RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3716
(436 letters)
>gnl|CDD|214803 smart00753, PAM, PCI/PINT associated module.
Length = 88
Score = 51.5 bits (124), Expect = 2e-08
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 4/87 (4%)
Query: 276 ENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHI 335
+L +KI L L++L+ +S +++++ L + EVE L+ KA+ G + I
Sbjct: 3 VERLQRKIRLTNLLQLSEPY----SSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKI 58
Query: 336 DQVDESFNVTWVQPRVLSKDQLAFKKI 362
DQV+ V PR + +
Sbjct: 59 DQVNGIVEFEEVDPRRSEPLAQFAETL 85
Score = 48.8 bits (117), Expect = 1e-07
Identities = 17/58 (29%), Positives = 28/58 (48%)
Query: 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVF 424
+S +++++ L + EVE L+ KA+ G + IDQV+ V PR F
Sbjct: 24 SISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRRSEPLAQF 81
>gnl|CDD|214509 smart00088, PINT, motif in proteasome subunits, Int-6, Nip-1 and
TRIP-15. Also called the PCI (Proteasome, COP9,
Initiation factor 3) domain. Unknown function.
Length = 88
Score = 51.5 bits (124), Expect = 2e-08
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 4/87 (4%)
Query: 276 ENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHI 335
+L +KI L L++L+ +S +++++ L + EVE L+ KA+ G + I
Sbjct: 3 VERLQRKIRLTNLLQLSEPY----SSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKI 58
Query: 336 DQVDESFNVTWVQPRVLSKDQLAFKKI 362
DQV+ V PR + +
Sbjct: 59 DQVNGIVEFEEVDPRRSEPLAQFAETL 85
Score = 48.8 bits (117), Expect = 1e-07
Identities = 17/58 (29%), Positives = 28/58 (48%)
Query: 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVF 424
+S +++++ L + EVE L+ KA+ G + IDQV+ V PR F
Sbjct: 24 SISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRRSEPLAQF 81
>gnl|CDD|216479 pfam01399, PCI, PCI domain. This domain has also been called the
PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
Length = 100
Score = 49.9 bits (120), Expect = 8e-08
Identities = 30/97 (30%), Positives = 50/97 (51%), Gaps = 7/97 (7%)
Query: 246 ELLRAFNAGDIEKF-ELMRPQWSAMNDIKANE--NKLSQKIALLCLMELAFKKIPGSHQL 302
+LLRAF +GD+ F E++ + D E L +KI L L LA +
Sbjct: 3 DLLRAFYSGDLSDFEEILADNEDELLDDGLAELLEDLRRKIRELNLRRLAKP----YSSI 58
Query: 303 SFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVD 339
S +++++ L + EVE ++ K + G ++G IDQV+
Sbjct: 59 SLSDLAKLLGLSVDEVEKILSKLIRDGRIRGKIDQVN 95
Score = 37.2 bits (87), Expect = 0.002
Identities = 12/40 (30%), Positives = 25/40 (62%)
Query: 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVD 405
+S +++++ L + EVE ++ K + G ++G IDQV+
Sbjct: 56 SSISLSDLAKLLGLSVDEVEKILSKLIRDGRIRGKIDQVN 95
>gnl|CDD|215575 PLN03100, PLN03100, Permease subunit of ER-derived-lipid
transporter; Provisional.
Length = 292
Score = 31.7 bits (72), Expect = 0.67
Identities = 17/37 (45%), Positives = 22/37 (59%), Gaps = 5/37 (13%)
Query: 209 FLIGLAA--LLADSVYNIGELLAHPILDSLQQTPNAW 243
F +G+AA LLADSVY + A+ ILDS + W
Sbjct: 196 FTVGMAASALLADSVYGVS---ANIILDSAARALRPW 229
>gnl|CDD|213992 cd07437, PHP_HisPPase_Ycdx_like, Polymerase and Histidinol
Phosphatase domain of Ycdx like. PHP Ycdx-like is a
stand alone PHP domain similar to Ycdx E. coli protein
with an unknown physiological role. The PHP (also called
histidinol phosphatase-2/HIS2) domain is associated with
several types of DNA polymerases, such as PolIIIA and
family X DNA polymerases, stand alone histidinol
phosphate phosphatases (HisPPases), and a number of
uncharacterized protein families. The PHP domain has
four conserved sequence motifs and contains an invariant
histidine that is involved in metal ion coordination. It
has also been shown that the PHP domain functions in DNA
repair. The PHP structures have a distorted
(beta/alpha)7 barrel fold with a trinuclear metal site
on the C-terminal side of the barrel. YcdX may be
involved in swarming.
Length = 233
Score = 30.1 bits (69), Expect = 1.9
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 7/43 (16%)
Query: 119 LCKILQAQMIMNKDA---DKPGSLDEVEKLIDEI----ELLVN 154
LCK +I+ DA G+ DE +L++EI EL++N
Sbjct: 178 LCKKYGVPVIVGSDAHIAYDIGNFDEALELLEEIGFPEELILN 220
>gnl|CDD|182415 PRK10370, PRK10370, formate-dependent nitrite reductase complex
subunit NrfG; Provisional.
Length = 198
Score = 29.5 bits (66), Expect = 2.5
Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 7 PTVYLTAKQEAYSKNPEISAQWLNLEELYNKKLW-HQLTLAVLAFVQNPAIQKEGELRDL 65
P L A Q+ NP+ S QW L E Y LW + A+LA+ Q A+Q GE +L
Sbjct: 55 PEAQLQALQDKIRANPQNSEQWALLGEYY---LWRNDYDNALLAYRQ--ALQLRGENAEL 109
Query: 66 Y 66
Y
Sbjct: 110 Y 110
>gnl|CDD|214886 smart00888, EF1_GNE, EF-1 guanine nucleotide exchange domain.
