RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2868
(289 letters)
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 44.6 bits (106), Expect = 4e-05
Identities = 27/130 (20%), Positives = 42/130 (32%), Gaps = 8/130 (6%)
Query: 125 VTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKP-----PVHTSHVTKPP 179
V + PV + V T P V + VT+ P + H V +P
Sbjct: 894 VVEEPVVVAEPQPEEVVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQ 953
Query: 180 VHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPP 239
T+ + T+ V V +P V T +P V + V +
Sbjct: 954 DETADIE-EAAETAEV--VVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEAT 1010
Query: 240 VHTSHVTKPL 249
V +H T P+
Sbjct: 1011 VEHNHATAPM 1020
Score = 41.2 bits (97), Expect = 6e-04
Identities = 27/138 (19%), Positives = 42/138 (30%), Gaps = 13/138 (9%)
Query: 121 THSYVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPV 180
TH V PV + + H V +P T+ + + V P
Sbjct: 915 THPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVAEPE 974
Query: 181 HTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPV 240
+ P V V T +P V + V + V +H T P +T+ P
Sbjct: 975 VVAQPAAPVVAEVAA---EVETVTAVEPEVAPAQVPEATVEHNHATAP------MTRAPA 1025
Query: 241 HTSHVTKPLHISHVTRWV 258
+V + S W
Sbjct: 1026 -PEYVPEAPRHSD---WQ 1039
>gnl|CDD|225549 COG3004, NhaA, Na+/H+ antiporter [Inorganic ion transport and
metabolism].
Length = 390
Score = 32.7 bits (75), Expect = 0.20
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 239 PVHTSHVTKPLH-ISHVTR-WVSYLIYPL 265
P+ T PL + H WV++ I PL
Sbjct: 241 PLKTKEGESPLERLEHALHPWVAFFILPL 269
>gnl|CDD|220340 pfam09678, Caa3_CtaG, Cytochrome c oxidase caa3 assembly factor
(Caa3_CtaG). Members of this family are the CtaG
protein required for assembly of active cytochrome c
oxidase of the caa3 type, as found in Bacillus subtilis.
Length = 241
Score = 30.7 bits (70), Expect = 0.68
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 83 ICYKTTCSHIHMLQNHLFTLHMLQNHLFTLHML 115
+ Y T S + + LF+ HM+Q HL L M+
Sbjct: 32 LLYLATSSPLDAYGHALFSAHMVQ-HL-LLSMV 62
>gnl|CDD|177614 PHA03377, PHA03377, EBNA-3C; Provisional.
Length = 1000
Score = 30.4 bits (68), Expect = 1.3
Identities = 22/85 (25%), Positives = 24/85 (28%), Gaps = 6/85 (7%)
Query: 126 TKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHV 185
T P V S P PPV T P V + T P T P
Sbjct: 551 TPPKVSPSDRGPPK------ASPPVMAPPSTGPRVMATPSTGPRDMAPPSTGPRQQAKCK 604
Query: 186 TKPPVHTSHVTKPPVHTSHVTKPPV 210
PP H +PP P V
Sbjct: 605 DGPPASGPHEKQPPSSAPRDMAPSV 629
Score = 30.4 bits (68), Expect = 1.3
Identities = 22/85 (25%), Positives = 24/85 (28%), Gaps = 6/85 (7%)
Query: 136 TKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHV 195
T P V S P PPV T P V + T P T P
Sbjct: 551 TPPKVSPSDRGPPK------ASPPVMAPPSTGPRVMATPSTGPRDMAPPSTGPRQQAKCK 604
Query: 196 TKPPVHTSHVTKPPVHTSHVTKPPV 220
PP H +PP P V
Sbjct: 605 DGPPASGPHEKQPPSSAPRDMAPSV 629
Score = 30.4 bits (68), Expect = 1.3
Identities = 22/85 (25%), Positives = 24/85 (28%), Gaps = 6/85 (7%)
Query: 146 TKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHV 205
T P V S P PPV T P V + T P T P
Sbjct: 551 TPPKVSPSDRGPPK------ASPPVMAPPSTGPRVMATPSTGPRDMAPPSTGPRQQAKCK 604
Query: 206 TKPPVHTSHVTKPPVHTSHVTKPPV 230
PP H +PP P V
Sbjct: 605 DGPPASGPHEKQPPSSAPRDMAPSV 629
Score = 30.4 bits (68), Expect = 1.3
Identities = 22/85 (25%), Positives = 24/85 (28%), Gaps = 6/85 (7%)
Query: 156 TKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHV 215
T P V S P PPV T P V + T P T P
Sbjct: 551 TPPKVSPSDRGPPK------ASPPVMAPPSTGPRVMATPSTGPRDMAPPSTGPRQQAKCK 604
Query: 216 TKPPVHTSHVTKPPVHTSHVTKPPV 240
PP H +PP P V
Sbjct: 605 DGPPASGPHEKQPPSSAPRDMAPSV 629
Score = 28.5 bits (63), Expect = 4.9
Identities = 22/91 (24%), Positives = 25/91 (27%), Gaps = 6/91 (6%)
Query: 166 TKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHV 225
T P V S P PPV T P V + T P T P
Sbjct: 551 TPPKVSPSDRGPPK------ASPPVMAPPSTGPRVMATPSTGPRDMAPPSTGPRQQAKCK 604
Query: 226 TKPPVHTSHVTKPPVHTSHVTKPLHISHVTR 256
PP H +PP P + R
Sbjct: 605 DGPPASGPHEKQPPSSAPRDMAPSVVRMFLR 635
>gnl|CDD|165431 PHA03160, PHA03160, hypothetical protein; Provisional.
