RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy986
(71 letters)
>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 = 42.5 bits (101), Expect = 3e-07
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
E + VP +LVG++IGK G I+EI +++G ++KI
Sbjct: 1 TERVLVPSSLVGRIIGKGGSTIKEIREETG-AKIKIPDSGSGSE 43
>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 = 39.9 bits (94), Expect = 3e-06
Identities = 15/41 (36%), Positives = 28/41 (68%), Gaps = 1/41 (2%)
Query: 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE 46
E + +P + VG++IGK G I+EI +++G V+++I D +
Sbjct: 1 TERILIPPDKVGRIIGKGGSNIKEIREETG-VKIRIPDDRD 40
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 38.0 bits (89), Expect = 1e-05
Identities = 13/46 (28%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTL 51
+ +P + VG +IGK G I++I +++G V++ I G + +
Sbjct: 4 TIEVLIPADKVGLIIGKGGSTIKKIEEETG-VKIDIPGPGSEERVV 48
>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like.
Members of this group possess KH domains in a tandem
arrangement. Most members, similar to the poly(C)
binding proteins (PCBPs) and Nova, containing three KH
domains, with the first and second domains, which are
represented here, in tandem arrangement, followed by a
large spacer region, with the third domain near the
C-terminal end of the protein. The poly(C) binding
proteins (PCBPs) can be divided into two groups, hnRNPs
K/J and the alphaCPs, which share a triple KH domain
configuration and poly(C) binding specificity. They
play roles in mRNA stabilization, translational
activation, and translational silencing. Nova-1 and
Nova-2 are nuclear RNA-binding proteins that regulate
splicing. This group also contains plant proteins that
seem to have two tandem repeat arrrangements, like
Hen4, a protein that plays a role in AGAMOUS (AG)
pre-mRNA processing and important step in plant
development. 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 = 65
Score = 37.1 bits (87), Expect = 3e-05
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 11 VPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
VP + G +IGK G I+EI +++G ++++ P T
Sbjct: 6 VPSSQAGSIIGKGGSTIKEIREETG-AKIRVSKSVLPGST 44
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 37.3 bits (88), Expect = 2e-04
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVV-------RVKIEGDNEPQ 48
E++++P + + VIG G+ I+EI +++G VKI +
Sbjct: 556 ETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAATDGEA 604
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 36.7 bits (86), Expect = 2e-04
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 11 VPRNLVGKVIGKNGRIIQEIVDKSGV-VRVKIEGDNEPQPTLPREEGQV 58
VP + KVIGK G+ I++I K G+ + V+ + + EE V
Sbjct: 487 VPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEPGEEAEEGEEVTV 535
>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 = 34.0 bits (79), Expect = 5e-04
Identities = 11/31 (35%), Positives = 22/31 (70%)
Query: 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGV 36
E +++P+ L +IGK G I++I++++GV
Sbjct: 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGV 31
>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 = 34.8 bits (81), Expect = 0.001
Identities = 12/38 (31%), Positives = 26/38 (68%), Gaps = 1/38 (2%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
E++++ + + VIG G++I+EI +++G ++ IE D
Sbjct: 553 ETIKINPDKIRDVIGPGGKVIREITEETG-AKIDIEDD 589
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 34.5 bits (80), Expect = 0.001
Identities = 13/46 (28%), Positives = 28/46 (60%), Gaps = 3/46 (6%)
Query: 1 MLEYSE--ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
+ Y+ E++++ + + VIG G+ I+ I +++G V++ IE D
Sbjct: 546 LSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETG-VKIDIEDD 590
>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 = 31.8 bits (73), Expect = 0.002
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 15 LVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
LVG +IGK G I+EI +++G +++I
Sbjct: 1 LVGAIIGKGGETIKEIREETG-AKIQIPKPEPGSG 34
>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 = 31.7 bits (73), Expect = 0.004
Identities = 13/38 (34%), Positives = 28/38 (73%), Gaps = 1/38 (2%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
E++++P + + VIG G+ I++I++++G V++ IE D
Sbjct: 4 ETMKIPPDKIRDVIGPGGKTIKKIIEETG-VKIDIEDD 40
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase
I/polynucleotide phosphorylase. Sohlberg, et al present
characterization of two proteins from Streptomyces
coelicolor. The protein in this family was shown to have
poly(A) polymerase activity and may be responsible for
polyadenylating RNA in this species. Reference 2 showed
that a nearly identical plasmid-encoded protein from
Streptomyces antibioticus is a bifunctional enzyme that
acts also as a guanosine pentaphosphate synthetase.
