RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1204
(71 letters)
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 28.2 bits (64), Expect = 0.24
Identities = 20/85 (23%), Positives = 29/85 (34%), Gaps = 37/85 (43%)
Query: 2 DMTPLWRQMDEEIASTPMPEEYKN-------VIL---------YVLCKDC---------- 35
DM L R + S P+ E K V+L ++LC+DC
Sbjct: 338 DMRELLRGENGSFLSPPLLEAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCD 397
Query: 36 -----HKESKVLYHIIGLKCEHCGS 55
H+ + L +C HCG
Sbjct: 398 ASLTLHRFQRRL------RCHHCGY 416
>gnl|CDD|218802 pfam05903, DUF862, PPPDE putative peptidase domain. The PPPDE
superfamily (after Permuted Papain fold Peptidases of
DsRNA viruses and Eukaryotes), consists of predicted
thiol peptidases with a circularly permuted papain-like
fold. The inference of the likely DUB function of the
PPPDE superfamily proteins is based on the fusions of
the catalytic domain to Ub-binding PUG (PUB)/UBA domains
and a novel alpha-helical Ub-associated domain (the PUL
domain, after PLAP, Ufd3p and Lub1p).
Length = 151
Score = 27.7 bits (62), Expect = 0.38
Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 13 EIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEH 52
E+ T + EE IL L ++ ++ Y++I C H
Sbjct: 76 ELGETELTEEEFREILNSLSEEYTGDT---YNLISKNCNH 112
>gnl|CDD|216754 pfam01873, eIF-5_eIF-2B, Domain found in IF2B/IF5. This family
includes the N terminus of eIF-5, and the C terminus of
eIF-2 beta. This region corresponds to the whole of the
archaebacterial eIF-2 beta homologue. The region
contains a putative zinc binding C4 finger.
Length = 125
Score = 26.9 bits (60), Expect = 0.57
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 16/48 (33%)
Query: 20 PEEYKNVI-----LYVLCKDC-------HKESKVLYHIIGLKCEHCGS 55
P++ ++V+ YVLC +C KE+++ I LKC+ CG+
Sbjct: 79 PKKLQDVLDDYIKEYVLCHECKSPDTELIKENRL----IFLKCKACGA 122
>gnl|CDD|235937 PRK07111, PRK07111, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 735
Score = 27.2 bits (61), Expect = 0.68
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 32 CKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNG 66
C C +I KC CGS N RI++ G
Sbjct: 683 CPVCGYL-----GVIEDKCPKCGSTNIQRIRRITG 712
>gnl|CDD|215713 pfam00094, VWD, von Willebrand factor type D domain.
Luciferin-2-monooxygenase from Vargula hilgendorfii
contains a vwd domain. Its function is unrelated but
the similarity is very strong by several methods.
Length = 159
Score = 27.0 bits (60), Expect = 0.71
Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 4/44 (9%)
Query: 16 STPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC 59
+ P Y + VL +DC E + ++ TC
Sbjct: 18 TFPGNCSY----VLVLAQDCSSEPSFKFSVLNKNVNDGAEGVTC 57
>gnl|CDD|129411 TIGR00311, aIF-2beta, translation initiation factor aIF-2, beta
subunit, putative. The trusted cutoff is set high
enough to select only archaeal members. The suggested
cutoff is set to include most eukaryotic members but
largely exclude the related eIF-5 [Protein synthesis,
Translation factors].
Length = 133
Score = 26.7 bits (59), Expect = 0.85
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 11/37 (29%)
Query: 26 VILYVLCKDCH-------KESKVLYHIIGLKCEHCGS 55
V YV+C++C+ KE +V LKCE CG+
Sbjct: 94 VRKYVICRECNRPDTRIIKEGRVSL----LKCEACGA 126
>gnl|CDD|214764 smart00653, eIF2B_5, domain present in translation initiation
factor eIF2B and eIF5.
