RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3939
(123 letters)
>gnl|CDD|201657 pfam01199, Ribosomal_L34e, Ribosomal protein L34e.
Length = 94
Score = 85.4 bits (212), Expect = 4e-23
Identities = 40/71 (56%), Positives = 48/71 (67%)
Query: 8 VKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCH 67
V+TPGGRLVYHY KK P+CG C L GI + R E R+S+ +K V R YGGVLCH
Sbjct: 23 VRTPGGRLVYHYEKKKPSKPKCGDCGKPLNGIPRLRPRELRRLSKTQKRVSRPYGGVLCH 82
Query: 68 KCVKEKFIYCF 78
KCV+E+ I F
Sbjct: 83 KCVRERIIRAF 93
>gnl|CDD|185429 PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional.
Length = 135
Score = 73.2 bits (180), Expect = 7e-18
Identities = 36/71 (50%), Positives = 46/71 (64%)
Query: 8 VKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCH 67
VKTPGGRLV KK P+CG C L GI+ R E ++SRR + V R+YGGVLCH
Sbjct: 23 VKTPGGRLVVQKRKKKSSGPKCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCH 82
Query: 68 KCVKEKFIYCF 78
KCV+++ + F
Sbjct: 83 KCVRDRIVRAF 93
>gnl|CDD|225085 COG2174, RPL34A, Ribosomal protein L34E [Translation, ribosomal
structure and biogenesis].
Length = 93
Score = 65.1 bits (159), Expect = 5e-15
Identities = 35/78 (44%), Positives = 44/78 (56%)
Query: 8 VKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCH 67
VKTPGGR V HY KK +P+C C L GI + R E R+S+ +K +R YGG LC
Sbjct: 16 VKTPGGRTVIHYEKKKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCA 75
Query: 68 KCVKEKFIYCFFYSHCKI 85
CV+E+ F KI
Sbjct: 76 NCVRERIKRAFRIEEQKI 93
>gnl|CDD|178710 PLN03166, PLN03166, 60S ribosomal protein L34; Provisional.
Length = 96
Score = 54.6 bits (131), Expect = 5e-11
Identities = 34/73 (46%), Positives = 43/73 (58%), Gaps = 2/73 (2%)
Query: 8 VKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIE--RSRMSRRRKMVKRSYGGVL 65
VKTPGG+LVY KK P+C ++ GI R E RSR+SR R+ V R+YGGVL
Sbjct: 23 VKTPGGKLVYQTTKKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVL 82
Query: 66 CHKCVKEKFIYCF 78
V+E+ I F
Sbjct: 83 SGSAVRERIIRAF 95
>gnl|CDD|179734 PRK04059, rpl34e, 50S ribosomal protein L34e; Validated.
Length = 88
Score = 54.2 bits (131), Expect = 5e-11
Identities = 26/69 (37%), Positives = 37/69 (53%)
Query: 8 VKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCH 67
V+TPGGR V HY +K +C C L G+ + R +E ++ + K +R YGG LC
Sbjct: 16 VRTPGGRTVIHYERKKPSKAKCAICGKPLNGVPRGRPVEIRKLGKTEKRPERPYGGYLCP 75
Query: 68 KCVKEKFIY 76
KC+K
Sbjct: 76 KCLKRLIKA 84
Score = 30.0 bits (68), Expect = 0.11
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 83 CKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKE 123
C L G+ + R +E ++ + K +R YGG LC KC+K
Sbjct: 40 CGKPLNGVPRGRPVEIRKLGKTEKRPERPYGGYLCPKCLKR 80
>gnl|CDD|235571 PRK05704, PRK05704, dihydrolipoamide succinyltransferase;
Validated.
Length = 407
Score = 28.6 bits (65), Expect = 0.74
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 37 PGIEKARSIERSRMSRRRKMVKR 59
P AR ER M+R RK +
Sbjct: 170 PAPLGARPEERVPMTRLRKTIAE 192
Score = 28.6 bits (65), Expect = 0.74
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 88 PGIEKARSIERSRMSRRRKMVKR 110
P AR ER M+R RK +
Sbjct: 170 PAPLGARPEERVPMTRLRKTIAE 192
>gnl|CDD|153136 cd01586, AcnA_IRP, Aconitase A catalytic domain. Aconitase A
catalytic domain. This is the major form of the TCA
cycle enzyme aconitate hydratase, also known as
aconitase and citrate hydrolyase. It includes bacterial
and archaeal aconitase A, and the eukaryotic cytosolic
form of aconitase. This group also includes sequences
that have been shown to act as an iron-responsive
element (IRE) binding protein in animals and may have
the same role in other eukaryotes.
