RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2081
(380 letters)
>gnl|CDD|220770 pfam10469, AKAP7_NLS, AKAP7 2'5' RNA ligase-like domain. AKAP7_NLS
is the N-terminal domain of the cyclic AMP-dependent
protein kinase A, PKA, anchor protein AKAP7. This
protein anchors PKA for its role in regulating
PKA-mediated gene transcription in both somatic cells
and oocytes. AKAP7_NLS carries the nuclear localisation
signal (NLS) KKRKK, that indicates the cellular destiny
of this anchor protein. Binding to the regulatory
subunits RI and RII of PKA is mediated via the family
AKAP7_RIRII_bdg. at the C-terminus. This family
represents a region that contains two 2'5' RNA ligase
like domains pfam02834. Presumably this domain carried
out some as yet unknown enzymatic function.
Length = 205
Score = 181 bits (461), Expect = 1e-55
Identities = 84/220 (38%), Positives = 128/220 (58%), Gaps = 19/220 (8%)
Query: 165 YTHLLSIPMNVPNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVE 224
TH LSIP+N P I+E +F+ +VLS + G++ESLF P +LH+T+ +L+L D E
Sbjct: 1 PTHFLSIPLNSPEIRERLKEFQESVLS---QDPGLDESLFIPPEKLHLTLLVLVLLDQEE 57
Query: 225 RDQAVEVLQKCGNNIILPILRSQRIKINLKGLEIMNDDPAEVDILYAKVVDD-SGLVQKL 283
+ A E LQ+C I + +++ KGLE NDDPA V +LYAKV +D S +QK+
Sbjct: 58 VEAAKEALQECKEEIKDILGNP--LELRFKGLETFNDDPA-VRVLYAKVEEDGSPRLQKI 114
Query: 284 CDDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYR--MRQNPSSDTNSEKRSTFNAKDI 341
D +++ F+ + L++K + VK+H+TLM ++Y ++ R +F+A +I
Sbjct: 115 ADRLLRAFVEKGLLAKDNNE-FDVKLHLTLMKTRYAPKKKKK--------GRESFDAPEI 165
Query: 342 LESLGDFEFGETFVYCVHLSQRHTHD-MDGYFKPSAVISL 380
LE GDF+FGE V +HL + D DGY+ I L
Sbjct: 166 LEDFGDFDFGEQKVNEIHLCSMGSTDSSDGYYHTEGSIPL 205
>gnl|CDD|177724 PLN00108, PLN00108, unknown protein; Provisional.
Length = 257
Score = 89.7 bits (222), Expect = 1e-20
Identities = 62/221 (28%), Positives = 115/221 (52%), Gaps = 23/221 (10%)
Query: 165 YTHLLSIPMNV-PNIQENFAKFKATVLSDFSRC----------RGIEESLFQEPGRLHIT 213
+TH +S+P+ + P++++N F+ +VL + + GIE+S+F P H+T
Sbjct: 36 FTHFVSLPLAIYPDLKKNIEAFQNSVLGNNDKDPLKFQSTLAEMGIEKSIFVSPKTFHLT 95
Query: 214 MGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIKINLKGLEIMNDDPAEVDILYAKV 273
+ ML L ++ +A +L+ +N+ L+ + + I L+GL+ MN + +LYA V
Sbjct: 96 VVMLKLENNESVVKAQNILKSICSNV-RQALKDRPVFIRLRGLDCMNGSLDKTRVLYAPV 154
Query: 274 --VDDSGLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMRQNPSSDTNSE 331
V G + C ++ F + K + +K+H TLMN+ YR + S+
Sbjct: 155 EEVGHEGRLLNACHVIIDAFENAGFAGKDAKS--RLKLHATLMNASYRKDK-------SK 205
Query: 332 KRSTFNAKDILESLGDFEFGETFVYCVHLSQRHTHDMDGYF 372
K TF+A++I + + ++G + H+SQR+ +D +GYF
Sbjct: 206 KMDTFDAREIHKEFENKDWGTYLIREAHISQRYKYDPNGYF 246
>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding
domain_vigilin_like. The vigilin family is a large and
extended family of multiple KH-domain proteins,
including vigilin, also called high density lipoprotein
binding protien (HBP), fungal Scp160 and bicaudal-C.
