RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031427
(160 letters)
>gnl|CDD|235522 PRK05591, rplQ, 50S ribosomal protein L17; Validated.
Length = 113
Score = 167 bits (427), Expect = 7e-55
Identities = 59/113 (52%), Positives = 79/113 (69%)
Query: 1 MTKFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAA 60
K RKL R + HR +MLR + + L++HERIETT+ KAKE+RR+ + ++ L K+G L A
Sbjct: 1 RKKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHAR 60
Query: 61 RRAAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFV 113
R+A A +R + +HKLF E+A RY DR GGYTR+L+ R GD APMA IE V
Sbjct: 61 RQAFARLRDKEAVHKLFDEIAPRYADRNGGYTRILKLGFRRGDNAPMAIIELV 113
>gnl|CDD|223281 COG0203, RplQ, Ribosomal protein L17 [Translation, ribosomal
structure and biogenesis].
Length = 116
Score = 150 bits (380), Expect = 9e-48
Identities = 57/112 (50%), Positives = 76/112 (67%)
Query: 2 TKFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAAR 61
K RKL R + HR +MLR + + L++HERIETT+ KAKE+RR+ + ++ L K+G L R
Sbjct: 5 KKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLANRR 64
Query: 62 RAAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFV 113
A A +R D + KLF E+A RY +R GGYTR+L+ R GD APMA IE V
Sbjct: 65 LAFARLRDKDAVKKLFDEIAPRYAERNGGYTRILKLGFRRGDNAPMAIIELV 116
>gnl|CDD|216356 pfam01196, Ribosomal_L17, Ribosomal protein L17.
Length = 97
Score = 146 bits (372), Expect = 1e-46
Identities = 51/97 (52%), Positives = 71/97 (73%)
Query: 17 MLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKL 76
+LR + + L++HERIETT+AKAKE+R A+ ++ L K+G L A R+A +F+R +++ KL
Sbjct: 1 LLRNLATSLIRHERIETTLAKAKELRPYAEKLITLAKKGDLHARRQALSFLRDKELVKKL 60
Query: 77 FTELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFV 113
F ELA RY DR GGYTR+++ R GD APMA IE V
Sbjct: 61 FDELAPRYADRNGGYTRIIKLGPRRGDNAPMAIIELV 97
>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 = 128 bits (324), Expect = 3e-39
Identities = 54/111 (48%), Positives = 79/111 (71%)
Query: 4 FRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRA 63
+RKL R + HR ++LR + S L++HE+I+TT+AKAKE+RR+ + ++ L K + R A
Sbjct: 2 YRKLGRTSAHRKALLRNLASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNRREA 61
Query: 64 AAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFVD 114
A++R +++HKLF+E+A RY R GGYTR+L+ R GDAA MA IE VD
Sbjct: 62 KAYIRNKEIVHKLFSEIAPRYAQRPGGYTRILKLGPRRGDAAEMAIIELVD 112
>gnl|CDD|173371 PTZ00076, PTZ00076, 60S ribosomal protein L17; Provisional.
Length = 253
Score = 87.6 bits (217), Expect = 8e-22
Identities = 41/122 (33%), Positives = 75/122 (61%), Gaps = 1/122 (0%)
Query: 4 FRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRA 63
FR+ + HR ++ + +L+++ R+E T+ +AKE+++ A+ ++ L K+ + + +
Sbjct: 19 FRRAHGQPHHRWDSIKNQLDELLRYGRLELTLPRAKELQQYAEELIYLAKKDTPESNLKV 78
Query: 64 AAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRS-RIRVGDAAPMAYIEFVDRENELRQS 122
+ +R KL+ + Y+DR +TR++ R+R+ DAAPMAYIEFVDR E+R +
Sbjct: 79 ESMLRTPQGRRKLYEKYVPLYRDRPFFFTRVVNQWRLRLRDAAPMAYIEFVDRPGEIRPA 138
Query: 123 KP 124
KP
Sbjct: 139 KP 140
>gnl|CDD|237254 PRK12899, secA, preprotein translocase subunit SecA; Reviewed.