Length = 719
Score = 29.8 bits (67), Expect = 0.083
Identities = 13/37 (35%), Positives = 26/37 (70%), Gaps = 1/37 (2%)
Query: 8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
++++P + +G+VIG G++I +I D++G + IE D
Sbjct: 581 TVKIPVDKIGEVIGPKGKMINQIQDETG-AEISIEDD 616
>gnl|CDD|224750 COG1837, COG1837, Predicted RNA-binding protein (contains KH
domain) [General function prediction only].
Length = 76
Score = 28.3 bits (64), Expect = 0.10
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 16 VGKVIGKNGRIIQEI 30
+GKVIGK GR IQ I
Sbjct: 41 MGKVIGKQGRTIQAI 55
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 29.3 bits (66), Expect = 0.13
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 11 VPRNLVGKVIGKNGRIIQEIVDKSGV-VRVKIEGDNEPQPTLPRE 54
VP + KVIGK G+ I+EI K G+ + VK + E +P E
Sbjct: 492 VPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEEGEKVPVE 536
>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 180
Score = 27.9 bits (63), Expect = 0.32
Identities = 12/42 (28%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDN 45
E +++P++ +G +IGK G +EI +++G V+++I+ +
Sbjct: 2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTG-VKLEIDSET 42
>gnl|CDD|100095 cd05802, GlmM, GlmM is a bacterial phosphoglucosamine mutase (PNGM)
that belongs to the alpha-D-phosphohexomutase
superfamily. It is required for the interconversion of
glucosamine-6-phosphate and glucosamine-1-phosphate in
the biosynthetic pathway of UDP-N-acetylglucosamine, an
essential precursor to components of the cell envelope.
In order to be active, GlmM must be phosphorylated,
which can occur via autophosphorylation or by the
Ser/Thr kinase StkP. GlmM functions in a classical
ping-pong bi-bi mechanism with
glucosamine-1,6-diphosphate as an intermediate. Other
members of the alpha-D-phosphohexomutase superfamily
include phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 434
Score = 27.8 bits (63), Expect = 0.32
Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 6/32 (18%)
Query: 18 KVIGKNGRIIQEIVDKSG---VVRVKIEGDNE 46
K +G GR++ V SG ++RV +EG++E
Sbjct: 395 KELGGEGRVL---VRPSGTEPLIRVMVEGEDE 423
>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase;
Provisional.
Length = 891
Score = 26.4 bits (58), Expect = 1.1
Identities = 9/36 (25%), Positives = 21/36 (58%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
++V V +IG G+ ++ I++++GV + + D
Sbjct: 689 MKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD 724
>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 = 26.4 bits (59), Expect = 1.1
Identities = 12/47 (25%), Positives = 28/47 (59%), Gaps = 10/47 (21%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEI---------VD-KSGVVRVKIEGDN 45
+++P++ +G +IGK G +EI +D ++G V+++ E ++
Sbjct: 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDED 48
>gnl|CDD|236787 PRK10887, glmM, phosphoglucosamine mutase; Provisional.
Length = 443
Score = 26.3 bits (59), Expect = 1.2
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 6/49 (12%)
Query: 3 EYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSG---VVRVKIEGDNEPQ 48
E+++ V +G GR++ + KSG ++RV +EG++E Q
Sbjct: 382 PLESEAVKAALAEVEAELGGRGRVL---LRKSGTEPLIRVMVEGEDEAQ 427
>gnl|CDD|221909 pfam13083, KH_4, KH domain.
Length = 71
Score = 25.1 bits (56), Expect = 1.6
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 16 VGKVIGKNGRIIQEI 30
+GK+IGK GR + +
Sbjct: 39 LGKLIGKRGRTLDAL 53
>gnl|CDD|222894 PHA02588, cd, deoxycytidylate deaminase; Provisional.