Length = 110
Score = 26.1 bits (58), Expect = 1.2
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 11/34 (32%)
Query: 29 YVLCKDC-------HKESKVLYHIIGLKCEHCGS 55
YVLC +C KE+++ + LKCE CG+
Sbjct: 80 YVLCPECGSPDTELIKENRLFF----LKCEACGA 109
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 26.4 bits (59), Expect = 1.3
Identities = 8/37 (21%), Positives = 13/37 (35%), Gaps = 6/37 (16%)
Query: 20 PEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSY 56
+ I C C KE+ +C CG++
Sbjct: 617 KGTIEVEIGRRKCPSCGKET------FYRRCPFCGTH 647
>gnl|CDD|235189 PRK03988, PRK03988, translation initiation factor IF-2 subunit
beta; Validated.
Length = 138
Score = 26.0 bits (58), Expect = 1.3
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 11/34 (32%)
Query: 29 YVLCKDCH-------KESKVLYHIIGLKCEHCGS 55
YV+C +C KE ++ LKCE CG+
Sbjct: 102 YVICPECGSPDTKLIKEGRIWV----LKCEACGA 131
>gnl|CDD|214566 smart00216, VWD, von Willebrand factor (vWF) type D domain. Von
Willebrand factor contains several type D domains: D1
and D2 are present within the N-terminal propeptide
whereas the remaining D domains are required for
multimerisation.
Length = 163
Score = 25.8 bits (57), Expect = 1.7
Identities = 12/34 (35%), Positives = 14/34 (41%), Gaps = 3/34 (8%)
Query: 29 YVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62
YVL +DC E + LK CG TC
Sbjct: 36 YVLAQDCSSEPTF---SVLLKNVPCGGGATCLKS 66
>gnl|CDD|215773 pfam00180, Iso_dh, Isocitrate/isopropylmalate dehydrogenase.
Length = 349
Score = 25.7 bits (57), Expect = 1.7
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 4/28 (14%)
Query: 1 MDMTPLWRQMDEEIASTPMPEEYKNVIL 28
+ + LWR++ EE+A EY +V L
Sbjct: 192 LKSSRLWRKIVEEVAK----AEYPDVEL 215
>gnl|CDD|173359 PTZ00064, PTZ00064, histone acetyltransferase; Provisional.
Length = 552
Score = 25.7 bits (56), Expect = 2.0
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 15/56 (26%)
Query: 17 TPMPEEYKNVILYVLCKDCHK----ESKVLYHIIGLKCEHCGSYNTCRIKKPNGQE 68
+P+P+EY+NV C+ C E +++ H+ C+++ P G E
Sbjct: 268 SPLPDEYQNVDTLHFCEYCLDFFCFEDELIRHLSR-----------CQLRHPPGNE 312
>gnl|CDD|222462 pfam13934, ELYS, Nuclear pore complex assembly. ELYS (embryonic
large molecule derived from yolk sac) is conserved from
fungi such Aspergillus nidulans and Schizosaccharomyces
pombe to human. It is important for the assembly of the
nuclear pore complex.
Length = 225
Score = 25.6 bits (57), Expect = 2.1
Identities = 6/30 (20%), Positives = 12/30 (40%)
Query: 14 IASTPMPEEYKNVILYVLCKDCHKESKVLY 43
I + +K+ ++Y L D + L
Sbjct: 36 ILLSDSDLLHKHALIYYLLLDLDQTRTELS 65
>gnl|CDD|224517 COG1601, GCD7, Translation initiation factor 2, beta subunit
(eIF-2beta)/eIF-5 N-terminal domain [Translation,
ribosomal structure and biogenesis].
Length = 151
Score = 25.4 bits (56), Expect = 2.2
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 8/44 (18%)
Query: 20 PEEYKNVI-----LYVLCKDCHK---ESKVLYHIIGLKCEHCGS 55
E N I YV CK+C E ++ LKCE CG+
Sbjct: 91 DSEIVNEIERYIAEYVKCKECGSPDTELIKEERLLFLKCEACGA 134
>gnl|CDD|237038 PRK12286, rpmF, 50S ribosomal protein L32; Reviewed.
