RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8979
(142 letters)
>gnl|CDD|215637 PLN03223, PLN03223, Polycystin cation channel protein; Provisional.
Length = 1634
Score = 32.2 bits (73), Expect = 0.083
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 38 EAQRNRERKELEDRVSVRRALLE-QKMDMETQQFLGERQERIRLLHERQERELE 90
E + ++ ++ LE V+R L E Q +E Q+ + ERQ R+ L + LE
Sbjct: 1577 EKEVDQLQQSLERLAEVQRELAEGQVKVIEGQKQMAERQSRLSQLENKILGVLE 1630
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 30.9 bits (71), Expect = 0.21
Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 11/87 (12%)
Query: 11 ECHHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDR----VSVRRALLEQKMDM- 65
E H L+ EL + +N++Q +R +++E DR + R LE+K
Sbjct: 65 EIHKLRNEFEKELR-----ERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKEL 119
Query: 66 -ETQQFLGERQERIRLLHERQERELES 91
+ QQ L +++E + L E Q +ELE
Sbjct: 120 EQKQQELEKKEEELEELIEEQLQELER 146
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 30.7 bits (70), Expect = 0.23
Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 11/87 (12%)
Query: 11 ECHHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDR----VSVRRALLEQKMD-- 64
E H L+ L EL+ + +N++Q +R +R+E DR + + LE+K
Sbjct: 59 EVHKLRAELERELK-----ERRNELQRLERRLLQREETLDRKMESLDKKEENLEKKEKEL 113
Query: 65 METQQFLGERQERIRLLHERQERELES 91
++ L E++E + L Q ELE
Sbjct: 114 SNKEKNLDEKEEELEELIAEQREELER 140
>gnl|CDD|225803 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell
envelope biogenesis, outer membrane].
Length = 835
Score = 30.4 bits (69), Expect = 0.29
Identities = 19/94 (20%), Positives = 31/94 (32%), Gaps = 29/94 (30%)
Query: 34 KMQAEAQRNRERKELEDRV-----------SVRRA-------LLEQK-----MDMETQQF 70
++ A A +R+ L ++ +V R LL+Q +QF
Sbjct: 80 RLNALASDDRQLANLLLQLLQSSRTIREQIAVLRGSLLLSRILLQQLGPLPEAGQPQEQF 139
Query: 71 LGERQERIRLLHERQ-----ERELESFDQESNRM 99
QER L E+ E + E E +
Sbjct: 140 EVT-QERDALQAEKAYINALEGQAEQLTAEVRDI 172
>gnl|CDD|221371 pfam12004, DUF3498, Domain of unknown function (DUF3498). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 433 to 538 amino acids in length. This domain is
found associated with pfam00616, pfam00168. This domain
has two conserved sequence motifs: DLQ and PLSFQNP.
Length = 489
Score = 29.7 bits (66), Expect = 0.48
Identities = 27/115 (23%), Positives = 42/115 (36%), Gaps = 27/115 (23%)
Query: 3 RLDESQEVECHHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQK 62
E E E LKERL + L Y+ + Q + QK
Sbjct: 363 TQAEKYEQEIARLKERLRVSVRRLEEYERRLLGQEQQM--------------------QK 402
Query: 63 MDMETQQFLGERQERIRLLHERQERELESFDQESNRMGFSALAIAEASKESYPDM 117
+ E Q L + +ER+R R+ E D + + +A+ E K+ + DM
Sbjct: 403 LLQEYQARLEDSEERLR-------RQQEEKDSQMKSIISRLMAVEEELKKDHADM 450
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 29.5 bits (66), Expect = 0.63
Identities = 23/95 (24%), Positives = 37/95 (38%), Gaps = 22/95 (23%)
Query: 15 LKERLHYELEILMAYQSKNKMQAEAQRNRE---------RKELEDRVSVRRALLEQKM-- 63
L E ELE L +++ + QAE QR RE R + + V RR L+ +
Sbjct: 250 LLEEKRRELEKLAKEEAERERQAEEQRRREEEKAAMEADRAQAKAEVEKRREKLQNLLKK 309
Query: 64 ---------DMETQQFLGERQERIRLLHERQEREL 89
+E +F + ++L + R L
Sbjct: 310 ASRSADNVWYIEPSEFKAG--DTVKLYYNRSSGPL 342
>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional.