Length = 970
Score = 32.1 bits (73), Expect = 0.11
Identities = 43/148 (29%), Positives = 64/148 (43%), Gaps = 33/148 (22%)
Query: 22 VSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELA 81
+S++++ RIE TV AK + A+ + GK G++ A A RG D+ KL E
Sbjct: 584 LSRILRQNRIEHTVLNAKNHAQEAEIIAGAGKLGAVTVATNMAG--RGTDI--KLDEEAV 639
Query: 82 ----------YRYKDRAGGYTRLLRSRI-RVGD-AAPMAYIEFVDRENELRQSKPAVPQP 129
R++ R R LR R R+GD A ++ F DR L S
Sbjct: 640 AVGGLYVIGTSRHQSRR--IDRQLRGRCARLGDPGAAKFFLSFEDRLMRLFAS------- 690
Query: 130 PPRAALDPWTRSRLTKNFAPPKQEKSSD 157
P+ + L ++F PP+ E SD
Sbjct: 691 -PKL-------NTLIRHFRPPEGEAMSD 710
>gnl|CDD|183859 PRK13103, secA, preprotein translocase subunit SecA; Reviewed.
Length = 913
Score = 29.9 bits (67), Expect = 0.69
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 22 VSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVI 73
+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 = 1.0
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 21 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVI 73
++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 = 4.1
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 21 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVI 73
++++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 = 25.6 bits (57), Expect = 5.3
Identities = 7/25 (28%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 90 GYTRLLRSRIRVGDAAPMAYIEFVD 114
G+ RL ++ P+ ++EF D
Sbjct: 28 GFRRL---KMHNKGGGPVCFVEFED 49
>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 = 26.8 bits (60), Expect = 5.8
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 33 TTVAKAKEVRRLADNMVQLGKEGSLCAAR 61
TT+ +RR + +L + G + AA+
Sbjct: 178 TTMKSPALLRRQIALLPELAERGLVHAAK 206
>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 = 26.1 bits (58), Expect = 6.0
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 10/46 (21%)
Query: 109 YIEFVDRENELRQSKP-----AVPQPPPRAALDPW--TRSRLTKNF 147
Y EFV L P +PQ PP+ PW +R L K +
Sbjct: 45 YSEFVQLREALLDEFPRHKRNEIPQLPPK---VPWYDSRVNLNKAW 87
>gnl|CDD|227250 COG4913, COG4913, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 1104
Score = 26.5 bits (58), Expect = 7.6
Identities = 27/132 (20%), Positives = 44/132 (33%), Gaps = 21/132 (15%)
Query: 5 RKLNRPTGHRM--SMLRTMVSQL-VKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAAR 61
+K G+R+ T+V Q V+ + ++ V AK A M L A
Sbjct: 285 KKALPTVGNRIKKEEQETLVRQFTVEQTQAKSKVESAKIETDRAREMETL--------AH 336
Query: 62 RAAAFVRGDDV------IHKLFTELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFVDR 115
+ G + RAG L++ +G AAP + E ++
Sbjct: 337 DNVKQIVGAQHGILSAKREGAVDKRRTISTARAG-LDALVK---GLGGAAPESAEELLEL 392
Query: 116 ENELRQSKPAVP 127
N R + P
Sbjct: 393 NNAARLTVDEYP 404
>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 = 25.5 bits (56), Expect = 7.9
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 123 KPAVPQPPPRAALDPWTR 140
P VP P ++ PW+R
Sbjct: 19 TPRVPTAAPSSSDLPWSR 36
>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 = 26.1 bits (58), Expect = 9.2
Identities = 18/84 (21%), Positives = 23/84 (27%), Gaps = 12/84 (14%)
Query: 74 HKLFTELAYRYK----DRAGGYTRLLRSRIRVGDAAPMAYIEFVDRENELRQSKPAVPQP 129
HK F RY D RLL+S + E + EL VP
Sbjct: 114 HKFFV----RYDEFTEDNPL--NRLLKSALERLLKLTR-SSENLRLLRELLFLLDEVPDS 166
Query: 130 P-PRAALDPWTRSRLTKNFAPPKQ 152
W +RL +
Sbjct: 167 KISAKDFQKWRLNRLNARYELLLP 190
>gnl|CDD|236149 PRK08088, PRK08088, 4-aminobutyrate aminotransferase; Validated.
Length = 425
Score = 26.3 bits (58), Expect = 9.4
Identities = 15/41 (36%), Positives = 18/41 (43%), Gaps = 10/41 (24%)
Query: 60 ARRAAAFVRGDDVIHKLFTELA----------YRYKDRAGG 90
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
0.320 0.132 0.381
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,260,119
Number of extensions: 764207
Number of successful extensions: 777
Number of sequences better than 10.0: 1
Number of HSP's gapped: 774
Number of HSP's successfully gapped: 33
Length of query: 160
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 71
Effective length of database: 6,990,096
Effective search space: 496296816
Effective search space used: 496296816
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: 55 (24.8 bits)