Yeast Scp160p has been shown to bind RNA and to
associate with both soluble and membrane-bound
polyribosomes as a mRNP component. Bicaudal-C is a
RNA-binding molecule believed to function in embryonic
development at the post-transcriptional level. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA.
Length = 62
Score = 58.7 bits (143), Expect = 2e-11
Identities = 20/60 (33%), Positives = 29/60 (48%)
Query: 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRL 152
+ IPK + FIIG KGS R+I ET ++ P G D I + + + AK +
Sbjct: 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEI 61
>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA. There are two different KH domains that belong
to different protein folds, but they share a single KH
motif. The KH motif is folded into a beta alpha alpha
beta unit. In addition to the core, type II KH domains
(e.g. ribosomal protein S3) include N-terminal extension
and type I KH domains (e.g. hnRNP K) contain C-terminal
extension.
Length = 64
Score = 46.0 bits (110), Expect = 6e-07
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 97 IPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD--IIISSYSERGIASAKRRL 152
+P S IIG GST + I ET ++ IP G + I+ + + + AK +
Sbjct: 6 VPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63
>gnl|CDD|215657 pfam00013, KH_1, KH domain. KH motifs bind RNA in vitro.
Autoantibodies to Nova, a KH domain protein, cause
paraneoplastic opsoclonus ataxia.
Length = 59
Score = 42.9 bits (102), Expect = 6e-06
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 97 IPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRL 152
IP IIG GS + I ET ++ IP + IS E+ + AK +
Sbjct: 6 IPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR-DDTVTISGTPEQ-VEKAKELI 59
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 42.7 bits (101), Expect = 9e-06
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 2/64 (3%)
Query: 90 QYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDII-ISSYSERGIASA 148
+ IP IIG GST ++IE ET ++ IP G ++ I+ E + A
Sbjct: 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPE-NVEKA 60
Query: 149 KRRL 152
+
Sbjct: 61 AELI 64
>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 180
Score = 40.6 bits (96), Expect = 4e-04
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 97 IPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISS 139
IPK +IG KG TK+ IE T +L I +TG++II
Sbjct: 9 IPKDRIGVLIGKKGETKKEIEERTGVKLEI--DSETGEVIIEP 49
Score = 28.7 bits (65), Expect = 3.4
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 105 IIGVKGSTKRRIESETNTQLSI 126
IIG G T+R IE T +S+
Sbjct: 109 IIGEGGKTRRIIEELTGVDISV 130
>gnl|CDD|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain
protein. This family of proteins is universal among the
41 archaeal genomes analyzed in and is not observed
outside of the archaea. The proteins contain a single KH
domain (pfam00013) which is likely to confer the ability
to bind RNA.
Length = 172
Score = 37.2 bits (87), Expect = 0.005
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 97 IPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIII 137
IPK +IG G TK+ IE T +L I +TG++ I
Sbjct: 4 IPKDRIGVLIGKGGETKKEIEERTGVKLDI--DSETGEVKI 42
Score = 28.3 bits (64), Expect = 4.4
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 105 IIGVKGSTKRRIESETNTQLSI 126
IIG G T+R IE T +S+
Sbjct: 103 IIGEGGKTRRIIEELTGVSISV 124
>gnl|CDD|221895 pfam13014, KH_3, KH domain. KH motifs bind RNA in vitro. This
RNA-binding domain is required for the efficient
anchoring of ASH1-mRNA to the distal tip of the daughter
cell. ASH1 is a specific repressor of transcription that
localizes asymmetrically to the daughter cell nucleus.
RNA localisation is a widespread mechanism for achieving
localised protein synthesis.
Length = 42
Score = 34.1 bits (79), Expect = 0.005
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 3/41 (7%)
Query: 101 FYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD---IIIS 138
IIG G T + I ET ++ IP+ + I+
Sbjct: 1 LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTIT 41
>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology
RNA-binding domain (KH). Splicing factor 1 (SF1)
specifically recognizes the intron branch point sequence
(BPS) UACUAAC in the pre-mRNA transcripts during
spliceosome assembly. We show that the KH-QUA2 region of
SF1 defines an enlarged KH (hnRNP K) fold which is
necessary and sufficient for BPS binding. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA.