Length = 1021
Score = 29.3 bits (65), Expect = 0.68
Identities = 27/98 (27%), Positives = 49/98 (50%), Gaps = 5/98 (5%)
Query: 28 AYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDMETQQFLGERQERIRLLHERQER 87
A++ +M+ ++ ER E E+R + R +E+ +E ++ ER ER RL +R ER
Sbjct: 445 AHRKALEMKILEKKRIERLEREERERLERERMER---IERERLERERLERERLERDRLER 501
Query: 88 E-LESFDQES-NRMGFSALAIAEASKESYPDMDGSLSG 123
+ L+ ++E +R+ L A + M+ LS
Sbjct: 502 DRLDRLERERVDRLERDRLEKARRNSYFLKGMENGLSA 539
>gnl|CDD|220186 pfam09335, SNARE_assoc, SNARE associated Golgi protein. This is a
family of SNARE associated Golgi proteins. The yeast
member of this family localises with the t-SNARE Tlg2.
Length = 123
Score = 28.4 bits (64), Expect = 0.73
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 70 FLGERQERIRLLHERQERELESFDQESNRMGFSALAIA 107
+LG R R RLL E+ + L+ ++ R GF AL +
Sbjct: 40 YLGRRALRRRLLKEKAFQRLQRVERLVERYGFKALLLL 77
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 28.8 bits (65), Expect = 0.95
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 13/87 (14%)
Query: 16 KERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQKMDMETQQFLGERQ 75
E E E+L Q + + EAQ ++ + L +KM+ E ++ L E Q
Sbjct: 213 AEAAEAEQELLREKQKEEEQMMEAQERSYQEHV--------KQLIEKMEAEREKLLAE-Q 263
Query: 76 ERIRLLHERQERE---LESFDQESNRM 99
ER+ L H+ QE+E E F E+ +
Sbjct: 264 ERM-LEHKLQEQEELLKEGFKTEAESL 289
>gnl|CDD|130587 TIGR01524, ATPase-IIIB_Mg, magnesium-translocating P-type ATPase.
This model describes the magnesium translocating P-type
ATPase found in a limited number of bacterial species
and best described in Salmonella typhimurium, which
contains two isoforms. These transporters are active in
low external Mg2+ concentrations and pump the ion into
the cytoplasm. The magnesium ATPases have been
classified as type IIIB by a phylogenetic analysis
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 867
Score = 28.3 bits (63), Expect = 1.8
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 7/71 (9%)
Query: 41 RNRERKELEDRVSVRRAL----LEQKMDMETQQFLGERQERIRLLHERQERELESFDQES 96
R R +E+R V R + +E+ + + T + + L E ++ EL+ E
Sbjct: 418 RRRLSVVVENRAEVTRLICKGAVEEMLTVCTHK---RFGGAVVTLSESEKSELQDMTAEM 474
Query: 97 NRMGFSALAIA 107
NR G +A+A
Sbjct: 475 NRQGIRVIAVA 485
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 27.7 bits (62), Expect = 2.1
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 7/78 (8%)
Query: 17 ERLHYE------LEILMAYQSKN-KMQAEAQRNRERKELEDRVSVRRALLEQKMDMETQQ 69
E L YE L L + K EA+ N E +EL+ + + + E++++ Q
Sbjct: 280 ENLLYENYRTEKLSGLKNSGEPSLKEIHEARLNEEERELKKKFTEKIREKEKRLEELEQN 339
Query: 70 FLGERQERIRLLHERQER 87
+ ER+E L E Q++
Sbjct: 340 LIEERKELNSKLEEIQKK 357
>gnl|CDD|184696 PRK14474, PRK14474, F0F1 ATP synthase subunit B; Provisional.
