCCCSHHHHTTCTTTTTTTTTTSSSHHHHHHHTTSCCSSHHHHTTT
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccHHHHhhCCHHHHHHHHHHHHHHHHHHhChhhccchhhhhhc
Confidence            344 6999999996222111   344699999999999999999999999999999999999999999999999999999


Q ss_pred             CChHHHHHhhcChHHHHHHHHHHHHHHHHHHHhHHhhhc
Q psy14481        140 IDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQAAVKK  178 (179)
Q Consensus       140 md~sELL~mLes~e~L~~KV~EA~~vL~~~q~~~~~~~~  178 (179)
                      ||++|||+||+|++.|++||+||++||++|+.++.+++.
T Consensus        96 md~~ell~lL~~~~~L~~kV~EA~~vL~~~~~~~~~~~~  134 (144)
T d1g9la_          96 IDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAAQKA  134 (144)
T ss_dssp             SSSHHHHHHHHCTTHHHHHHHHHHHHHHTTSSSTTCCCC
T ss_pred             CCHHHHHHHHcCHHHHHHHHHHHHHHHHHHhccHHHHHh
Confidence            999999999999999999999999999999998876553

>d1nmra_ a.144.1.1 (A:) poly(A) binding protein {Protozoan (Trypanosoma cruzi) [TaxId: 5693]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Protozoan (Trypanosoma cruzi) [TaxId: 5693]

Probab=99.97  E-value=1.7e-33  Score=206.36  Aligned_cols=81  Identities=47%  Similarity=0.708  Sum_probs=76.9

Q ss_pred             ccccCCCCCCChhHhhcCChHHHHHHhhhhhhhhHhhhCCCCCCCceeeccCCChHHHHHhhcChHHHHHHHHHHHHHHH
Q psy14481         88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQ  167 (179)
Q Consensus        88 ~~~~~g~epl~~s~La~a~peeQKq~LGErLyplV~~l~p~~AgKITGMLLEmd~sELL~mLes~e~L~~KV~EA~~vL~  167 (179)
                      +++.+|++  ++++|++++|++|||+|||+|||+|++++|++||||||||||||++||++||+|++.|+.||+||++||+
T Consensus         3 ~~~~~g~~--~a~~la~~~p~eqK~~LGE~Lyp~V~~~~p~~AgKITGMLLEm~~~ell~lL~~~~~L~~kV~EA~~vL~   80 (85)
T d1nmra_           3 SLASQGQN--LSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDAKVQEALEVLN   80 (85)
T ss_dssp             CCCCCCCT--THHHHTTCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHCSCTHHHHHHTTCCTHHHHHHHHHHHHHHTT
T ss_pred             cccccchH--HHHHHhhCCHHHHHHHHHHHHHHHHHHHCcccccchhHHhhCCCHHHHHHHHCCHHHHHHHHHHHHHHHH
Confidence            35667776  8999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHH
Q psy14481        168 AHQ  170 (179)
Q Consensus       168 ~~q  170 (179)
                      +|+
T Consensus        81 ~h~   83 (85)
T d1nmra_          81 RHM   83 (85)
T ss_dssp             CCC
T ss_pred             Hhc
Confidence            876

>d1ifwa_ a.144.1.1 (A:) poly(A) binding protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.96  E-value=1.1e-31  Score=199.10  Aligned_cols=83  Identities=30%  Similarity=0.436  Sum_probs=77.6

Q ss_pred             CCCChhHhhcCChHHHHHHhhhhhhhhHhhh--CCCCCCCceeeccCCChHHHHHhhcChHHHHHHHHHHHHHHHHHHHh
Q psy14481         95 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRM--YPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAK  172 (179)
Q Consensus        95 epl~~s~La~a~peeQKq~LGErLyplV~~l--~p~~AgKITGMLLEmd~sELL~mLes~e~L~~KV~EA~~vL~~~q~~  172 (179)
                      .|.++++++.+++++||++|||+|||+|+++  +|++||||||||||||++||++||+|++.|+.||+||++||++|+++
T Consensus         5 ~p~~~~~~~~~~~~~qk~~LGe~Lyp~V~~~~~~pe~A~KITGMLLEm~~~ell~lL~~~~~L~~kV~EA~~vL~~~~~~   84 (92)
T d1ifwa_           5 SPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAAYESFKKE   84 (92)
T ss_dssp             CSSCCSSCCSCSCHHHHHHHHHHHHHHHGGGCCCHHHHHHHHHHHTTSCHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCChHHHhhcCHHHHHHHHHHHHHHHHHHhccCccccccchhhhcCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHhc
Confidence            3578889999999999999999999999998  68999999999999999999999999999999999999999999998


Q ss_pred             HHhhh
Q psy14481        173 QAAVK  177 (179)
Q Consensus       173 ~~~~~  177 (179)
                      +.+..
T Consensus        85 ~~~~~   89 (92)
T d1ifwa_          85 QEQQT   89 (92)
T ss_dssp             CTTSC
T ss_pred             ccccc
Confidence            76543

>d1i2ta_ a.144.1.1 (A:) hyperplastic discs protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: hyperplastic discs protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=4.2e-30  Score=178.20  Aligned_cols=61  Identities=49%  Similarity=0.835  Sum_probs=59.7

Q ss_pred             HHHHhhhhhhhhHhhhCCCCCCCceeeccCCChHHHHHhhcChHHHHHHHHHHHHHHHHHH
Q psy14481        110 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQ  170 (179)
Q Consensus       110 QKq~LGErLyplV~~l~p~~AgKITGMLLEmd~sELL~mLes~e~L~~KV~EA~~vL~~~q  170 (179)
                      |||+|||+|||+|++++|++||||||||||||++|+++||+|++.|++||+||++||++|.
T Consensus         1 qk~~LGE~Ly~~V~~~~p~~A~KITGMLLEm~~~ell~lL~~~~~L~~kV~EA~~vL~~hg   61 (61)
T d1i2ta_           1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAHG   61 (61)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGHHHHHHHHTTSCHHHHHHHHHCHHHHHHHHHHHHHHHHHHC
T ss_pred             ChHHHHHHhHHHHHHHChhhhcchhHHHhcCCHHHHHHHHCCHHHHHHHHHHHHHHHHHcC
Confidence            7999999999999999999999999999999999999999999999999999999999883