RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy833
(642 letters)
>gnl|CDD|219525 pfam07699, GCC2_GCC3, GCC2 and GCC3.
Length = 48
Score = 67.4 bits (165), Expect = 2e-14
Identities = 21/48 (43%), Positives = 27/48 (56%)
Query: 15 GTFAGINQKTCTPCPRGFYQNNDRQGVCLKCPMGTYTREEGSKAVQEC 62
GT++ K C PCPRG YQ + Q C+ CP GT T GS + +C
Sbjct: 1 GTYSNSGLKPCEPCPRGTYQPEEGQDSCIPCPPGTTTLSPGSTSESDC 48
Score = 52.0 bits (125), Expect = 5e-09
Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 69 GTYSPTGLVPCLECPRNSYTGEPPVGGHKDCEACPANMFTYQPAAPARNFC 119
GTYS +GL PC CPR +Y P G C CP T P + + + C
Sbjct: 1 GTYSNSGLKPCEPCPRGTYQ---PEEGQDSCIPCPPGTTTLSPGSTSESDC 48
>gnl|CDD|111397 pfam02494, HYR, HYR domain. This domain is known as the HYR
(Hyalin Repeat) domain, after the protein hyalin that is
composed exclusively of this repeat. This domain
probably corresponds to a new superfamily in the
immunoglobulin fold. The function of this domain is
uncertain it may be involved in cell adhesion.
Length = 81
Score = 47.0 bits (112), Expect = 7e-07
Identities = 32/86 (37%), Positives = 36/86 (41%), Gaps = 7/86 (8%)
Query: 489 VDNEPPVFQNCPQQPIIVRKGPNGIEPVNI--TEPVAVDNSGSIARLEIKPQSFKTPMIT 546
VD PP NCP IVR G VN+ TEP A DNSG + Q
Sbjct: 1 VDTTPPTV-NCPNN--IVRTVELGTSTVNVFFTEPTASDNSGQAILISRTLQP--GDFFP 55
Query: 547 FHDMAVKYIAYDFDGNVAICEINITV 572
+ V Y A D GN A C +TV
Sbjct: 56 VGETTVTYTATDNAGNTASCTFTVTV 81
>gnl|CDD|238014 cd00057, FA58C, Coagulation factor 5/8 C-terminal domain, discoidin
domain; Cell surface-attached carbohydrate-binding
domain, present in eukaryotes and assumed to have
horizontally transferred to eubacterial genomes.
Length = 143
Score = 39.6 bits (93), Expect = 0.001
Identities = 34/163 (20%), Positives = 57/163 (34%), Gaps = 33/163 (20%)
Query: 319 PLGLASGRIPDSSINATSES-----PYLVRVNA----CSVPLIPGPRVQ-ELLAEKNVRL 368
PLG+ SG D I A+S R+N+ P +Q +L + V
Sbjct: 2 PLGMESGL-ADDQITASSSYSSGWEASRARLNSDNAWTPAVNDPPQWLQVDLGKTRRVTG 60
Query: 369 FNVLRTLANMEVYVYRLAILVKGVVTNDIVGRPTEIRFFYKQAESENFVVYFPNFNLTMR 428
++T KG +++ V T + Y + E + Y
Sbjct: 61 ---IQTQ------------GRKGGGSSEWV---TSYKVQYSL-DGETWTTYKDKGEE-KV 100
Query: 429 DPGNYGELAMIT--LPKFVQARFVILGIVSYMDNACLKFELMG 469
GN +T P + AR++ + ++ N L+ EL G
Sbjct: 101 FTGNSDGSTPVTNDFPPPIVARYIRILPTTWNGNISLRLELYG 143
>gnl|CDD|238109 cd00185, TNFR, Tumor necrosis factor receptor (TNFR) domain;
superfamily of TNF-like receptor domains. When bound to
TNF-like cytokines, TNFRs trigger multiple signal
transduction pathways, they are involved in
inflammation response, apoptosis, autoimmunity and
organogenesis. TNFRs domains are elongated with
generally three tandem repeats of cysteine-rich domains
(CRDs). They fit in the grooves between protomers
within the ligand trimer. Some TNFRs, such as NGFR and
HveA, bind ligands with no structural similarity to TNF
and do not bind ligand trimers.
Length = 98
Score = 36.3 bits (84), Expect = 0.006
Identities = 25/98 (25%), Positives = 29/98 (29%), Gaps = 26/98 (26%)
Query: 12 CPAGTFAGINQKTCTPCPRGFYQNND----RQGVCLKCPMGTYTRE-------------- 53
C G + C CP G Y + D VC CP GTYT
Sbjct: 1 CREGEYYYTGGLCCDQCPPGTYLSKDCTPGSDTVCEPCPPGTYTDSWNHLPKCLSCRTCD 60
Query: 54 EGSKAVQECVP----VCG--YGTY--SPTGLVPCLECP 83
G C VCG G Y + C+ C
Sbjct: 61 SGLVEKAPCTATRNTVCGCKPGFYCLTKASCEMCVPCS 98
>gnl|CDD|146106 pfam03302, VSP, Giardia variant-specific surface protein.
