RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3462
(795 letters)
>gnl|CDD|216358 pfam01198, Ribosomal_L31e, Ribosomal protein L31e.
Length = 83
Score = 116 bits (292), Expect = 4e-31
Identities = 40/62 (64%), Positives = 47/62 (75%), Gaps = 1/62 (1%)
Query: 121 NEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGI 180
EVVTR+YTI++ KR V FKKRAPRAIK +R F K M T+DVRID +LNK IWS+GI
Sbjct: 1 EEVVTREYTINLRKR-KGVPFKKRAPRAIKEIRKFAAKHMKTDDVRIDPKLNKAIWSRGI 59
Query: 181 NN 182
N
Sbjct: 60 RN 61
>gnl|CDD|199209 cd00463, Ribosomal_L31e, Eukaryotic/archaeal ribosomal protein L31.
Ribosomal protein L31e, which is present in archaea and
eukaryotes, binds the 23S rRNA and is one of six protein
components encircling the polypeptide exit tunnel. It is
a component of the eukaryotic 60S (large) ribosomal
subunit, and the archaeal 50S (large) ribosomal subunit.
Length = 83
Score = 106 bits (266), Expect = 2e-27
Identities = 38/62 (61%), Positives = 45/62 (72%), Gaps = 1/62 (1%)
Query: 121 NEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGI 180
EVV R+YTI++ KR H V KKRAPRAIK +R F K M TEDVRID +LN+ IWS+GI
Sbjct: 2 EEVVEREYTINLRKRKH-VPRKKRAPRAIKEIRKFAAKHMKTEDVRIDPKLNEAIWSRGI 60
Query: 181 NN 182
Sbjct: 61 EK 62
>gnl|CDD|225008 COG2097, RPL31A, Ribosomal protein L31E [Translation, ribosomal
structure and biogenesis].
Length = 89
Score = 87.4 bits (217), Expect = 6e-21
Identities = 31/61 (50%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 122 EVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGIN 181
VV R YTI + R KV KRAPRA+K++R FV + M E+VRID LN+ IW +GI
Sbjct: 5 VVVERIYTIPLR-RAKKVPRTKRAPRAVKIIRKFVARHMKAEEVRIDPSLNEKIWERGIE 63
Query: 182 N 182
Sbjct: 64 K 64
>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain. This domain
is the second of two tandem AAA domains found in a wide
variety of helicase enzymes.
Length = 165
Score = 76.1 bits (188), Expect = 5e-16
Identities = 22/57 (38%), Positives = 35/57 (61%)
Query: 612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQ 668
G ++Y QA R LNQA+GR IRH D+G ++L+D+R +++ + L KW+
Sbjct: 109 GKDGFREYYLPQAIRKLNQAIGRLIRHEDDYGVVILLDERLLTRSYGKLLLKWLPPG 165
>gnl|CDD|234916 PRK01192, PRK01192, 50S ribosomal protein L31e; Reviewed.
Length = 89
Score = 64.2 bits (157), Expect = 1e-12
Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 121 NEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTE--DVRIDTRLNKHIWSK 178
EV R YTI + + + KV KRA RA+K+VR F+ + + V+ID +N+ IW +
Sbjct: 3 KEVEERIYTIPL-RDVKKVPRTKRADRAVKLVREFLARHFKADEDKVKIDPSINEKIWER 61
Query: 179 GINN 182
G
Sbjct: 62 GREK 65
>gnl|CDD|140220 PTZ00193, PTZ00193, 60S ribosomal protein L31; Provisional.