Length = 499
Score = 29.7 bits (66), Expect = 1.9
Identities = 22/86 (25%), Positives = 33/86 (38%), Gaps = 10/86 (11%)
Query: 118 HLFTHSYVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTK 177
H F++ Y + P H P + PP+ S + P+ HV +
Sbjct: 382 HHFSNPY-SFDPGHAPFFRYAPYGAPKNDHHLL-------PPLACSQ--QLPMQPLHVQQ 431
Query: 178 PPVHTSHVTKPPVHTSHVTKPPVHTS 203
P+ HV PP+ HV +P V S
Sbjct: 432 APMQAPHVAPPPMQPPHVQQPRVLPS 457
Score = 29.7 bits (66), Expect = 2.2
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 164 HVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTS 213
H PP+ S + P+ HV + P+ HV PP+ HV +P V S
Sbjct: 410 HHLLPPLACSQ--QLPMQPLHVQQAPMQAPHVAPPPMQPPHVQQPRVLPS 457
Score = 29.7 bits (66), Expect = 2.2
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 174 HVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTS 223
H PP+ S + P+ HV + P+ HV PP+ HV +P V S
Sbjct: 410 HHLLPPLACSQ--QLPMQPLHVQQAPMQAPHVAPPPMQPPHVQQPRVLPS 457
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 29.9 bits (67), Expect = 1.9
Identities = 28/167 (16%), Positives = 46/167 (27%), Gaps = 11/167 (6%)
Query: 126 TKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHV 185
+PPV T PP +P +P +PP
Sbjct: 2879 ARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPR 2938
Query: 186 TKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHV 245
+PP+ + S P + V P +
Sbjct: 2939 PQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLT- 2997
Query: 246 TKPLHISHVTRWVSYLIY------PLLTLKIHKTIQKSGEIENTDRD 286
+S V+ W S L P ++LK +T+ + E++D D
Sbjct: 2998 --GHSLSRVSSWASSLALHEETDPPPVSLK--QTLWPPDDTEDSDAD 3040
>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional.
Length = 991
Score = 30.0 bits (67), Expect = 1.9
Identities = 26/133 (19%), Positives = 40/133 (30%), Gaps = 1/133 (0%)
Query: 117 NHLFTHSYVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVT-KPPVHTSHV 175
N L + P V + H+ P T T P+ + T +PP
Sbjct: 644 NVLVFPTPHQPPQVEITPYKPTWTQIGHIPYQPSPTGANTMLPIQWAPGTMQPPPRAPTP 703
Query: 176 TKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHV 235
+PP + P + +PP +PP +PP +PP
Sbjct: 704 MRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGR 763
Query: 236 TKPPVHTSHVTKP 248
+PP P
Sbjct: 764 ARPPAAAPGAPTP 776
>gnl|CDD|216257 pfam01034, Syndecan, Syndecan domain. Syndecans are transmembrane
heparin sulfate proteoglycans which are implicated in
the binding of extracellular matrix components and
growth factors.