Length = 250
Score = 27.5 bits (61), Expect = 2.4
Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 4/77 (5%)
Query: 6 ESQEVECHHLKERLHYELEILMAYQ----SKNKMQAEAQRNRERKELEDRVSVRRALLEQ 61
E ++ E ER + + L + ++ + A+ QR E + V+ R +
Sbjct: 49 EQRQQEAGQEAERYRQKQQSLEQQRASFMAQAQEAADEQRQHLLNEAREDVATARDEWLE 108
Query: 62 KMDMETQQFLGERQERI 78
+++ E Q+F Q++
Sbjct: 109 QLEREKQEFFKALQQQT 125
>gnl|CDD|187671 cd09811, 3b-HSD_HSDB1_like_SDR_e, human 3beta-HSD (hydroxysteroid
dehydrogenase) and HSD3B1(delta 5-delta
4-isomerase)-like, extended (e) SDRs. This
extended-SDR subgroup includes human 3 beta-HSD/HSD3B1
and C(27) 3beta-HSD/
[3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase;
HSD3B7], and related proteins. These proteins have the
characteristic active site tetrad and NAD(P)-binding
motif of extended SDRs. 3 beta-HSD catalyzes the
oxidative conversion of delta 5-3 beta-hydroxysteroids
to the delta 4-3-keto configuration; this activity is
essential for the biosynthesis of all classes of
hormonal steroids. C(27) 3beta-HSD is a membrane-bound
enzyme of the endoplasmic reticulum, it catalyzes the
isomerization and oxidation of 7alpha-hydroxylated
sterol intermediates, an early step in bile acid
biosynthesis. Mutations in the human gene encoding
C(27) 3beta-HSD underlie a rare autosomal recessive
form of neonatal cholestasis. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid sythase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 354
Score = 27.5 bits (61), Expect = 2.5
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 4/27 (14%)
Query: 70 FLGERQERIRLLHERQER--ELESFDQ 94
FLG+ IRLL ER+E E+ D+
Sbjct: 10 FLGQHI--IRLLLERKEELKEIRVLDK 34
>gnl|CDD|224640 COG1726, NqrA, Na+-transporting NADH:ubiquinone oxidoreductase,
subunit NqrA [Energy production and conversion].
Length = 447
Score = 27.4 bits (61), Expect = 2.6
Identities = 11/56 (19%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 70 FLGERQERIRLLHERQERELESFDQ-ESNRMGFSALAIAEASKESYPDMDGSLSGS 124
+LG +I +L E +E+EL + + +N+ + + K + +++G
Sbjct: 316 YLGRYHLQISVLEEGREKELFGWLRPGANKYSVTRTYLGHFFKRKLFNFTTNMNGG 371
>gnl|CDD|233646 TIGR01936, nqrA, NADH:ubiquinone oxidoreductase,
Na(+)-translocating, A subunit. This model represents
the NqrA subunit of the six-protein, Na(+)-pumping
NADH-quinone reductase of a number of marine and
pathogenic Gram-negative bacteria. This oxidoreductase
complex functions primarily as a sodium ion pump
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 447
Score = 27.4 bits (61), Expect = 2.9
Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 10/65 (15%)
Query: 66 ETQQFLGERQERIRLLHERQERELESFDQESNRMGFSALAIAEA------SKESYPDMDG 119
+ + +LG R +I +L E REL + R G + ++ K +MD
Sbjct: 311 KEEAYLGRRDLQISVLPEGDVRELFGW----LRPGLNKYSVTRTYLSGLFKKRKEYNMDT 366
Query: 120 SLSGS 124
+ +G
Sbjct: 367 NTNGG 371
>gnl|CDD|129911 TIGR00831, a_cpa1, Na+/H+ antiporter, bacterial form. The
Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC
2.A.36) The CPA1 family is a large family of proteins
derived from Gram-positive and Gram-negative bacteria,
blue green bacteria, yeast, plants and animals.