Length = 188
Score = 65.4 bits (159), Expect = 4e-12
Identities = 33/66 (50%), Positives = 44/66 (66%), Gaps = 2/66 (3%)
Query: 115 TKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKH 174
T +KP N ++ + TIH+ K L K F KRAP AIK ++AFV + M T+D RID LN +
Sbjct: 77 TGRKPDN--ISMEATIHLSKLLKKKTFHKRAPIAIKRIKAFVGRLMKTKDNRIDASLNTY 134
Query: 175 IWSKGI 180
IW KG+
Sbjct: 135 IWHKGV 140
>gnl|CDD|233047 TIGR00604, rad3, DNA repair helicase (rad3). All proteins in this
family for which funcitons are known are DNA-DNA
helicases that funciton in the initiation of
transcription and nucleotide excision repair as part of
the TFIIH complex. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 705
Score = 65.1 bits (159), Expect = 8e-11
Identities = 24/67 (35%), Positives = 41/67 (61%), Gaps = 3/67 (4%)
Query: 618 DWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTSSHNT 677
D+Y+ A RA+NQA+GR IRH+ D+G+I+L+D+R+ N ++ L KW++ S +
Sbjct: 641 DFYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDKRYARSNKRKKLPKWIQ---DTIQSSDL 697
Query: 678 FMENLRN 684
+
Sbjct: 698 NGMAISL 704
Score = 43.9 bits (104), Expect = 3e-04
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 41 NCLLESPTGSGKTLALLCSVLAWQRKEKELV-------QQKMFEQRTQDLQKTSFVF 90
+LE P+G+GKT++LL +LA+Q+++ E+ EQ T++L+K
Sbjct: 31 EAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKLMSYR 87
Score = 41.2 bits (97), Expect = 0.002
Identities = 18/52 (34%), Positives = 32/52 (61%), Gaps = 7/52 (13%)
Query: 293 NCLLESPTGSGKTLALLCSVLAWQRKEKELV-------QQKMFEQRTQDLQK 337
+LE P+G+GKT++LL +LA+Q+++ E+ EQ T++L+K
Sbjct: 31 EAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRK 82
>gnl|CDD|214693 smart00488, DEXDc2, DEAD-like helicases superfamily.
Length = 289
Score = 57.4 bits (139), Expect = 8e-09
Identities = 29/105 (27%), Positives = 44/105 (41%), Gaps = 33/105 (31%)
Query: 244 VEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSG 303
FP + YP Q M ++ + ++ K +LESPTG+G
Sbjct: 3 FYFPYEPYPIQYEFMEELKRVLDR-----------------------GKIGILESPTGTG 39
Query: 304 KTLALLCSVLAWQRKEKELVQ----------QKMFEQRTQDLQKI 338
KTL+LLC L W R E +Q E+R ++L+K+
Sbjct: 40 KTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL 84
Score = 56.6 bits (137), Expect = 1e-08
Identities = 23/58 (39%), Positives = 31/58 (53%), Gaps = 10/58 (17%)
Query: 40 KNCLLESPTGSGKTLALLCSVLAWQRKEKELVQ----------QKMFEQRTQDLQKTS 87
K +LESPTG+GKTL+LLC L W R E +Q E+R ++L+K
Sbjct: 28 KIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKLM 85
>gnl|CDD|214694 smart00491, HELICc2, helicase superfamily c-terminal domain.
Length = 142
Score = 54.2 bits (131), Expect = 1e-08
Identities = 17/35 (48%), Positives = 26/35 (74%)
Query: 618 DWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRF 652
+ Y A RAL QA+GR IRH+ D+G ++L+D+R+
Sbjct: 106 EVYLFDAMRALAQAIGRAIRHKNDYGVVVLLDKRY 140
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 54.4 bits (131), Expect = 2e-07
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 618 DWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQ 670
++Y A L QA+GR IR D G I+L+D+R+ +K + L + +
Sbjct: 584 EFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDKRYATKRYGKLLLDSLPPFPK 636
Score = 46.3 bits (110), Expect = 5e-05
Identities = 23/83 (27%), Positives = 33/83 (39%), Gaps = 24/83 (28%)
Query: 239 IGGVKVEFP-VKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLE 297
G + V FP + P Q M V+ + + L+E
Sbjct: 4 DGYLAVAFPGFEPRPEQREMAEAVAEALK-----------------------GGEGLLIE 40
Query: 298 SPTGSGKTLALLCSVLAWQRKEK 320
+PTG+GKTLA L LA+ R+E
Sbjct: 41 APTGTGKTLAYLLPALAYAREEG 63
Score = 45.6 bits (108), Expect = 1e-04
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 14/75 (18%)
Query: 37 NKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDF 96
+ L+E+PTG+GKTLA L LA+ R+E + V + RT+ LQ+
Sbjct: 32 KGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKV---IISTRTKALQE----------- 77
Query: 97 FLLFRERRISDTMVK 111
LL + I + K
Sbjct: 78 QLLEEDLPIHKLLKK 92
>gnl|CDD|217380 pfam03133, TTL, Tubulin-tyrosine ligase family. Tubulins and
microtubules are subjected to several post-translational
modifications of which the reversible
detyrosination/tyrosination of the carboxy-terminal end
of most alpha-tubulins has been extensively analysed.
