RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032454
(140 letters)
>gnl|CDD|216356 pfam01196, Ribosomal_L17, Ribosomal protein L17.
Length = 97
Score = 141 bits (359), Expect = 5e-45
Identities = 49/93 (52%), Positives = 68/93 (73%)
Query: 1 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTEL 60
+ + L++HERIETT+AKAKE+R A+ ++ L K+G L A R+A +F+R +++ KLF EL
Sbjct: 5 LATSLIRHERIETTLAKAKELRPYAEKLITLAKKGDLHARRQALSFLRDKELVKKLFDEL 64
Query: 61 AYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFV 93
A RY DR GGYTR+++ R GD APMA IE V
Sbjct: 65 APRYADRNGGYTRIIKLGPRRGDNAPMAIIELV 97
>gnl|CDD|235522 PRK05591, rplQ, 50S ribosomal protein L17; Validated.
Length = 113
Score = 141 bits (359), Expect = 8e-45
Identities = 49/93 (52%), Positives = 67/93 (72%)
Query: 1 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTEL 60
+ + L++HERIETT+ KAKE+RR+ + ++ L K+G L A R+A A +R + +HKLF E+
Sbjct: 21 LATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHARRQAFARLRDKEAVHKLFDEI 80
Query: 61 AYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFV 93
A RY DR GGYTR+L+ R GD APMA IE V
Sbjct: 81 APRYADRNGGYTRILKLGFRRGDNAPMAIIELV 113
>gnl|CDD|223281 COG0203, RplQ, Ribosomal protein L17 [Translation, ribosomal
structure and biogenesis].
Length = 116
Score = 130 bits (330), Expect = 2e-40
Identities = 47/93 (50%), Positives = 64/93 (68%)
Query: 1 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTEL 60
+ + L++HERIETT+ KAKE+RR+ + ++ L K+G L R A A +R D + KLF E+
Sbjct: 24 LATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLANRRLAFARLRDKDAVKKLFDEI 83
Query: 61 AYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFV 93
A RY +R GGYTR+L+ R GD APMA IE V
Sbjct: 84 APRYAERNGGYTRILKLGFRRGDNAPMAIIELV 116
>gnl|CDD|129169 TIGR00059, L17, ribosomal protein L17. Eubacterial and
mitochondrial. The mitochondrial form, from yeast,
contains an additional 110 amino acids C-terminal to the
region found by this model [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 112
Score = 110 bits (277), Expect = 2e-32
Identities = 46/94 (48%), Positives = 67/94 (71%)
Query: 1 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTEL 60
+ S L++HE+I+TT+AKAKE+RR+ + ++ L K + R A A++R +++HKLF+E+
Sbjct: 19 LASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNRREAKAYIRNKEIVHKLFSEI 78
Query: 61 AYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFVD 94
A RY R GGYTR+L+ R GDAA MA IE VD
Sbjct: 79 APRYAQRPGGYTRILKLGPRRGDAAEMAIIELVD 112
>gnl|CDD|173371 PTZ00076, PTZ00076, 60S ribosomal protein L17; Provisional.
Length = 253
Score = 77.5 bits (191), Expect = 3e-18
Identities = 37/104 (35%), Positives = 67/104 (64%), Gaps = 1/104 (0%)
Query: 2 VSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELA 61
+ +L+++ R+E T+ +AKE+++ A+ ++ L K+ + + + + +R KL+ +
Sbjct: 37 LDELLRYGRLELTLPRAKELQQYAEELIYLAKKDTPESNLKVESMLRTPQGRRKLYEKYV 96
Query: 62 YRYKDRAGGYTRLLRS-RIRVGDAAPMAYIEFVDRENELRQSKP 104
Y+DR +TR++ R+R+ DAAPMAYIEFVDR E+R +KP
Sbjct: 97 PLYRDRPFFFTRVVNQWRLRLRDAAPMAYIEFVDRPGEIRPAKP 140
>gnl|CDD|237254 PRK12899, secA, preprotein translocase subunit SecA; Reviewed.