Length = 120
Score = 32.2 bits (74), Expect = 0.15
Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 6/38 (15%)
Query: 95 CHIPKSFYP---F---IIGVKGSTKRRIESETNTQLSI 126
+IP YP F I+G +G+T +++E ET ++SI
Sbjct: 4 VYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISI 41
>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K
homology RNA-binding domain (KH). PNPase is a
polyribonucleotide nucleotidyl transferase that degrades
mRNA in prokaryotes and plant chloroplasts. The
C-terminal region of PNPase contains domains homologous
to those in other RNA binding proteins: a KH domain and
an S1 domain. KH domains bind single-stranded RNA and
are found in a wide variety of proteins including
ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 61
Score = 29.8 bits (68), Expect = 0.29
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 96 HIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLD 153
IP +IG G T ++I ET ++ I G + I++ + AK+ ++
Sbjct: 7 KIPPDKIRDVIGPGGKTIKKIIEETGVKIDI---EDDGTVYIAASDKEAAEKAKKMIE 61
>gnl|CDD|235467 PRK05441, murQ, N-acetylmuramic acid-6-phosphate etherase;
Reviewed.
Length = 299
Score = 30.9 bits (71), Expect = 1.1
Identities = 8/29 (27%), Positives = 16/29 (55%)
Query: 216 MLMLADSVERDQAVEVLQKCGNNIILPIL 244
++M A V R++A L+ ++ L I+
Sbjct: 241 IVMEATGVSREEAEAALEAADGSVKLAIV 269
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 31.0 bits (71), Expect = 1.3
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 105 IIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLD 153
+IG G T + I ET ++ I G + I++ AK R++
Sbjct: 566 VIGPGGKTIKAITEETGVKIDI---EDDGTVKIAASDGESAKKAKERIE 611
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 30.8 bits (71), Expect = 1.4
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 3/56 (5%)
Query: 96 HIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRR 151
IP +IG G T R I ET ++ I G + I++ +AK R
Sbjct: 559 KIPPDKIRDVIGPGGKTIREITEETGAKIDI---EDDGTVKIAATDGEAAEAAKER 611
>gnl|CDD|237142 PRK12570, PRK12570, N-acetylmuramic acid-6-phosphate etherase;
Reviewed.
Length = 296
Score = 30.4 bits (69), Expect = 1.5
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 216 MLMLADSVERDQAVEVLQKCGNNIILPIL 244
++M A D+A E+L++ N++ L IL
Sbjct: 237 IVMQATGCSEDEAKELLKESDNDVKLAIL 265
>gnl|CDD|131555 TIGR02503, type_III_SycN, type III secretion chaperone SycN.
Members of this protein family are part of the machinery
of bacterial type III secretion in a number of bacteria
that target animal cells. In the well-studied system
from Yersinia, a complex of this protein (SycN) and YscB
(pfam07329) acts as a chaperone for the export of YopN
(PMID:10094626). YopN then acts to control effector
protein secretion, in response to calcium levels, so
that secretion occurs only after contact with the
targeted eukaryotic cell [Protein fate, Protein folding
and stabilization, Cellular processes, Pathogenesis].
Length = 119
Score = 29.0 bits (65), Expect = 1.8
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 13/58 (22%)
Query: 190 LSDFSRCRGIEESLF---------QEPGRLHIT----MGMLMLADSVERDQAVEVLQK 234
L+ F + G+ ++ GRL++ +L LA S+E QA E L++
Sbjct: 5 LAQFCQDLGLPTPAPLPRLAQLSMEQSGRLYVEQHDGTLLLWLARSLEWHQAEEALKR 62
>gnl|CDD|182070 PRK09776, PRK09776, putative diguanylate cyclase; Provisional.
Length = 1092
Score = 30.4 bits (69), Expect = 2.1
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 191 SDFSRCRGIEESLFQEPGRLHITM 214
D + R + E+LFQE RLHIT+
Sbjct: 519 MDMTEVRQLNEALFQEKERLHITL 542
>gnl|CDD|240140 cd05007, SIS_Etherase, N-acetylmuramic acid 6-phosphate etherase.