This modification cycle involves a specific
carboxypeptidase and the activity of the
tubulin-tyrosine ligase (TTL). The true physiological
function of TTL has so far not been established.
Tubulin-tyrosine ligase (TTL) catalyzes the
ATP-dependent post-translational addition of a tyrosine
to the carboxy terminal end of detyrosinated
alpha-tubulin. In normally cycling cells, the
tyrosinated form of tubulin predominates. However, in
breast cancer cells, the detyrosinated form frequently
predominates, with a correlation to tumour
aggressiveness. On the other hand, 3-nitrotyrosine has
been shown to be incorporated, by TTL, into the carboxy
terminal end of detyrosinated alpha-tubulin. This
reaction is not reversible by the carboxypeptidase
enzyme. Cells cultured in 3-nitrotyrosine rich medium
showed evidence of altered microtubule structure and
function, including altered cell morphology, epithelial
barrier dysfunction, and apoptosis. Bacterial homologs
of TTL are predicted to form peptide tags. Some of these
are fused to a 2-oxoglutarate Fe(II)-dependent
dioxygenase domain.
Length = 291
Score = 40.0 bits (94), Expect = 0.003
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 522 CFQLIQLDLMLDEHLNPYVLKVKDTP-----CIEDLVLKRNIFYDTL 563
CF+L D M+DE+L P++L+V +P D LK + D L
Sbjct: 233 CFELYGFDFMIDENLKPWLLEVNASPSLHSTTKLDARLKEQLIDDVL 279
Score = 29.6 bits (67), Expect = 5.5
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 474 MESSVAFDQLIQLDLMLDEHLNPYVLKVKDTP 505
++ +L D M+DE+L P++L+V +P
Sbjct: 227 VQPLYNCFELYGFDFMIDENLKPWLLEVNASP 258
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 37.9 bits (89), Expect = 0.023
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 38 KAKNCLLESPTGSGKTLALLCSVL 61
+ KN L+ SPTGSGKTLA +++
Sbjct: 46 EGKNVLISSPTGSGKTLAAFLAII 69
Score = 37.9 bits (89), Expect = 0.023
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 290 KAKNCLLESPTGSGKTLALLCSVL 313
+ KN L+ SPTGSGKTLA +++
Sbjct: 46 EGKNVLISSPTGSGKTLAAFLAII 69
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 37.2 bits (87), Expect = 0.038
Identities = 29/111 (26%), Positives = 46/111 (41%), Gaps = 34/111 (30%)
Query: 252 PSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLA-LLC 310
Q MM +V H L+E+ TG+GK+LA LL
Sbjct: 260 EGQQEMMKEVYTALRDSEH-----------------------ALIEAGTGTGKSLAYLLP 296
Query: 311 SVLAWQRKEKELV--------QQKMFEQRTQDLQKI-PFRKLKISRLKAKD 352
+ ++KE+ +V QQ++ E+ LQKI PF ++ + LK +
Sbjct: 297 AAYFAKKKEEPVVISTYTIQLQQQLLEKDIPLLQKIFPF-PVEAALLKGRS 346
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 34.9 bits (81), Expect = 0.076
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 12/48 (25%)
Query: 40 KNCLLESPTGSGKTLA----LLCSVLAWQRK--------EKELVQQKM 75
K+ L+++PTGSGKTLA +L ++L + +EL +Q
Sbjct: 15 KDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQIY 62
Score = 34.9 bits (81), Expect = 0.076
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 12/48 (25%)
Query: 292 KNCLLESPTGSGKTLA----LLCSVLAWQRK--------EKELVQQKM 327
K+ L+++PTGSGKTLA +L ++L + +EL +Q
Sbjct: 15 KDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQIY 62
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 35.9 bits (83), Expect = 0.096
Identities = 26/106 (24%), Positives = 47/106 (44%), Gaps = 19/106 (17%)
Query: 295 LLESPTGSGKTLALLCSVLAWQRKEKELV--------QQKMFEQRTQDLQKIPFRKLKIS 346
L+E+PTG+GKTL L L + EK +V Q ++ E+ L +I K+ +
Sbjct: 268 LIEAPTGTGKTLGYLLPALYYAITEKPVVISTNTKVLQSQLLEKDIPLLNEILNFKINAA 327