Length = 207
Score = 29.3 bits (66), Expect = 1.9
Identities = 16/87 (18%), Positives = 23/87 (26%), Gaps = 8/87 (9%)
Query: 128 PPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPV-HTSHVT 186
+ PV TS +T S+ T TS T P V T T
Sbjct: 59 GATPSDDEDSEPVTTSA------TPPKLTTTSSSPSNDTTT-ASTSTKTSPTVSTTVTTT 111
Query: 187 KPPVHTSHVTKPPVHTSHVTKPPVHTS 213
P T ++ ++
Sbjct: 112 TSPSETDTEEATTTVSTETPTEGGSSA 138
Score = 29.3 bits (66), Expect = 1.9
Identities = 16/87 (18%), Positives = 23/87 (26%), Gaps = 8/87 (9%)
Query: 138 PPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPV-HTSHVT 196
+ PV TS +T S+ T TS T P V T T
Sbjct: 59 GATPSDDEDSEPVTTSA------TPPKLTTTSSSPSNDTTT-ASTSTKTSPTVSTTVTTT 111
Query: 197 KPPVHTSHVTKPPVHTSHVTKPPVHTS 223
P T ++ ++
Sbjct: 112 TSPSETDTEEATTTVSTETPTEGGSSA 138
Score = 29.3 bits (66), Expect = 1.9
Identities = 16/87 (18%), Positives = 23/87 (26%), Gaps = 8/87 (9%)
Query: 148 PPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPV-HTSHVT 206
+ PV TS +T S+ T TS T P V T T
Sbjct: 59 GATPSDDEDSEPVTTSA------TPPKLTTTSSSPSNDTTT-ASTSTKTSPTVSTTVTTT 111
Query: 207 KPPVHTSHVTKPPVHTSHVTKPPVHTS 233
P T ++ ++
Sbjct: 112 TSPSETDTEEATTTVSTETPTEGGSSA 138
Score = 29.3 bits (66), Expect = 1.9
Identities = 16/87 (18%), Positives = 23/87 (26%), Gaps = 8/87 (9%)
Query: 158 PPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPV-HTSHVT 216
+ PV TS +T S+ T TS T P V T T
Sbjct: 59 GATPSDDEDSEPVTTSA------TPPKLTTTSSSPSNDTTT-ASTSTKTSPTVSTTVTTT 111
Query: 217 KPPVHTSHVTKPPVHTSHVTKPPVHTS 243
P T ++ ++
Sbjct: 112 TSPSETDTEEATTTVSTETPTEGGSSA 138
Score = 28.6 bits (64), Expect = 3.4
Identities = 16/78 (20%), Positives = 22/78 (28%), Gaps = 8/78 (10%)
Query: 127 KPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPV-HTSHVTKPPVHTSHV 185
PV TS +T S+ T TS T P V T T P T
Sbjct: 68 SEPVTTSA------TPPKLTTTSSSPSNDTTT-ASTSTKTSPTVSTTVTTTTSPSETDTE 120
Query: 186 TKPPVHTSHVTKPPVHTS 203
++ ++
Sbjct: 121 EATTTVSTETPTEGGSSA 138
Score = 27.4 bits (61), Expect = 6.8
Identities = 19/82 (23%), Positives = 23/82 (28%), Gaps = 10/82 (12%)
Query: 168 PPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPV-HTSHVT 226
+ PV TS +T S+ T TS T P V T T
Sbjct: 59 GATPSDDEDSEPVTTSA------TPPKLTTTSSSPSNDTTT-ASTSTKTSPTVSTTVTTT 111
Query: 227 KPPVHTSHVTKPPVHTSHVTKP 248
P T T+ T P
Sbjct: 112 TSPSET--DTEEATTTVSTETP 131
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 29.7 bits (66), Expect = 2.1
Identities = 31/152 (20%), Positives = 47/152 (30%), Gaps = 11/152 (7%)
Query: 127 KPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVH--------TSHVTKP 178
K P H + P S++ PP + P H PP+ S +P
Sbjct: 363 KHPPHLQGPSPFPQMPSNLPPPPALKPLSSLPTHHPPSAHPPPLQLMPQSQPLQSVPAQP 422
Query: 179 PVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKP 238
PV T + PP ++H P H + P + TS P
Sbjct: 423 PVLTQSQSLPPKASTH---PHSGLHSGPPQSPFAQHPFTSGGLPAIGPPPSLPTSTPAAP 479
Query: 239 PVHTSHVTKPLHISHVTRWVSYLIYPLLTLKI 270
P +S P + + PL ++I
Sbjct: 480 PRASSGSQPPGSALPSSGGCAGPGPPLPPIQI 511
>gnl|CDD|216788 pfam01923, Cob_adeno_trans, Cobalamin adenosyltransferase.
Cobalamin adenosyltransferase This family contains the
gene products of PduO and EutT which are both cobalamin
adenosyltransferases. PduO is a protein with
ATP:cob(I)alamin adenosyltransferase activity. The main
role of this protein is the conversion of inactive
cobalamins to AdoCbl for 1,2-propanediol degradation.The
EutT enzyme appears to be an adenosyl transferase,
converting CNB12 to AdoB12.