Translation elongation factors are responsible for two
main processes during protein synthesis on the ribosome.
EF1A (or EF-Tu) is responsible for the selection and
binding of the cognate aminoacyl-tRNA to the A-site
(acceptor site) of the ribosome. EF2 (or EF-G) is
responsible for the translocation of the peptidyl-tRNA
from the A-site to the P-site (peptidyl-tRNA site) of
the ribosome, thereby freeing the A-site for the next
aminoacyl-tRNA to bind. Elongation factors are
responsible for achieving accuracy of translation and
both EF1A and EF2 are remarkably conserved throughout
evolution. Elongation factor EF1B (also known as EF-Ts
or EF-1beta/gamma/delta) is a nucleotide exchange factor
that is required to regenerate EF1A from its inactive
form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is
then ready to interact with a new aminoacyl-tRNA to
begin the cycle again. EF1B is more complex in
eukaryotes than in bacteria, and can consist of three
subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or
EF-1gamma) and EF1B-beta (or EF-1delta). This entry
represents the guanine nucleotide exchange domain of the
beta (EF-1beta, also known as EF1B-alpha) and delta
(EF-1delta, also known as EF1B-beta) chains of EF1B
proteins from eukaryotes and archaea. The beta and delta
chains have exchange activity, which mainly resides in
their homologous guanine nucleotide exchange domains,
found in the C-terminal region of the peptides. Their
N-terminal regions may be involved in interactions with
the gamma chain (EF-1gamma).
Length = 88
Score = 28.2 bits (64), Expect = 2.5
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 18/75 (24%)
Query: 103 LQSFEDKVKNNLEAKSLCKI--------------LQAQMIMNKDADKPGSLDEVEKLIDE 148
L+ E+KVK+ L L LQ +++ D G DE+E+ I+E
Sbjct: 17 LEELEEKVKSILPMDGLLWGAGIELEPIAFGLKALQIYVVVE---DDEGGTDELEEAIEE 73
Query: 149 IELLVN-DIEGVTAI 162
+E + + ++E V+ +
Sbjct: 74 VEGVQSVEVEAVSRL 88
>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
Length = 338
Score = 28.6 bits (64), Expect = 6.2
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 220 SVYNIGELLAHPILDSLQQTPNAWLVELLRAFN 252
S Y +L+ IL LQ+ W + LLR FN
Sbjct: 147 SPYGKSKLMVEQILTDLQKAQPDWSIALLRYFN 179
>gnl|CDD|106506 PRK13560, PRK13560, hypothetical protein; Provisional.
Length = 807
Score = 28.9 bits (64), Expect = 6.5
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 98 EALVLLQSFEDKVKNNLEAKSLCKILQAQMIMNKDA 133
E VLL+ +VKNNL+ S LQA+ + +++A
Sbjct: 604 EKEVLLKEIHHRVKNNLQIISSLLDLQAEKLHDEEA 639
>gnl|CDD|217382 pfam03135, CagE_TrbE_VirB, CagE, TrbE, VirB family, component of
type IV transporter system. This family includes the
Helicobacter pylori protein CagE, which together with
other proteins from the cag pathogenicity island (PAI),
encodes a type IV transporter secretion system. The
precise role of CagE is not known, but studies in animal
models have shown that it is essential for pathogenesis
in Helicobacter pylori induced gastritis and peptic
ulceration. Indeed, the expression of the cag PAI has
been shown to be essential for stimulating human gastric
epithelial cell apoptosis in vitro. Similar type IV
transport systems are also found in other bacteria. This
family includes the TrbE and VirB proteins from the
respective trb and Vir conjugal transfer systems in
Agrobacterium tumefaciens. Homologues of VirB proteins
from other species are also members of this family, e.g.
VirB from Brucella suis.
Length = 205
Score = 28.0 bits (63), Expect = 8.8
Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 6/94 (6%)
Query: 89 ITNHLSDQEEALVLLQSFEDKVKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDE 148
+ L D + +L QSF K K +AKS K Q ++I D + ++E+L +
Sbjct: 82 ALDVLLDLDFEFILTQSFSFKSKQ--KAKSFLKRFQKRLISISD----DAKSQIEELEEA 135
Query: 149 IELLVNDIEGVTAIHSRFYLVASTLYRKQAKLSL 182
++ L + + H + A + A LS
Sbjct: 136 LDELRSGDFVLGLHHLSLVVFAEDKEKLDASLSE 169
>gnl|CDD|236791 PRK10902, PRK10902, FKBP-type peptidyl-prolyl cis-trans isomerase;
Provisional.
Length = 269
Score = 28.2 bits (63), Expect = 9.4
Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 12/42 (28%)
Query: 93 LSDQEEALVLLQSFEDKVKNNLEAKSLCKILQAQMIMNKDAD 134
LSDQE L Q+FE +VK+ +AK M KDA
Sbjct: 93 LSDQEIEQTL-QAFEARVKSAAQAK-----------MEKDAA 122
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 0.134 0.378
Gapped
Lambda K H
0.267 0.0827 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,547,253
Number of extensions: 2260768
Number of successful extensions: 2108
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2103
Number of HSP's successfully gapped: 45
Length of query: 436
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 336
Effective length of database: 6,502,202
Effective search space: 2184739872
Effective search space used: 2184739872
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: 60 (26.7 bits)