Query: 347 RLKAKDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKVL 392
+K +N + L + I + + + + K++VL
Sbjct: 328 LIK----GKSNYLS---LGKFSQILKDNTDNYE----FNIFKMQVL 362
Score = 34.0 bits (78), Expect = 0.36
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 623 QAYRALNQALGRCIRHRYDWGAILLVDQRFYSKN 656
A L QALGR IR D G+I+++D+R K
Sbjct: 786 MAIIRLRQALGRLIRRENDRGSIVILDRRLVGKR 819
Score = 31.3 bits (71), Expect = 2.3
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 43 LLESPTGSGKTLALLCSVLAWQRKEKELV 71
L+E+PTG+GKTL L L + EK +V
Sbjct: 268 LIEAPTGTGKTLGYLLPALYYAITEKPVV 296
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 33.2 bits (76), Expect = 0.29
Identities = 18/76 (23%), Positives = 30/76 (39%), Gaps = 13/76 (17%)
Query: 40 KNCLLESPTGSGKTLALLCSVLAWQRKE-----------KELVQQ--KMFEQRTQDLQKT 86
++ +L +PTGSGKTLA L L ++ +EL +Q + ++ L
Sbjct: 25 RDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLK 84
Query: 87 SFVFCGRSDFFLLFRE 102
G R+
Sbjct: 85 VVGLYGGDSKREQLRK 100
Score = 32.8 bits (75), Expect = 0.46
Identities = 28/148 (18%), Positives = 54/148 (36%), Gaps = 24/148 (16%)
Query: 292 KNCLLESPTGSGKTLALLCSVLAWQRKE-----------KELVQQ--KMFEQRTQDLQKI 338
++ +L +PTGSGKTLA L L ++ +EL +Q + ++ L
Sbjct: 25 RDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLK 84
Query: 339 PFRKLKISRLKAKDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKVL------ 392
+ + +G L +TT + D L K + + ++
Sbjct: 85 VVGLYGGDSKREQLRKLESGKTDIL---VTTPGRLLDLLEN--DKLSLSNVDLVILDEAH 139
Query: 393 NGRSKNLVSSIDFILGLLYKGIQTCITT 420
++ +L LL K +Q + +
Sbjct: 140 RLLDGGFGDQLEKLLKLLPKNVQLLLLS 167
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 34.3 bits (79), Expect = 0.31
Identities = 13/22 (59%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 38 KAKNCLLESPTGSGKTL-ALLC 58
+N L+ +PTGSGKTL ALL
Sbjct: 46 SDENVLISAPTGSGKTLIALLA 67
Score = 34.3 bits (79), Expect = 0.31
Identities = 13/22 (59%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 290 KAKNCLLESPTGSGKTL-ALLC 310
+N L+ +PTGSGKTL ALL
Sbjct: 46 SDENVLISAPTGSGKTLIALLA 67
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 34.2 bits (79), Expect = 0.35
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 40 KNCLLESPTGSGKTLALLCSVL 61
+N L+ +PTGSGKT A V+
Sbjct: 38 ENVLIIAPTGSGKTEAAFLPVI 59
Score = 34.2 bits (79), Expect = 0.35
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 292 KNCLLESPTGSGKTLALLCSVL 313
+N L+ +PTGSGKT A V+
Sbjct: 38 ENVLIIAPTGSGKTEAAFLPVI 59
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 32.3 bits (74), Expect = 0.45
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 16/65 (24%)
Query: 292 KNCLLESPTGSGKTLA----LLCSVLAWQRK-------EKELVQQKMFEQRTQDLQKIPF 340
++ LL +PTGSGKTLA +L + + + +EL Q + L+++
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVA-----ERLKELFG 55
Query: 341 RKLKI 345
+K+
Sbjct: 56 EGIKV 60
Score = 31.9 bits (73), Expect = 0.58
Identities = 13/22 (59%), Positives = 17/22 (77%)
Query: 40 KNCLLESPTGSGKTLALLCSVL 61
++ LL +PTGSGKTLA L +L
Sbjct: 1 RDVLLAAPTGSGKTLAALLPIL 22
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 32.1 bits (74), Expect = 1.2
Identities = 10/36 (27%), Positives = 22/36 (61%)
Query: 683 RNFVRRRMEIQLEEERVKREEANLNEEEEVMDDTDR 718
+ RR E+Q E+R+ ++E NL+ + E+++ +
Sbjct: 75 KELRERRNELQKLEKRLLQKEENLDRKLELLEKREE 110
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription
/ Translation, ribosomal structure and biogenesis].