Members of this family contain the SIS (Sugar ISomerase)
domain. The SIS domain is found in many phosphosugar
isomerases and phosphosugar binding proteins. The
bacterial cell wall sugar N-acetylmuramic acid carries a
unique D-lactyl ether substituent at the C3 position.
The etherase catalyzes the cleavage of the lactyl ether
bond of N-acetylmuramic acid 6-phosphate.
Length = 257
Score = 29.8 bits (68), Expect = 2.2
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 216 MLMLADSVERDQAVEVLQKCGNNIILPIL 244
++M A V RD+A L++ G ++ IL
Sbjct: 228 IVMEATGVSRDEAEAALEQAGGDVKTAIL 256
>gnl|CDD|227429 COG5098, COG5098, Chromosome condensation complex Condensin,
subunit D2 [Chromatin structure and dynamics / Cell
division and chromosome partitioning].
Length = 1128
Score = 29.9 bits (67), Expect = 2.8
Identities = 10/58 (17%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 265 EVDILYAKVVDD-SGLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMR 321
+++ + + + S L Q L + +I + +IS+ + Y K +L+ + +
Sbjct: 611 LINLSFEASLAELSSLEQLLGMMYARRYIDKTVISELWSMYSLQKFDFSLLQASGSII 668
>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model
TIGR02696 for an exception clade, within this family)
[Transcription, Degradation of RNA].
Length = 684
Score = 29.8 bits (68), Expect = 2.9
Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 3/57 (5%)
Query: 97 IPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLD 153
I +IG G R I ET ++ I G + I++ +A + ++
Sbjct: 557 INPDKIRDVIGPGGKVIREITEETGAKIDI---EDDGTVKIAASDGEAAEAAIKMIE 610
>gnl|CDD|218565 pfam05346, DUF747, Eukaryotic membrane protein family. This family
is a family of eukaryotic membrane proteins. It was
previously annotated as including a putative receptor
for human cytomegalovirus gH but this has has since been
disputed. Analysis of the mouse Tapt1 protein
(transmembrane anterior posterior transformation 1) has
shown it to be involved in patterning of the vertebrate
axial skeleton.
Length = 320
Score = 29.6 bits (67), Expect = 3.0
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 16/50 (32%)
Query: 178 IQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQ 227
+ FA+ K++V F + ESLFQ IT AD VER Q
Sbjct: 129 LSNQFAEIKSSVFKKFDK-----ESLFQ------ITC-----ADVVERFQ 162
>gnl|CDD|132208 TIGR03164, UHCUDC, OHCU decarboxylase. Previously thought to only
proceed spontaneously, the decarboxylation of
2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU)
has been recently been shown to be catalyzed by this
enzyme in Mus musculus. Homologs of this enzyme are
found adjacent to and fused with uricase in a number of
prokaryotes and are represented by this model.
Length = 157
Score = 28.9 bits (65), Expect = 3.1
Identities = 16/67 (23%), Positives = 27/67 (40%), Gaps = 17/67 (25%)
Query: 69 EEDDGGLS--EDEDLDIYLGKDGQYKYQCHIPKSF-YPFIIGVKGSTK--------RRIE 117
E+ GL E+ + + Y+ F +PFI+ VKG TK R+
Sbjct: 79 EQASAGLDQLSQEEFARFTRLNNAYR------ARFGFPFIMAVKGKTKQSILAAFEARLN 132
Query: 118 SETNTQL 124
++ T+
Sbjct: 133 NDRETEF 139
>gnl|CDD|221882 pfam12984, DUF3868, Domain of unknown function, B. Theta Gene
description (DUF3868). Based on Bacteroides
thetaiotaomicron gene BT_1065, a putative
uncharacterized protein As seen in gene expression
experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22
31), It appears to be upregulated in the presence of
host or other bacterial species vs when in culture.