Length = 970
Score = 32.1 bits (73), Expect = 0.076
Identities = 43/148 (29%), Positives = 64/148 (43%), Gaps = 33/148 (22%)
Query: 2 VSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELA 61
+S++++ RIE TV AK + A+ + GK G++ A A RG D+ KL E
Sbjct: 584 LSRILRQNRIEHTVLNAKNHAQEAEIIAGAGKLGAVTVATNMAG--RGTDI--KLDEEAV 639
Query: 62 ----------YRYKDRAGGYTRLLRSRI-RVGD-AAPMAYIEFVDRENELRQSKPAVPQP 109
R++ R R LR R R+GD A ++ F DR L S
Sbjct: 640 AVGGLYVIGTSRHQSRR--IDRQLRGRCARLGDPGAAKFFLSFEDRLMRLFAS------- 690
Query: 110 PPRAALDPWTRSRLTKNFAPPKQEKSSD 137
P+ + L ++F PP+ E SD
Sbjct: 691 -PKL-------NTLIRHFRPPEGEAMSD 710
>gnl|CDD|183859 PRK13103, secA, preprotein translocase subunit SecA; Reviewed.
Length = 913
Score = 29.5 bits (66), Expect = 0.53
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 2 VSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVI 53
+S L+K E IE V AK + A+ + Q G+ G+L A A RG D++
Sbjct: 465 MSNLLKKEGIEHKVLNAKYHEKEAEIIAQAGRPGALTIATNMAG--RGTDIL 514
>gnl|CDD|233212 TIGR00963, secA, preprotein translocase, SecA subunit. The
proteins SecA-F and SecY, not all of which are
necessary, comprise the standard prokaryotic protein
translocation apparatus. Other, specialized
translocation systems also exist but are not as broadly
distributed. This model describes SecA, an essential
member of the apparatus. This model excludes SecA2 of
the accessory secretory system [Protein fate, Protein
and peptide secretion and trafficking].
Length = 745
Score = 29.2 bits (66), Expect = 0.77
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 1 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVI 53
++S L+K I V AK R A+ + Q G++G++ A A RG D+
Sbjct: 420 LLSNLLKERGIPHNVLNAKNHEREAEIIAQAGRKGAVTIATNMAG--RGTDIK 470
>gnl|CDD|183863 PRK13107, PRK13107, preprotein translocase subunit SecA; Reviewed.
Length = 908
Score = 27.2 bits (60), Expect = 3.4
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 1 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVI 53
++++L+ E+I V AK R A+ + Q G+ G++ A A RG D++
Sbjct: 464 LLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGAVTIATNMAG--RGTDIV 514
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family
including yeast cell wall integrity protein scw1, yeast
Whi3 protein, yeast Whi4 protein and similar proteins.
The strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates
septation and cell-wall structure in fission yeast. It
may function as an inhibitor of septum formation, such
that its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3),
a G1 cyclin that promotes transcription of many genes
to trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict
Cln3 synthesis to modulate cell cycle progression.
Moreover, Whi3 plays a key role in cell fate
determination in budding yeast. The RRM domain is
essential for Whi3 function. Whi4 is a partially
redundant homolog of Whi3, also containing one RRM.
Some uncharacterized family members of this subfamily
contain two RRMs; their RRM1 shows high sequence
homology to the RRM of RNA-binding protein with
multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 26.0 bits (58), Expect = 3.4
Identities = 7/25 (28%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 70 GYTRLLRSRIRVGDAAPMAYIEFVD 94
G+ RL ++ P+ ++EF D
Sbjct: 28 GFRRL---KMHNKGGGPVCFVEFED 49
>gnl|CDD|132813 cd07280, PX_YPT35, The phosphoinositide binding Phox Homology
domain of the fungal protein YPT35. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions such as cell signaling,
vesicular trafficking, protein sorting, and lipid
modification, among others. This subfamily is composed
of YPT35 proteins from the fungal subkingdom Dikarya.
The PX domain is involved in targeting of proteins to
PI-enriched membranes, and may also be involved in
protein-protein interaction. The PX domain of YPT35
binds to phosphatidylinositol 3-phosphate (PI3P). It
also serves as a protein interaction domain, binding to
members of the Yip1p protein family, which localize to
the ER and Golgi. YPT35 is mainly associated with
endosomes and together with Yip1p proteins, may be
involved in a specific function in the endocytic
pathway.