Length = 513
Score = 32.1 bits (73), Expect = 1.4
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 30 LQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA 62
L I ++ L ++ TG+GKT A L +L
Sbjct: 57 LAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQ 89
Score = 32.1 bits (73), Expect = 1.4
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 282 LQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA 314
L I ++ L ++ TG+GKT A L +L
Sbjct: 57 LAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQ 89
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 32.1 bits (74), Expect = 1.5
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 40 KNCLLESPTGSGKTLALLCSVLA 62
++ LL +PTGSGKTLA L
Sbjct: 29 RSGLLIAPTGSGKTLAGFLPSLI 51
Score = 32.1 bits (74), Expect = 1.5
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 292 KNCLLESPTGSGKTLALLCSVLA 314
++ LL +PTGSGKTLA L
Sbjct: 29 RSGLLIAPTGSGKTLAGFLPSLI 51
>gnl|CDD|233879 TIGR02468, sucrsPsyn_pln, sucrose phosphate synthase/possible
sucrose phosphate phosphatase, plant. Members of this
family are sucrose-phosphate synthases of plants. This
enzyme is known to exist in multigene families in
several species of both monocots and dicots. The
N-terminal domain is the glucosyltransferase domain.
Members of this family also have a variable linker
region and a C-terminal domain that resembles sucrose
phosphate phosphatase (SPP) (EC 3.1.3.24) (see
TIGR01485), the next and final enzyme of sucrose
biosynthesis. The SPP-like domain likely serves a
binding and not a catalytic function, as the reported
SPP is always encoded by a distinct protein.
Length = 1050
Score = 31.7 bits (72), Expect = 2.0
Identities = 26/110 (23%), Positives = 47/110 (42%), Gaps = 23/110 (20%)
Query: 664 WVR-NQVQNTSSHNTFMENL--R--NFVRRRMEI-----------QLEEERVKRE-EANL 706
WV+ ++ NT +EN+ R N R++ ++ +LE ER +RE A++
Sbjct: 61 WVKAVATRSPQERNTRLENMCWRIWNLARKKKQLEWEEAQRLAKRRLERERGRREATADM 120
Query: 707 NEE------EEVMDDTDRASSSQESTGGTQSQNSTVMPQRWAYLSLLKKL 750
+E+ +V D A + G +S + + W+ KKL
Sbjct: 121 SEDLSEGEKGDVAGDISVAGGEPSTKGRLPRISSNLEMETWSDQQKEKKL 170
>gnl|CDD|225497 COG2946, COG2946, Putative phage replication protein RstA [DNA
replication, recombination, and repair].
Length = 377
Score = 31.3 bits (71), Expect = 2.0
Identities = 10/22 (45%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 651 RFYSKNSQQG--LSKWVRNQVQ 670
R Y K Q G S WVR +V+
Sbjct: 229 RIYEKGKQLGDKDSPWVRFEVE 250
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 31.0 bits (71), Expect = 2.4
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 683 RNFVRRRMEIQLEEERVKREEANLNEEEEVMDDTDRASSSQE 724
R RR E+Q E R+ + E L+ + E +D + +E
Sbjct: 69 RELKERRNELQRLERRLLQREETLDRKMESLDKKEENLEKKE 110
>gnl|CDD|220710 pfam10351, Apt1, Golgi-body localisation protein domain. This is
the C-terminus of a family of proteins conserved from
plants to humans. The plant members are localised to the
Golgi proteins and appear to regulate membrane
trafficking, as they are required for rapid vesicle
accumulation at the tip of the pollen tube. The
C-terminus probably contains the Golgi localisation
signal and it is well-conserved.