Length = 162
Score = 28.6 bits (65), Expect = 2.6
Identities = 13/54 (24%), Positives = 18/54 (33%), Gaps = 8/54 (14%)
Query: 67 HLFTHSYVTK--PPVHTFICYKTTCSHIHMLQNHL------FTLHMLQNHLFTL 112
L V K P + + S I + + L L +QN LF L
Sbjct: 12 SLGGGERVPKDDPRIEAYGTVDELNSAIGLARALLPDEDLRELLERIQNDLFDL 65
>gnl|CDD|222831 PHA01747, PHA01747, putative ATP-dependent protease.
Length = 425
Score = 29.0 bits (65), Expect = 3.2
Identities = 24/72 (33%), Positives = 31/72 (43%), Gaps = 11/72 (15%)
Query: 5 HLFTHSYVTKPPVHTFICY-----KTTCSHIHMLQNHLFTHSYVTKPPVHTFICY--KTT 57
LFT S V+K PVH KTT ++ LF Y T+PP + + Y KT
Sbjct: 180 PLFT-SPVSKRPVHIIELSNRGTGKTT---TFVILQELFNFRYYTEPPTYANLVYDAKTN 235
Query: 58 CSHIHMLQNHLF 69
+ L N L
Sbjct: 236 ALGLVFLSNGLI 247
Score = 29.0 bits (65), Expect = 3.2
Identities = 24/72 (33%), Positives = 31/72 (43%), Gaps = 11/72 (15%)
Query: 36 HLFTHSYVTKPPVHTFICY-----KTTCSHIHMLQNHLFTHSYVTKPPVHTFICY--KTT 88
LFT S V+K PVH KTT ++ LF Y T+PP + + Y KT
Sbjct: 180 PLFT-SPVSKRPVHIIELSNRGTGKTT---TFVILQELFNFRYYTEPPTYANLVYDAKTN 235
Query: 89 CSHIHMLQNHLF 100
+ L N L
Sbjct: 236 ALGLVFLSNGLI 247
>gnl|CDD|225873 COG3336, COG3336, Predicted membrane protein [Function unknown].
Length = 299
Score = 28.2 bits (63), Expect = 4.5
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 6/31 (19%)
Query: 85 YKTTCSHIHMLQNHLFTLHMLQNHLFTLHML 115
Y S + + +F+LHM + HML
Sbjct: 60 YGAVGSPVRAYGHAMFSLHMAE------HML 84
>gnl|CDD|219392 pfam07382, HC2, Histone H1-like nucleoprotein HC2. This family
contains the bacterial histone H1-like nucleoprotein HC2
(approximately 200 residues long), which seems to be
found mostly in Chlamydia. HC2 functions in DNA
condensation, although it has been suggested that it
also has other roles.
Length = 187
Score = 27.8 bits (61), Expect = 5.1
Identities = 24/127 (18%), Positives = 29/127 (22%), Gaps = 6/127 (4%)
Query: 127 KPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVH-----TSHVTKPPVHTSHVTKPPVH 181
K + V KP + K V KP + K P K
Sbjct: 12 KTAAKKAAVRKPAAKKAAAKKTVVRKVAAKKPAARKTVAKKTVAAKKPAAKKAAKKAVAK 71
Query: 182 TSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVH 241
KP + K K V V K K V V + P
Sbjct: 72 KVVAKKPVAKKAVAKKATAKKV-AAKKVVAKKTVAKKAAAKKPAAKKAVAKKAVARKPAA 130
Query: 242 TSHVTKP 248
V K
Sbjct: 131 KKAVAKK 137
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 27.9 bits (62), Expect = 8.3
Identities = 16/75 (21%), Positives = 20/75 (26%), Gaps = 3/75 (4%)
Query: 175 VTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSHVTKPPVHTSH 234
+ P + +P S K + K PV T PPV
Sbjct: 360 LVPVPAPQPAKPTAAAPSP--VRPTPAPSTRPKAAAAANIPPKEPV-RETATPPPVPPRP 416
Query: 235 VTKPPVHTSHVTKPL 249
V P HT L
Sbjct: 417 VAPPVPHTPESAPKL 431
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.131 0.436
Gapped
Lambda K H
0.267 0.0703 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,699,301
Number of extensions: 1167675
Number of successful extensions: 1161
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1015
Number of HSP's successfully gapped: 100
Length of query: 289
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 193
Effective length of database: 6,679,618
Effective search space: 1289166274
Effective search space used: 1289166274
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (26.2 bits)