Length = 57
Score = 24.4 bits (54), Expect = 2.5
Identities = 9/28 (32%), Positives = 11/28 (39%), Gaps = 5/28 (17%)
Query: 30 VLCKDCHKESKVLYHIIGLKCEHCGSYN 57
V C +C L H + C CG Y
Sbjct: 28 VECPNCG--EPKLPHRV---CPSCGYYK 50
>gnl|CDD|182885 PRK10991, fucI, L-fucose isomerase; Provisional.
Length = 588
Score = 25.3 bits (56), Expect = 2.5
Identities = 9/23 (39%), Positives = 14/23 (60%), Gaps = 3/23 (13%)
Query: 2 DMTPLWRQMDEEIASTPMPEEYK 24
DMT L R++D++I EE +
Sbjct: 207 DMTELRRRIDQKIYD---EEELE 226
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 25.4 bits (56), Expect = 2.7
Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 21/42 (50%)
Query: 29 YVLCKDC---------------HKESKVLYHIIGLKCEHCGS 55
+LC+DC HK + L +C +CG
Sbjct: 435 LLLCRDCGYIAECPNCDSPLTLHKATGQL------RCHYCGY 470
>gnl|CDD|225037 COG2126, RPL37A, Ribosomal protein L37E [Translation, ribosomal
structure and biogenesis].
Length = 61
Score = 24.3 bits (53), Expect = 3.5
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 24 KNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQ 67
+N ++ C+ C + S YH+ C CG + R++ N Q
Sbjct: 11 RNKKTHIRCRRCGRRS---YHVRKKYCAACGFGRSARMRSYNWQ 51
>gnl|CDD|224245 COG1326, COG1326, Uncharacterized archaeal Zn-finger protein
[General function prediction only].
Length = 201
Score = 24.7 bits (54), Expect = 4.1
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 8/45 (17%)
Query: 27 ILYVLCKDCHKESKVLYHIIG-------LKCEHCGSYNTCRIKKP 64
+Y+ C C E +V + +I ++CE CG+ + IK P
Sbjct: 4 EIYIECPSCGSE-EVSHEVIKERGREPLVRCEECGTVHPAIIKTP 47
>gnl|CDD|179504 PRK02935, PRK02935, hypothetical protein; Provisional.
Length = 110
Score = 24.6 bits (54), Expect = 4.3
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 30 VLCKDCHKESKVLYHIIGLKCEHCG 54
V+C C K +K+L + C HC
Sbjct: 71 VICPSCEKPTKMLGRVDA--CMHCN 93
>gnl|CDD|131061 TIGR02006, IscS, cysteine desulfurase IscS. This model represents
IscS, one of several cysteine desulfurases from a larger
protein family designated (misleadingly, in this case)
class V aminotransferases. IscS is one of at least 6
enzymes characteristic of the IscSUA-hscAB-fsx system of
iron-sulfur cluster assembly. Scoring almost as well as
proteobacterial sequences included in the model are
mitochondrial cysteine desulfurases, apparently from an
analogous system in eukaryotes. The sulfur, taken from
cysteine, may be used in other systems as well, such as
tRNA base modification and biosynthesis of other
cofactors [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other, Protein synthesis, tRNA and rRNA
base modification].
Length = 402
Score = 24.8 bits (54), Expect = 4.7
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 44 HIIGLKCEHCGSYNTCR 60
HII K EH +TCR
Sbjct: 94 HIITSKTEHKAVLDTCR 110
>gnl|CDD|184450 PRK14012, PRK14012, cysteine desulfurase; Provisional.
Length = 404
Score = 24.5 bits (54), Expect = 4.7
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 44 HIIGLKCEHCGSYNTCR 60
HII K EH +TCR
Sbjct: 96 HIITSKTEHKAVLDTCR 112
>gnl|CDD|224462 COG1545, COG1545, Predicted nucleic-acid-binding protein
containing a Zn-ribbon [General function prediction
only].