Length = 168
Score = 25.9 bits (57), Expect = 1.8
Identities = 10/12 (83%), Positives = 10/12 (83%)
Query: 16 VGKVIGKNGRII 27
VG VI KNGRII
Sbjct: 24 VGAVIEKNGRII 35
>gnl|CDD|205365 pfam13184, KH_5, NusA-like KH domain.
Length = 67
Score = 24.9 bits (55), Expect = 2.0
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 16 VGKVIGKNGRIIQEIVDKSGVVRVKI 41
VG +GK G I+ I D+ ++ +
Sbjct: 17 VGACVGKKGSRIRAISDELNGEKIDV 42
>gnl|CDD|222404 pfam13829, DUF4191, Domain of unknown function (DUF4191).
Length = 223
Score = 25.6 bits (57), Expect = 2.5
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 54 EEGQVPFMVLTKTVYRLK 71
EGQVP L KT+ +L
Sbjct: 164 GEGQVPLRKLQKTLMKLP 181
>gnl|CDD|214485 smart00044, CYCc, Adenylyl- / guanylyl cyclase, catalytic domain.
Present in two copies in mammalian adenylyl cyclases.
Eubacterial homologues are known. Two residues (Asn,
Arg) are thought to be involved in catalysis. These
cyclases have important roles in a diverse range of
cellular processes.
Length = 194
Score = 24.9 bits (55), Expect = 3.7
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 26 IIQEIVDKSGVVRVKIEGD 44
+I+D+ G +VK GD
Sbjct: 69 RFDQIIDRHGGYKVKTIGD 87
>gnl|CDD|179040 PRK00468, PRK00468, hypothetical protein; Provisional.
Length = 75
Score = 24.3 bits (53), Expect = 3.9
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEI 30
L+V +GKVIGK GRI + I
Sbjct: 34 LKVAPEDMGKVIGKQGRIAKAI 55
>gnl|CDD|178206 PLN02596, PLN02596, hexokinase-like.
Length = 490
Score = 24.8 bits (54), Expect = 4.1
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 36 VVRVKIEGDNEPQPTLPREEGQVPFMVLTKTVYRL 70
++R ++ G NEP L REE +P VL T L
Sbjct: 110 LLRARLGGKNEPISDLYREEISIPSNVLNGTSQEL 144
>gnl|CDD|188365 TIGR03675, arCOG00543, arCOG00543 universal archaeal
KH-domain/beta-lactamase-domain protein. This family of
proteins is universal in the archaea and consistsof an
N-terminal type-1 KH-domain (pfam00013) a central
beta-lactamase-domain (pfam00753) with a C-terminal
motif associated with RNA metabolism (pfam07521).
KH-domains are associated with RNA-binding, so taken
together, this protein is a likely metal-dependent
RNAase. This family was defined in as arCOG01782.
Length = 630
Score = 24.9 bits (55), Expect = 4.3
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 4/26 (15%)
Query: 17 GKVIGKNGRIIQEIVDKSG----VVR 38
G VIGK G ++EI ++G VVR
Sbjct: 105 GLVIGKGGSTLREITKETGWTPKVVR 130
>gnl|CDD|217309 pfam02990, EMP70, Endomembrane protein 70.
Length = 518
Score = 24.6 bits (54), Expect = 4.7
Identities = 8/40 (20%), Positives = 14/40 (35%)
Query: 22 KNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
+ RI+ V V + PQ +E ++ F
Sbjct: 128 DDYRIVGIEVTPRSVKPSGCSTTSSPQELDEGKENELTFT 167
>gnl|CDD|173796 cd04857, Peptidases_S8_Tripeptidyl_Aminopeptidase_II, Peptidase S8
family domain in Tripeptidyl aminopeptidases_II.
Tripeptidyl aminopeptidases II are member of the
peptidase S8 or Subtilase family. Subtilases, or
subtilisin-like serine proteases, have an Asp/His/Ser
catalytic triad similar to that found in trypsin-like
proteases, but do not share their three-dimensional
structure (an example of convergent evolution).
Tripeptidyl aminopeptidase II removes tripeptides from
the free N terminus of oligopeptides as well as having
endoproteolytic activity. Some tripeptidyl
aminopeptidases have been shown to cleave tripeptides
and small peptides, e.g. angiotensin II and glucagon,
while others are believed to be involved in MHC I
processing.