Length = 397
Score = 37.6 bits (87), Expect = 0.018
Identities = 20/80 (25%), Positives = 25/80 (31%), Gaps = 7/80 (8%)
Query: 6 VPRCLHCPA--GTFAGINQKTCTPCPRGFYQNNDRQGVCLKCPMGTYTREEGSKAVQECV 63
+ C T N+K C C + + QG C C G Y + E
Sbjct: 55 IDDCAKIGNYYYTTNANNKKICKECTVANCKTCEDQGQCQACNDGFYKSGDACSPCHESC 114
Query: 64 PVCGYGTYSPTGLVPCLECP 83
C GT S C EC
Sbjct: 115 KTCSGGTAS-----DCTECL 129
>gnl|CDD|214572 smart00231, FA58C, Coagulation factor 5/8 C-terminal domain,
discoidin domain. Cell surface-attached
carbohydrate-binding domain, present in eukaryotes and
assumed to have horizontally transferred to eubacterial
genomes.
Length = 139
Score = 34.8 bits (80), Expect = 0.047
Identities = 13/65 (20%), Positives = 25/65 (38%)
Query: 406 FFYKQAESENFVVYFPNFNLTMRDPGNYGELAMITLPKFVQARFVILGIVSYMDNACLKF 465
+ N+ Y + + G + + P + AR+V + + N L+
Sbjct: 75 KLEYSDDGVNWTTYKDGNSKVFPGNSDAGTVVLNDFPPPIVARYVRILPTGWNGNIILRV 134
Query: 466 ELMGC 470
EL+GC
Sbjct: 135 ELLGC 139
>gnl|CDD|153056 cd00033, CCP, Complement control protein (CCP) modules (aka short
consensus repeats SCRs or SUSHI repeats) have been
identified in several proteins of the complement system.
SUSHI repeats (short complement-like repeat, SCR) are
abundant in complement control proteins. The complement
control protein (CCP) modules (also known as short
consensus repeats SCRs or SUSHI repeats) contain
approximately 60 amino acid residues and have been
identified in several proteins of the complement system.
Typically, 2 to 4 modules contribute to a binding site,
implying that the orientation of the modules to each
other is critical for function.
Length = 57
Score = 31.3 bits (71), Expect = 0.13
Identities = 18/63 (28%), Positives = 24/63 (38%), Gaps = 13/63 (20%)
Query: 260 CSDPGRPVDGYQVATSYEQVRYDDEQGSEVQFGCNKPGYILINPRPITCVR-------EP 312
C P P +G + + Y GS V + CN GY L+ ITC P
Sbjct: 1 CPPPPVPENGT---VTGSKGSY--SYGSTVTYSCN-EGYTLVGSSTITCTENGGWSPPPP 54
Query: 313 ECK 315
C+
Sbjct: 55 TCE 57
Score = 29.7 bits (67), Expect = 0.53
Identities = 17/76 (22%), Positives = 24/76 (31%), Gaps = 19/76 (25%)
Query: 181 CSDPGRPVDGYQVATSYEQVRYDDEQYGNFLDTRYQSSFFFGCQDTFKLAGQTDKNDNVV 240
C P P +G V Y Y S+ + C + + L G + +
Sbjct: 1 CPPPPVPENGT--------VTGSKGSY------SYGSTVTYSCNEGYTLVGS-----STI 41
Query: 241 RCQANGIWDFGDLRCE 256
C NG W CE
Sbjct: 42 TCTENGGWSPPPPTCE 57
Score = 29.0 bits (65), Expect = 1.1
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 5/45 (11%)
Query: 133 DTRYQSSFFFGCQDTFKLAGQTDKNDNVVRCQANGIWDFGDLRCE 177
Y S+ + C + + L G + + C NG W CE
Sbjct: 18 SYSYGSTVTYSCNEGYTLVGS-----STITCTENGGWSPPPPTCE 57
>gnl|CDD|219467 pfam07562, NCD3G, Nine Cysteines Domain of family 3 GPCR. This
conserved sequence contains several highly-conserved
Cys residues that are predicted to form disulphide
bridges. It is predicted to lie outside the cell
membrane, tethered to the pfam00003 in several receptor
proteins.