Length = 140
Score = 24.2 bits (53), Expect = 5.2
Identities = 5/14 (35%), Positives = 8/14 (57%)
Query: 43 YHIIGLKCEHCGSY 56
++G KC+ CG
Sbjct: 25 GKLLGTKCKKCGRV 38
>gnl|CDD|220202 pfam09359, VTC, VTC domain. This presumed domain is found in the
yeast vacuolar transport chaperone proteins VTC2, VTC3
and VTC4. This domain is also found in a variety of
bacterial proteins.
Length = 239
Score = 24.2 bits (53), Expect = 6.6
Identities = 6/34 (17%), Positives = 12/34 (35%), Gaps = 4/34 (11%)
Query: 2 DMTPLWRQMDEEIASTPM----PEEYKNVILYVL 31
++ +W + D ++ P E VL
Sbjct: 168 NLRMIWHRTDIDLNVKPFKLLRKGEVSRFPYAVL 201
>gnl|CDD|193407 pfam12934, FTO_CTD, FTO C-terminal domain. This domain is found at
the C-terminus of the FTO protein which was shown to be
associated with increased BMI and obesity risk in
humans. The N-terminal domain of this protein is a DNA
demethylase and this domain is found to associate with
the N-terminal domain in the crystal structure. This
domain is alpha helical with three helices that form a
bundle.
Length = 172
Score = 24.3 bits (53), Expect = 6.6
Identities = 7/23 (30%), Positives = 11/23 (47%), Gaps = 3/23 (13%)
Query: 5 PLWRQMDEEIASTPMPEEYKNVI 27
P W D+ P+P + + VI
Sbjct: 146 PYW---DDSSKKMPLPFDLEPVI 165
>gnl|CDD|225328 COG2608, CopZ, Copper chaperone [Inorganic ion transport and
metabolism].
Length = 71
Score = 23.5 bits (51), Expect = 7.2
Identities = 5/16 (31%), Positives = 7/16 (43%)
Query: 38 ESKVLYHIIGLKCEHC 53
K + G+ C HC
Sbjct: 1 MMKTTLKVEGMTCGHC 16
>gnl|CDD|220946 pfam11023, DUF2614, Protein of unknown function (DUF2614). This
is a family of proteins conserved in the Bacillaceae
family. Some members are annotated as being protein
YgzB. The function is not known.
Length = 114
Score = 23.9 bits (52), Expect = 7.6
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 30 VLCKDCHKESKVLYHIIGLKCEHC 53
V+C +C K +K+L + C HC
Sbjct: 70 VVCPNCGKPTKMLGRVD--ACMHC 91
>gnl|CDD|220551 pfam10071, DUF2310, Zn-ribbon-containing, possibly
nucleic-acid-binding protein (DUF2310). Members of this
family of proteobacterial zinc ribbon proteins are
thought to bind to nucleic acids, however their exact
function has not as yet been defined.
Length = 259
Score = 23.8 bits (52), Expect = 9.8
Identities = 7/26 (26%), Positives = 12/26 (46%), Gaps = 3/26 (11%)
Query: 31 LCKDCHKESKV---LYHIIGLKCEHC 53
C C + ++ L+ I KC+ C
Sbjct: 223 KCPSCGGDWRLAEPLHDIFDFKCDKC 248
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
0.319 0.135 0.439
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,439,360
Number of extensions: 233490
Number of successful extensions: 343
Number of sequences better than 10.0: 1
Number of HSP's gapped: 342
Number of HSP's successfully gapped: 39
Length of query: 71
Length of database: 10,937,602
Length adjustment: 41
Effective length of query: 30
Effective length of database: 9,119,088
Effective search space: 273572640
Effective search space used: 273572640
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 (21.7 bits)
S2: 53 (24.1 bits)