Length = 115
Score = 28.1 bits (63), Expect = 3.7
Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 9/52 (17%)
Query: 202 SLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIKINL 253
SL Q+ +++ M + + V+ Q+V+ + P+L S K+ L
Sbjct: 36 SLEQKGDSVYLNMDIDLSGVKVKSRQSVD---------LTPVLVSASSKLLL 78
>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein. This family consists of several
NOA36 proteins which contain 29 highly conserved
cysteine residues. The function of this protein is
unknown.
Length = 314
Score = 28.8 bits (64), Expect = 4.4
Identities = 10/28 (35%), Positives = 10/28 (35%)
Query: 55 SEYDAGCPGGNQPYEEDDGGLSEDEDLD 82
S G N YE DD S D D
Sbjct: 258 SNKYGDFKGVNYGYESDDDEGSSSNDYD 285
>gnl|CDD|220936 pfam11006, DUF2845, Protein of unknown function (DUF2845). This
bacterial family of proteins has no known function.
Length = 85
Score = 26.9 bits (60), Expect = 5.2
Identities = 10/23 (43%), Positives = 11/23 (47%), Gaps = 4/23 (17%)
Query: 226 DQAVEVLQKCGNNIILPILRSQR 248
D EVL KCG P + QR
Sbjct: 17 DSKAEVLAKCGE----PASKDQR 35
>gnl|CDD|202610 pfam03380, DUF282, Caenorhabditis protein of unknown function,
DUF282.
Length = 370
Score = 28.6 bits (63), Expect = 5.6
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 61 CPGGNQPYEEDDGGLSEDEDLDIYLGKDGQYKY 93
CP G ++ G + DE+L Y G D Y +
Sbjct: 192 CPAGTVAVFDNGGTVIPDEELGNYYGLDTVYAF 224
>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 28.0 bits (63), Expect = 6.3
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 105 IIGVKGSTKRRIESETNTQLSIPRQGQTGDII 136
IIG +G T+R IE T +S+ G+T II
Sbjct: 116 IIGREGKTRRAIEELTGVYISV--YGKTVAII 145
>gnl|CDD|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4;
Provisional.
Length = 235
Score = 27.9 bits (63), Expect = 8.1
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 103 PFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGI 145
P +IG KGS ++ ET + + GQ G I I E
Sbjct: 157 PRVIGKKGSMINMLKEETGCDIIV---GQNGRIWIKGPDEEDE 196
>gnl|CDD|171440 PRK12365, PRK12365, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 1046
Score = 28.4 bits (63), Expect = 8.3
Identities = 24/133 (18%), Positives = 57/133 (42%), Gaps = 18/133 (13%)
Query: 227 QAVEVLQKCGNNIIL-PILRSQRIKINLKGLEIMNDDP-----AEVDILYAKVVDDSGLV 280
Q++ V+++ G + P+ S ++ + + + E++ L +V++ +
Sbjct: 116 QSLSVIRRDGTVVHFNPMKISAALEKAFRATDKIEGMTPSSVLEEINALTQNIVEE---I 172
Query: 281 QKLCD-------DVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMRQNPSSDTNSEKR 333
+ C + +Q + Q L+ + YD K ++ ++ R+R N D ++EK
Sbjct: 173 LECCSQEDRIDIEKIQDIVEQQLMVVGH--YDVAKNYILYREARARVRDNKEEDGSTEKT 230
Query: 334 STFNAKDILESLG 346
A ++L G
Sbjct: 231 IAEEAYEVLSKDG 243
>gnl|CDD|214938 smart00958, 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 = 114
Score = 26.6 bits (60), Expect = 9.8
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 12/35 (34%)
Query: 11 RTKHLF----DYDVVNPKIEIID--------GRRY 33
R LF DY V + ++ I+D GRR+
Sbjct: 71 RAHKLFKRDVDYIVRDGEVVIVDEFTGRVMPGRRW 105
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 0.137 0.399
Gapped
Lambda K H
0.267 0.0863 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,461,895
Number of extensions: 1879457
Number of successful extensions: 1467
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1458
Number of HSP's successfully gapped: 40
Length of query: 380
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 281
Effective length of database: 6,546,556
Effective search space: 1839582236
Effective search space used: 1839582236
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: 60 (26.6 bits)