Length = 404
Score = 28.0 bits (63), Expect = 1.1
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 6 PSVKT---PGGRLVYHYLKKAGKVP 27
P VKT PG R+V YL+ +G +P
Sbjct: 303 PYVKTSLAPGSRVVTKYLEASGLLP 327
>gnl|CDD|236445 PRK09277, PRK09277, aconitate hydratase; Validated.
Length = 888
Score = 27.4 bits (62), Expect = 2.2
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 6 PSVKT---PGGRLVYHYLKKAG 24
P VKT PG ++V YL+KAG
Sbjct: 458 PWVKTSLAPGSKVVTDYLEKAG 479
>gnl|CDD|237246 PRK12881, acnA, aconitate hydratase; Provisional.
Length = 889
Score = 27.2 bits (61), Expect = 2.2
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 6 PSVKT---PGGRLVYHYLKKAG 24
P VKT PG ++V YL++AG
Sbjct: 459 PWVKTSLAPGSKVVTEYLERAG 480
>gnl|CDD|233883 TIGR02475, CobW, cobalamin biosynthesis protein CobW. The family
of proteins identified by this model is generally found
proximal to the trimeric cobaltochelatase subunit CobN
which is essential for vitamin B12 (cobalamin)
biosynthesis. The protein contains an P-loop
nucleotide-binding loop in the N-terminal domain and a
histidine-rich region in the C-terminal portion
suggesting a role in metal binding, possibly as an
intermediary between the cobalt transport and chelation
systems. A broader CobW family is delineated by two PFAM
models which identify the N- and C-terminal domains
(pfam02492 and pfam07683) [Biosynthesis of cofactors,
prosthetic groups, and carriers, Heme, porphyrin, and
cobalamin].
Length = 341
Score = 26.6 bits (59), Expect = 3.6
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 38 GIEKARSIERSRMSRRRKMVKRSYGGV 64
G+ + R+ + + R K+V+ S+G V
Sbjct: 190 GLARVRAEIAAELPRAVKIVEASHGEV 216
Score = 26.6 bits (59), Expect = 3.6
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 89 GIEKARSIERSRMSRRRKMVKRSYGGV 115
G+ + R+ + + R K+V+ S+G V
Sbjct: 190 GLARVRAEIAAELPRAVKIVEASHGEV 216
>gnl|CDD|132783 cd06873, PX_SNX13, The phosphoinositide binding Phox Homology
domain of Sorting Nexin 13. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions. Sorting nexins (SNXs)
make up the largest group among PX domain containing
proteins. They are involved in regulating membrane
traffic and protein sorting in the endosomal system. The
PX domain of SNXs binds PIs and targets the protein to
PI-enriched membranes. SNXs differ from each other in
PI-binding specificity and affinity, and the presence of
other protein-protein interaction domains, which help
determine subcellular localization and specific function
in the endocytic pathway. SNX13, also called RGS-PX1,
contains an N-terminal PXA domain, a regulator of G
protein signaling (RGS) domain, a PX domain, and a
C-terminal domain that is conserved in some SNXs. It
specifically binds to the stimulatory subunit of the
heterotrimeric G protein G(alpha)s, serving as its
GTPase activating protein, through the RGS domain. It
preferentially binds phosphatidylinositol-3-phosphate
(PI3P) through the PX domain and is localized in early
endosomes. SNX13 is involved in endosomal sorting of
EGFR into multivesicular bodies (MVB) for delivery to
the lysosome.
Length = 120
Score = 25.7 bits (57), Expect = 4.8
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 67 HKCVKEKFIYCFFYSHCKIKLPGIEKARSIERSRMSRRRKM 107
H +KEKF + K+ PG + +++R+ + +RRKM
Sbjct: 54 HMRLKEKF-----PNLSKLSFPGKKTFNNLDRAFLEKRRKM 89
>gnl|CDD|233363 TIGR01341, aconitase_1, aconitate hydratase 1. This model
represents one form of the TCA cycle enzyme aconitate
hydratase, also known as aconitase and citrate
hydro-lyase. It is found in bacteria, archaea, and
eukaryotic cytosol. It has been shown to act also as an
iron-responsive element binding protein in animals and
may have the same role in other eukaryotes [Energy
metabolism, TCA cycle].
Length = 876
Score = 26.3 bits (58), Expect = 4.8
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 6 PSVKT---PGGRLVYHYLKKAGKVP 27
P VKT PG ++V YL ++G +P
Sbjct: 448 PYVKTSLAPGSKVVTDYLAESGLLP 472
>gnl|CDD|236888 PRK11263, PRK11263, cardiolipin synthase 2; Provisional.