Length = 451
Score = 31.1 bits (71), Expect = 2.9
Identities = 23/115 (20%), Positives = 41/115 (35%), Gaps = 12/115 (10%)
Query: 690 MEIQLEEERVK---------REEANLNEEEEVMDDTDRASSSQESTGGTQSQNST--VMP 738
++I+LEEE K R+ + E+ + + + S S+ G++ +ST
Sbjct: 276 LKIKLEEETGKKLMEYLFPGRDSSLSEEDSDSSKREEDSDISSSSSSGSRRSSSTSRSSS 335
Query: 739 QRWAYLSLLKKLSPLAPTWGPPLKIQSVPQVIFHKPCDNKSIFKLISIKYMLIRD 793
+ LS LS + + + D+ S KYM R
Sbjct: 336 SSSSLLSSSSILSK-SSDKSKDKRFSLKLSKSEKEESDDLEEMISRSSKYMSFRY 389
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 30.5 bits (69), Expect = 3.1
Identities = 18/94 (19%), Positives = 31/94 (32%), Gaps = 25/94 (26%)
Query: 558 IFYDTLMLCDVQTKETKHRDSVKQVMGKGNLELCKGVFWTRFPNTCQYSVVYPTGLLKGG 617
+ +DT L D + K+ +HR + + K +L V W L+K
Sbjct: 90 VLWDTPGLGDGKDKDAEHRQLYRDYLPKLDL-----VLW----------------LIKAD 128
Query: 618 DWYQIQAYRALNQALGRCIRHRYDWGAILLVDQR 651
D L + + R + +V Q
Sbjct: 129 DRALGTDEDFLRDVIILGLDKR----VLFVVTQA 158
>gnl|CDD|213361 cd12827, EcCorA_ZntB-like_u2, uncharacterized bacterial subfamily
of the Escherichia coli CorA-Salmonella typhimurium ZntB
family. A uncharacterized subfamily of the Escherichia
coli CorA-Salmonella typhimurium ZntB (EcCorA-ZntB_like)
family of the MIT superfamily of essential membrane
proteins involved in transporting divalent cations
(uptake or efflux) across membranes.The EcCorA-ZntB-like
family includes the Mg2+ transporters Escherichia coli
and Salmonella typhimurium CorAs, which can also
transport Co2+, and Ni2+. Structures of the
intracellular domain of EcCorA-ZntB-like family members,
Vibrio parahaemolyticus and Salmonella typhimurium ZntB,
form funnel-shaped homopentamers, the tip of the funnel
is formed from two C-terminal transmembrane (TM) helices
from each monomer, and the large opening of the funnel
from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport through Salmonella typhimurium CorA. Natural
variants such as GVN and GIN, such as occur in some ZntB
family proteins, may be associated with the transport of
different divalent cations, such as zinc and cadmium.
The functional diversity of MIT transporters may also be
due to minor structural differences regulating gating,
substrate selection, and transport.
Length = 289
Score = 30.5 bits (70), Expect = 3.3
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 7/56 (12%)
Query: 386 VDKLKVLNGRSKNLVSSIDFILGLLYKGIQ---TCITTINQQ----EDELRQSTKK 434
+D ++ + S F+L +LY+ + IN++ E ELR+STK
Sbjct: 89 LDDFLEGRVKNFDTSSKTRFLLQILYRIATSYLKYLRQINKERDELEQELRKSTKN 144
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 30.1 bits (69), Expect = 5.2
Identities = 14/22 (63%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 41 NCLLESPTGSGKTLALLCSVLA 62
N LL PTGSGKT LL LA
Sbjct: 110 NILLIGPTGSGKT--LLAQTLA 129
Score = 30.1 bits (69), Expect = 5.2
Identities = 14/22 (63%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 293 NCLLESPTGSGKTLALLCSVLA 314
N LL PTGSGKT LL LA
Sbjct: 110 NILLIGPTGSGKT--LLAQTLA 129
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 30.1 bits (68), Expect = 5.8
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 18/65 (27%)
Query: 268 PNHFLKYSSC----KILH--------------LQVIQGCNKAKNCLLESPTGSGKTLALL 309
P L +SSC K+L +Q I ++ L+ + TGSGKT + L
Sbjct: 117 PPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFL 176
Query: 310 CSVLA 314
+++
Sbjct: 177 VPIIS 181
Score = 29.8 bits (67), Expect = 7.3
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 18/65 (27%)
Query: 16 PNYFLKYSSC----KILH--------------LQVIQGCNKAKNCLLESPTGSGKTLALL 57
P L +SSC K+L +Q I ++ L+ + TGSGKT + L
Sbjct: 117 PPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFL 176
Query: 58 CSVLA 62
+++
Sbjct: 177 VPIIS 181
>gnl|CDD|217779 pfam03885, DUF327, Protein of unknown function (DUF327). The
proteins in this family are around 140-170 residues in
length. The proteins contain many conserved residues.
with the most conserved motifs found in the central and
C-terminal region. The function of these proteins is
unknown.
