RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10458
(563 letters)
>gnl|CDD|143392 cd05402, NT_PAP_TUTase, Nucleotidyltransferase (NT) domain of
poly(A) polymerases and terminal uridylyl transferases.
Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail
synthesis, and terminal uridylyl transferases (TUTases)
uridylate RNA. PAPs in this subgroup include human PAP
alpha, mouse testis-specific cytoplasmic PAP beta, human
nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4
and-5, Schizosaccharomyces pombe caffeine-induced death
proteins -1, and -14, Caenorhabditis elegans Germ Line
Development-2, and Chlamydomonas reinhardtii MUT68. This
family also includes human U6 snRNA-specific TUTase1,
and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This
family belongs to the Pol beta-like NT superfamily. In
the majority of enzymes in this superfamily, two
carboxylates, Dx[D/E], together with a third more distal
carboxylate, coordinate two divalent metal cations
involved in a two-metal ion mechanism of nucleotide
addition. For the majority of proteins in this family,
these carboxylate residues are conserved.
Length = 114
Score = 88.4 bits (220), Expect = 3e-21
Identities = 35/144 (24%), Positives = 55/144 (38%), Gaps = 30/144 (20%)
Query: 159 LRFLVAYQVELALSGLFPLCAIFPFGSSVNNFGKLGCDLDLVLQLDLQSQGDNDQCRLMF 218
R V +++ + FP ++PFGS V G G D+DL L
Sbjct: 1 KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGP-------------- 46
Query: 219 HCKSSLGSERSQTLRHLETVGDLLQLFLPGCSQLFLPGCSQVKRILGARVPIIKYNHDMS 278
+ R L + LL+ +V+ I+ ARVPIIK+ +
Sbjct: 47 -------NHRVDREDFLRKLAKLLKKS---------GEVVEVEPIINARVPIIKFVDKPT 90
Query: 279 ALECDLSMTNLTALYMAELLYLFG 302
+E D+S NL + +LL +
Sbjct: 91 GIEVDISFNNLNGIRNTKLLRAYV 114
>gnl|CDD|227585 COG5260, TRF4, DNA polymerase sigma [DNA replication,
recombination, and repair].
Length = 482
Score = 72.9 bits (179), Expect = 1e-13
Identities = 90/433 (20%), Positives = 154/433 (35%), Gaps = 105/433 (24%)
Query: 137 NTITQQMTTLHNITKMNDINTRLRFLVAYQVELALSGLFPLCAIFPFGSSVNNFGKLGCD 196
+ +T ++ ++ +D + R + ++ L FP + FGS+ D
Sbjct: 55 DELTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSD 114
Query: 197 LDLVLQLDLQSQGDNDQCR---LMFHCKSSLGSERSQTLRHLETVGDLLQLFLPGCSQLF 253
+DL + D +G + L H ++ +
Sbjct: 115 IDLCIISD--PRGYKETRNAGSLASHLFKKNLAKEVVVVST------------------- 153
Query: 254 LPGCSQVKRILGARVPIIKYNHDMSALECDLSMTNLTALYMAELLYLFGEIDWRVRPLVF 313
ARVPIIK S L CD+S N + A+L+ + + D R+RPLV
Sbjct: 154 ------------ARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVL 201
Query: 314 TIKKWAKDINLTNPTPGRWITNFSLTLLVLFYLQSVKVLPPLKLLIDEASLKDRRISEDG 373
IK W K L + G +++++++ +VL +LQ P L D L
Sbjct: 202 IIKHWLKRRALNDVATGT-LSSYTISCMVLSFLQMH----PPFLFFDNGLLS-------- 248
Query: 374 VNCTFVRDITKLQFHPSIPEQSTDSLTTLLFGFFEFYS-QYDFNNQGISLYLGSPI-PKP 431
P ++ D+L L FFE Y ++++ +S+ G PK
Sbjct: 249 ---------------PLKYNKNIDNLGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPKY 293
Query: 432 EHGALYINNPL---------ERGLNVSKNVSFEELERLKVEVR------NASWTLESTAN 476
E G L + P +R ++S VSF + +R N +TL S
Sbjct: 294 EKGWLKPSKPNSLSIQDPGTDRNNDISA-VSFNIKDIKAAFIRAFELLSNKLFTLTSA-- 350
Query: 477 SNNKPSHTPSESWGLLELF-------KKQNLSEKAKSVFFSEKSRPKERMVSV------E 523
+++GLL F ++L E+ S + + P ER V +
Sbjct: 351 -------IKHDAYGLLIEFNEASYSNTSRSLKEEYDS-IYEKAPIPPERYNKVDPYIIRK 402
Query: 524 DLFSTETSEDSQV 536
L ++ Q
Sbjct: 403 CLILPDSDMSLQY 415
>gnl|CDD|217750 pfam03828, PAP_assoc, Cid1 family poly A polymerase. This domain
is found in poly(A) polymerases and has been shown to
have polynucleotide adenylyltransferase activity.
Proteins in this family have been located to both the
nucleus and the cytoplasm.
Length = 59
Score = 45.3 bits (108), Expect = 2e-06
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 398 SLTTLLFGFFEFYSQY-DFNNQGISLYLGSPIPKPEHGALYINN 440
+L LL GFFE+Y + D+ IS+ G + K E G L
Sbjct: 1 NLGELLIGFFEYYGREFDYEKVVISIRTGGALSKKEKGWLKDGR 44
>gnl|CDD|144583 pfam01043, SecA_PP_bind, SecA preprotein cross-linking domain. The
SecA ATPase is involved in the insertion and retraction
of preproteins through the plasma membrane. This domain
has been found to cross-link to preproteins, thought to
indicate a role in preprotein binding. The pre-protein
cross-linking domain is comprised of two sub domains
that are inserted within the ATPase domain.
Length = 113
Score = 28.2 bits (64), Expect = 4.4
Identities = 10/32 (31%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 502 EKAKSVFFSEKSRPK-ERMVSVEDLFSTETSE 532
EK++ V +E+ K E+++ +E+L+ E E
Sbjct: 29 EKSRQVELTEEGIEKAEKLLGIENLYDPENIE 60
>gnl|CDD|177602 PHA03365, PHA03365, hypothetical protein; Provisional.
Length = 419
Score = 28.9 bits (65), Expect = 7.5
Identities = 27/131 (20%), Positives = 50/131 (38%), Gaps = 23/131 (17%)
Query: 254 LPGCSQVKRILGARVPIIKYNHDMSALECDLSMTNLTALYMAELLYLFGEIDWRVRPLVF 313
LP C V +IL ++P ++ + + + T Y FG+ D V+
Sbjct: 65 LPPCPSVGQILKKQIP--NFSFNSTTYGSRGTTTA---------FYAFGDEDNPVKIKPM 113
Query: 314 TIKKWAKDIN--LTNPTPGRWITNFSLTLLVLFYLQSVKVLPP----LKLLIDEASLK-D 366
++ ++I L NP I SL FY+ + ++ L+ L D + +
Sbjct: 114 FVESSDQEIILRLLNPLELM-IPAGSLK----FYILPITLVKLDGLYLRCLPDRSPIIMT 168
Query: 367 RRISEDGVNCT 377
S++G
Sbjct: 169 TSCSQEGTRLN 179
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
0.320 0.135 0.401
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,819,576
Number of extensions: 2650933
Number of successful extensions: 2040
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2036
Number of HSP's successfully gapped: 13
Length of query: 563
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 461
Effective length of database: 6,413,494
Effective search space: 2956620734
Effective search space used: 2956620734
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 (21.8 bits)
S2: 62 (27.5 bits)