Length = 411
Score = 26.1 bits (58), Expect = 5.1
Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 5 LPSVKTPGGRLVYHYLKKAG 24
+P V+ G RL+Y+YL K G
Sbjct: 259 MPIVRV-GARLLYNYLLKGG 277
>gnl|CDD|165563 PHA03308, PHA03308, transcriptional regulator ICP4; Provisional.
Length = 1463
Score = 26.3 bits (57), Expect = 6.3
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 32 CKIKLPGIEKARSIERSRMSRRRKMVKRS 60
C LP +EK ++ R + R+ + V RS
Sbjct: 166 CPCPLPAVEKTTAVRRQEVVRKSERVARS 194
Score = 26.3 bits (57), Expect = 6.3
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 83 CKIKLPGIEKARSIERSRMSRRRKMVKRS 111
C LP +EK ++ R + R+ + V RS
Sbjct: 166 CPCPLPAVEKTTAVRRQEVVRKSERVARS 194
>gnl|CDD|185123 PRK15201, PRK15201, fimbriae regulatory protein FimW; Provisional.
Length = 198
Score = 25.8 bits (56), Expect = 7.4
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 64 VLCHKCVKEKFIYCFFYSHCKIKLPGIEKARSIE----RSRMSRRRKMVKRSYGGVLCHK 119
++C+KC KEK + + C LP I + +E + + ++ ++ S +CH
Sbjct: 73 IICNKCDKEKLM----FRPCLYMLPHIYREDDVEEITRKMILILHKRALRHSVPSGICHY 128
Query: 120 C 120
C
Sbjct: 129 C 129
>gnl|CDD|176118 cd08427, PBP2_LTTR_like_2, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator, contains the type 2 periplasmic binding fold.
LysR-transcriptional regulators comprise the largest
family of prokaryotic transcription factor. Homologs of
some of LTTRs with similar domain organizations are also
found in the archaea and eukaryotic organisms. The LTTRs
are composed of two functional domains joined by a
linker helix involved in oligomerization: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The genes controlled by the
LTTRs have diverse functional roles including amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to a name a few. This substrate-binding domain
shows significant homology to the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 195
Score = 25.2 bits (56), Expect = 8.7
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 11 PGGRLVYHYLKKAGKVPRC 29
GGRLV +L++ G R
Sbjct: 106 WGGRLVDRFLRRQGIRVRE 124
>gnl|CDD|239299 cd03001, PDI_a_P5, PDIa family, P5 subfamily; composed of
eukaryotic proteins similar to human P5, a PDI-related
protein with a domain structure of aa'b (where a and a'
are redox active TRX domains and b is a redox inactive
TRX-like domain). Like PDI, P5 is located in the
endoplasmic reticulum (ER) and displays both isomerase
and chaperone activities, which are independent of each
other. Compared to PDI, the isomerase and chaperone
activities of P5 are lower. The first cysteine in the
CXXC motif of both redox active domains in P5 is
necessary for isomerase activity. The P5 gene was first
isolated as an amplified gene from a
hydroxyurea-resistant hamster cell line. The zebrafish
P5 homolog has been implicated to play a critical role
in establishing left/right asymmetries in the embryonic
midline. Some members of this subfamily are P5-like
proteins containing only one redox active TRX domain.
Length = 103
Score = 24.9 bits (55), Expect = 9.1
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 27 PRCGHCKIKLPGIEKA 42
P CGHCK P +KA
Sbjct: 28 PWCGHCKNLAPEWKKA 43
>gnl|CDD|233282 TIGR01130, ER_PDI_fam, protein disulfide isomerase, eukaryotic.
This model represents eukaryotic protein disulfide
isomerases retained in the endoplasmic reticulum (ER)
and closely related forms. Some members have been
assigned alternative or additional functions such as
prolyl 4-hydroxylase and
dolichyl-diphosphooligosaccharide-protein
glycotransferase. Members of this family have at least
two protein-disulfide domains, each similar to
thioredoxin but with the redox-active disulfide in the
motif PWCGHCK, and an ER retention signal at the
extreme C-terminus (KDEL, HDEL, and similar motifs).
Length = 462
Score = 25.4 bits (56), Expect = 9.3
Identities = 10/16 (62%), Positives = 10/16 (62%)
Query: 27 PRCGHCKIKLPGIEKA 42
P CGHCK P EKA
Sbjct: 28 PWCGHCKSLAPEYEKA 43
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
0.328 0.140 0.444
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,150,859
Number of extensions: 515532
Number of successful extensions: 665
Number of sequences better than 10.0: 1
Number of HSP's gapped: 664
Number of HSP's successfully gapped: 38
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.2 bits)