Transporters from eukaryotes have been functionally
characterized, and all of these catalyze Na+:H+
exchange. Their primary physiological functions may be
in (1) cytoplasmic pH regulation, extruding the H+
generated during metabolism, and (2) salt tolerance (in
plants), due to Na+ uptake into vacuoles. This model is
specific for the bacterial members of this family
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 525
Score = 27.2 bits (60), Expect = 3.4
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 46 KELEDRVSVRRALLEQKMDMETQQFLGERQERIRLL-HERQE 86
EL+ R+ RA E+K+ + R+ R+ +L +R
Sbjct: 453 PELDARIEELRADGEEKIRSGMGEKNLRRRARLYVLDAKRSA 494
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 27.1 bits (61), Expect = 4.0
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 11/68 (16%)
Query: 45 RKELEDRVSVRRALLEQKMDMETQQFLGERQERIRLLHERQERELESFDQESNRMGFSAL 104
+ELE + E + E ++ E +E+ L E +++ LE ++E+ +
Sbjct: 529 ERELEQK----AEEAEALLK-EAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQ------ 577
Query: 105 AIAEASKE 112
AI EA KE
Sbjct: 578 AIKEAKKE 585
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 27.0 bits (61), Expect = 4.1
Identities = 26/87 (29%), Positives = 42/87 (48%), Gaps = 13/87 (14%)
Query: 15 LKERLHYELEILMAYQSKNKMQAEAQR-NRERKELEDRVSVRRALLEQKMDMET-QQFLG 72
L+ER + ELE L++ Q ++ ++E ELE V R + + D+E ++ L
Sbjct: 11 LEER-YEELEALLSDPEVISDQKRFRKLSKEYAELEPIVEAYREYKQAQEDLEEAKEMLE 69
Query: 73 ER---------QERIRLLHERQERELE 90
E +E ++ L ER E ELE
Sbjct: 70 EESDPEMREMAKEELKELEERLE-ELE 95
>gnl|CDD|131097 TIGR02042, sir, ferredoxin-sulfite reductase. Distantly related to
the iron-sulfur hemoprotein of sulfite reductase (NADPH)
found in Proteobacteria and Eubacteria, sulfite
reductase (ferredoxin) is a cyanobacterial and plant
monomeric enzyme that also catalyzes the reduction of
sulfite to sulfide [Central intermediary metabolism,
Sulfur metabolism].
Length = 577
Score = 26.7 bits (59), Expect = 5.0
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 73 ERQERIRLLHERQEREL-ESFDQESNRMGFSAL 104
E+ +H +Q R+ ESF +R+GF AL
Sbjct: 538 EKVLEPLFVHFKQSRQSGESFGDFCDRVGFDAL 570
>gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein
MsbA. This family consists of a single polypeptide
chain transporter in the ATP-binding cassette (ABC)
transporter family, MsbA, which exports lipid A. It may
also act in multidrug resistance. Lipid A, a part of
lipopolysaccharide, is found in the outer leaflet of the
outer membrane of most Gram-negative bacteria. Members
of this family are restricted to the Proteobacteria
(although lipid A is more broadly distributed) and often
are clustered with lipid A biosynthesis genes [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides, Transport and
binding proteins, Other].
Length = 571
Score = 26.2 bits (58), Expect = 6.7
Identities = 13/39 (33%), Positives = 16/39 (41%)
Query: 77 RIRLLHERQERELESFDQESNRMGFSALAIAEASKESYP 115
R+ L Q E FD SNR A+ + A S P
Sbjct: 204 RVVKLFGGQAYETRRFDAVSNRNRRLAMKMTSAGSISSP 242
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1042
Score = 26.5 bits (58), Expect = 6.9
Identities = 14/83 (16%), Positives = 23/83 (27%), Gaps = 2/83 (2%)
Query: 3 RLDESQEVECHHLKERLHYELEILMAYQSKNKMQAEAQRNRERKELEDRVSVRRALLEQK 62
R E L L + L QS ++ +A+ + + + +
Sbjct: 718 REFNEIENASSSLGSDLAAREDALN--QSLKELMHQARTVLKARTEAHFNNNEEVTAALQ 775
Query: 63 MDMETQQFLGERQERIRLLHERQ 85
E E Q RL E
Sbjct: 776 TGAELSHLAAEIQFFNRLREEDT 798
>gnl|CDD|161783 TIGR00237, xseA, exodeoxyribonuclease VII, large subunit. This
family consist of exodeoxyribonuclease VII, large
subunit XseA which catalyses exonucleolytic cleavage in
either the 5'->3' or 3'->5' direction to yield
5'-phosphomononucleotides. Exonuclease VII consists of
one large subunit and four small subunits [DNA
metabolism, Degradation of DNA].
Length = 432
Score = 26.3 bits (58), Expect = 7.2
Identities = 4/28 (14%), Positives = 11/28 (39%)
Query: 60 EQKMDMETQQFLGERQERIRLLHERQER 87
++ L +++ R+ L +R
Sbjct: 268 NVRLHRAFDTLLHQKKARLEQLVASLQR 295
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
0.313 0.127 0.338
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,030,971
Number of extensions: 638000
Number of successful extensions: 1002
Number of sequences better than 10.0: 1
Number of HSP's gapped: 937
Number of HSP's successfully gapped: 218
Length of query: 142
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 55
Effective length of database: 7,078,804
Effective search space: 389334220
Effective search space used: 389334220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (24.5 bits)