Length = 146
Score = 28.7 bits (65), Expect = 7.5
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 8/60 (13%)
Query: 351 KDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKVLNGRSKNLVSSIDFILGLL 410
K S + ++ T + I+++ +EL + D L +LN ID I GLL
Sbjct: 90 KSRSFDRRGRTRIYTIVKVIDEKLEELTEELLDEEKDNLDILN--------KIDEIKGLL 141
>gnl|CDD|182031 PRK09694, PRK09694, helicase Cas3; Provisional.
Length = 878
Score = 29.8 bits (67), Expect = 7.8
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 43 LLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQ 81
++E+PTGSGKT A L AW+ ++ L +F TQ
Sbjct: 305 IIEAPTGSGKTEAAL--AYAWRLIDQGLADSIIFALPTQ 341
Score = 29.8 bits (67), Expect = 7.8
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 295 LLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQ 333
++E+PTGSGKT A L AW+ ++ L +F TQ
Sbjct: 305 IIEAPTGSGKTEAAL--AYAWRLIDQGLADSIIFALPTQ 341
>gnl|CDD|221408 pfam12072, DUF3552, Domain of unknown function (DUF3552). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria, archaea and eukaryotes.
This domain is about 200 amino acids in length. This
domain is found associated with pfam00013, pfam01966.
This domain has a single completely conserved residue A
that may be functionally important.
Length = 201
Score = 29.0 bits (66), Expect = 8.3
Identities = 11/46 (23%), Positives = 26/46 (56%)
Query: 688 RRMEIQLEEERVKREEANLNEEEEVMDDTDRASSSQESTGGTQSQN 733
RR E+Q +E+R+ ++E L+ ++E ++ + + +E + Q
Sbjct: 76 RRNELQRQEKRLLQKEETLDRKDESLEKKEESLEEKEKELAARQQQ 121
>gnl|CDD|203903 pfam08312, cwf21, cwf21 domain. The cwf21 family is involved in
mRNA splicing. It has been isolated as a subcomplex of
the splicosome in Schizosaccharomyces pombe. The
function of the cwf21 domain is to bind directly to the
spliceosomal protein Prp8. Mutations in the cwf21 domain
prevent Prp8 from binding. The structure of this domain
has recently been solved which shows this domain to be
composed of two alpha helices.
Length = 46
Score = 26.4 bits (59), Expect = 8.5
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 687 RRRMEIQLEEERVKREEANLNEEE 710
+R +E++ E R K EE L+EEE
Sbjct: 6 KREIEVKCLELRDKLEEQGLSEEE 29
>gnl|CDD|227396 COG5064, SRP1, Karyopherin (importin) alpha [Intracellular
trafficking and secretion].
Length = 526
Score = 29.5 bits (66), Expect = 9.4
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 680 ENLRNFVRRRMEIQLEEERVKREEANLNEEEEVMDDTDRASSSQ 723
+ LR RRR E Q+E + KREE LN+ + D ++ A SS
Sbjct: 23 DELR---RRREEQQVELRKQKREE-LLNKRRNLADVSEEAESSF 62
>gnl|CDD|201951 pfam01749, IBB, Importin beta binding domain. This family consists
of the importin alpha (karyopherin alpha), importin beta
(karyopherin beta) binding domain. The domain mediates
formation of the importin alpha beta complex; required
for classical NLS import of proteins into the nucleus,
through the nuclear pore complex and across the nuclear
envelope. Also in the alignment is the NLS of importin
alpha which overlaps with the IBB domain.
Length = 97
Score = 27.3 bits (61), Expect = 9.9
Identities = 14/51 (27%), Positives = 22/51 (43%)
Query: 687 RRRMEIQLEEERVKREEANLNEEEEVMDDTDRASSSQESTGGTQSQNSTVM 737
RRR E+ +E + KREE L + D A E G + + ++
Sbjct: 25 RRREEVGVELRKNKREEQLLKRRNVGLPPEDGAEPESELDGSSDADQLSLE 75
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 0.134 0.393
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 38,666,035
Number of extensions: 3702517
Number of successful extensions: 3613
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3600
Number of HSP's successfully gapped: 78
Length of query: 795
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 690
Effective length of database: 6,280,432
Effective search space: 4333498080
Effective search space used: 4333498080
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: 63 (28.0 bits)