Length = 412
Score = 24.6 bits (54), Expect = 4.8
Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 24 GRII---QEIVDKSGVVRVKIEGDNEP 47
GRII E V+K GV+ V G+N P
Sbjct: 262 GRIIELMNEAVNKHGVIFVSSAGNNGP 288
>gnl|CDD|180696 PRK06793, fliI, flagellum-specific ATP synthase; Validated.
Length = 432
Score = 24.6 bits (53), Expect = 4.9
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 7 ESLQVPRN--LVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREE 55
E + +PR L+GKV+ NG ++ E + + ++K+ D P REE
Sbjct: 87 EDVVIPRGNHLLGKVLSANGEVLNEEAENIPLQKIKL--DAPPIHAFEREE 135
>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 = 24.4 bits (53), Expect = 6.4
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 7/41 (17%)
Query: 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDN 45
+EE+++ RN V ++IG + R EIV SG E +N
Sbjct: 45 AEEAVENARNQVAELIGADSR---EIVFTSGAT----ESNN 78
>gnl|CDD|235208 PRK04036, PRK04036, DNA polymerase II small subunit; Validated.
Length = 504
Score = 24.1 bits (53), Expect = 6.6
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 22 KNGRIIQEIVDKSGVVRVKIEGDNE 46
KNG I E+ D +G V I D E
Sbjct: 169 KNGHKIVELEDTTGTFPVLIMKDRE 193
>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 24.2 bits (53), Expect = 7.4
Identities = 13/36 (36%), Positives = 25/36 (69%)
Query: 1 MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGV 36
E S E++++P++ +G +IGK G + + I +K+GV
Sbjct: 4 FAEKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGV 39
>gnl|CDD|222539 pfam14097, SpoVAE, Stage V sporulation protein AE1. Members of
this family are all described as putative stage V
sporulation protein AE, although this could not be
confirmed. Proteins in this family are approximately 190
amino acids in length.
Length = 180
Score = 24.1 bits (53), Expect = 8.2
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 3/28 (10%)
Query: 20 IGKNGRIIQEIVDKSGVVRV---KIEGD 44
I +NG + + VDK GV + +I GD
Sbjct: 107 IDRNGELTEYGVDKEGVPEMEIGRINGD 134
>gnl|CDD|179216 PRK01064, PRK01064, hypothetical protein; Provisional.
Length = 78
Score = 23.3 bits (50), Expect = 8.5
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEI 30
L V + +GK+IGK GR I+ I
Sbjct: 34 LTVAKPDIGKIIGKEGRTIKAI 55
>gnl|CDD|221199 pfam11741, AMIN, AMIN domain. This N-terminal domain of various
bacterial protein families is crucial for the
targetting of periplasmic or extracellular proteins to
specific regions of the bacterial envelope. AMIN is
derived from the N-terminal domain of AmiC, an
N-acetylmuramoyl-l-alanine amidase of Escherichia coli
which localises to the septal ring during division and
plays a key role in the separation of daughter cells.
The AMIN domain is present in several protein families
besides amidases suggesting that AMIN may represent a
general targetting determinant involved in the
localisation of periplasmic protein complexes.
Length = 96
Score = 23.4 bits (51), Expect = 9.9
Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 3/45 (6%)
Query: 14 NLVGKVIGKNGRIIQEIVD---KSGVVRVKIEGDNEPQPTLPREE 55
NL K I I+ + + VRV ++ D P + +
Sbjct: 43 NLPLKRIENPSPGIKSVRVTQLDANTVRVVVDLDGSVLPKVELRD 87
>gnl|CDD|227495 COG5166, COG5166, Uncharacterized conserved protein [Function
unknown].
Length = 657
Score = 23.8 bits (51), Expect = 9.9
Identities = 9/32 (28%), Positives = 15/32 (46%)
Query: 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGV 36
+E + + + +IG G IQE + K V
Sbjct: 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAV 480
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
0.314 0.137 0.376
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,585,986
Number of extensions: 277150
Number of successful extensions: 351
Number of sequences better than 10.0: 1
Number of HSP's gapped: 349
Number of HSP's successfully gapped: 59
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.2 bits)