Length = 120
Score = 25.8 bits (57), Expect = 5.2
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 10/46 (21%)
Query: 89 YIEFVDRENELRQSKP-----AVPQPPPRAALDPW--TRSRLTKNF 127
Y EFV L P +PQ PP+ PW +R L K +
Sbjct: 45 YSEFVQLREALLDEFPRHKRNEIPQLPPK---VPWYDSRVNLNKAW 87
>gnl|CDD|100028 cd02192, PurM-like3, AIR synthase (PurM) related protein, subgroup
3 of unknown function. The family of PurM related
proteins includes Hydrogen expression/formation protein
HypE, AIR synthases, FGAM synthase and Selenophosphate
synthetase (SelD). They all contain two conserved
domains and seem to dimerize. The N-terminal domain
forms the dimer interface and is a putative ATP binding
domain.
Length = 283
Score = 26.4 bits (59), Expect = 5.6
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 13 TTVAKAKEVRRLADNMVQLGKEGSLCAAR 41
TT+ +RR + +L + G + AA+
Sbjct: 178 TTMKSPALLRRQIALLPELAERGLVHAAK 206
>gnl|CDD|220582 pfam10117, McrBC, McrBC 5-methylcytosine restriction system
component. Members of this family of bacterial proteins
modify the specificity of mcrB restriction by expanding
the range of modified sequences restricted.
Length = 317
Score = 26.4 bits (59), Expect = 6.2
Identities = 18/84 (21%), Positives = 23/84 (27%), Gaps = 12/84 (14%)
Query: 54 HKLFTELAYRYK----DRAGGYTRLLRSRIRVGDAAPMAYIEFVDRENELRQSKPAVPQP 109
HK F RY D RLL+S + E + EL VP
Sbjct: 114 HKFFV----RYDEFTEDNPL--NRLLKSALERLLKLTR-SSENLRLLRELLFLLDEVPDS 166
Query: 110 P-PRAALDPWTRSRLTKNFAPPKQ 132
W +RL +
Sbjct: 167 KISAKDFQKWRLNRLNARYELLLP 190
>gnl|CDD|216655 pfam01708, Gemini_mov, Geminivirus putative movement protein. This
family consists of putative movement proteins from Maize
streak and wheat dwarf virus.
Length = 92
Score = 25.1 bits (55), Expect = 8.3
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 103 KPAVPQPPPRAALDPWTR 120
P VP P ++ PW+R
Sbjct: 19 TPRVPTAAPSSSDLPWSR 36
>gnl|CDD|233250 TIGR01052, top6b, DNA topoisomerase VI, B subunit. This model
describes DNA topoisomerase VI, an archaeal type II DNA
topoisomerase (DNA gyrase) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 488
Score = 25.9 bits (57), Expect = 8.7
Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 8/65 (12%)
Query: 57 FTELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFVD---RENELRQSKPAVPQPPPRA 113
F ++YR + + G Y L R+ + A P A I VD +S +P+PP
Sbjct: 171 FKGVSYR-RSKQGVYEYLRRTAV----ANPHAKIVLVDPDGEIYVFPRSTDEIPKPPKEM 225
Query: 114 ALDPW 118
P
Sbjct: 226 KPHPH 230
>gnl|CDD|236149 PRK08088, PRK08088, 4-aminobutyrate aminotransferase; Validated.
Length = 425
Score = 25.9 bits (57), Expect = 8.9
Identities = 15/41 (36%), Positives = 18/41 (43%), Gaps = 10/41 (24%)
Query: 40 ARRAAAFVRGDDVIHKLFTELA----------YRYKDRAGG 70
RR+AA RG IH +F + A Y D AGG
Sbjct: 9 QRRSAAVPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGG 49
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
0.318 0.132 0.379
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,264,975
Number of extensions: 668475
Number of successful extensions: 664
Number of sequences better than 10.0: 1
Number of HSP's gapped: 662
Number of HSP's successfully gapped: 32
Length of query: 140
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 53
Effective length of database: 7,078,804
Effective search space: 375176612
Effective search space used: 375176612
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: 54 (24.6 bits)