Length = 54
Score = 30.8 bits (70), Expect = 0.21
Identities = 10/27 (37%), Positives = 11/27 (40%)
Query: 24 TCTPCPRGFYQNNDRQGVCLKCPMGTY 50
C PCP G N C CP G +
Sbjct: 27 DCIPCPEGEISNTTDSTTCTPCPEGQW 53
Score = 26.9 bits (60), Expect = 4.6
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 11/52 (21%)
Query: 27 PCPRGFYQNNDRQGV------CLKCPMGTYTREEGSKAVQECVPVCGYGTYS 72
PCP G + ++G C+ CP G + S C P C G +S
Sbjct: 8 PCPPGTRKK-VQKGQPVCCWDCIPCPEGEISNTTDS---TTCTP-CPEGQWS 54
>gnl|CDD|215703 pfam00084, Sushi, Sushi domain (SCR repeat).
Length = 56
Score = 30.6 bits (69), Expect = 0.27
Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 8/61 (13%)
Query: 119 CRVPTP---GAEYGNFLDTRYQSSFFFGCQDTFKLAGQTDKNDNVVRCQANGIWDFGDLR 175
C P P G + S + C + L G +V+ CQ +G W
Sbjct: 1 CPAPPPIPHGVISTTKNSYQVGSVVRYECDPGYVLVGS-----SVITCQDDGTWSPPLPE 55
Query: 176 C 176
C
Sbjct: 56 C 56
Score = 29.5 bits (66), Expect = 0.70
Identities = 10/44 (22%), Positives = 16/44 (36%), Gaps = 5/44 (11%)
Query: 212 DTRYQSSFFFGCQDTFKLAGQTDKNDNVVRCQANGIWDFGDLRC 255
+ S + C + L G +V+ CQ +G W C
Sbjct: 18 SYQVGSVVRYECDPGYVLVGS-----SVITCQDDGTWSPPLPEC 56
>gnl|CDD|214478 smart00032, CCP, Domain abundant in complement control proteins;
SUSHI repeat; short complement-like repeat (SCR). The
complement control protein (CCP) modules (also known as
short consensus repeats SCRs or SUSHI repeats) contain
approximately 60 amino acid residues and have been
identified in several proteins of the complement system.
A missense mutation in seventh CCP domain causes
deficiency of the b subunit of factor XIII.
Length = 56
Score = 29.8 bits (67), Expect = 0.52
Identities = 17/49 (34%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 260 CSDPGRPVDGYQVATSYEQVRYDDEQGSEVQFGCNKPGYILINPRPITC 308
C P +G V +S Y G V + C+ PGY LI ITC
Sbjct: 1 CPPPPDIENGT-VTSSSGTYSY----GDTVTYSCD-PGYTLIGSSTITC 43
Score = 27.1 bits (60), Expect = 4.7
Identities = 14/75 (18%), Positives = 20/75 (26%), Gaps = 19/75 (25%)
Query: 181 CSDPGRPVDGYQVATSYEQVRYDDEQYGNFLDTRYQSSFFFGCQDTFKLAGQTDKNDNVV 240
C P +G V Y Y + + C + L G + +
Sbjct: 1 CPPPPDIENGT--------VTSSSGTY------SYGDTVTYSCDPGYTLIG-----SSTI 41
Query: 241 RCQANGIWDFGDLRC 255
C NG W C
Sbjct: 42 TCLENGTWSPPPPTC 56
>gnl|CDD|132699 TIGR03660, T1SS_rpt_143, T1SS-143 repeat domain. This model
represents a domain of about 143 amino acids that may
occur singly or in up to 23 tandem repeats in very large
proteins in the genus Vibrio, and in related species
such as Legionella pneumophila, Photobacterium
profundum, Rhodopseudomonas palustris, Shewanella
pealeana, and Aeromonas hydrophila. Proteins with these
domains represent a subset of a broader set of proteins
with a particular signal for type 1 secretion,
consisting of several glycine-rich repeats modeled by
pfam00353, followed by a C-terminal domain modeled by
TIGR03661. Proteins with this domain tend to share
several properties with the RtxA (Repeats in Toxin)
protein of Vibrio cholerae, including a large size often
containing tandemly repeated domains and a C-terminal
signal for type 1 secretion [Cellular processes,
Pathogenesis].
Length = 137
Score = 31.1 bits (71), Expect = 0.77
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 555 IAYDFDGNVAICEINITVVDETP 577
IA DFDG+ + + +T+VD+ P
Sbjct: 92 IATDFDGDTSSITLPVTIVDDVP 114
>gnl|CDD|238021 cd00064, FU, Furin-like repeats. Cysteine rich region. Exact
function of the domain is not known. Furin is a
serine-kinase dependent proprotein processor. Other
members of this family include endoproteases and cell
surface receptors.
Length = 49
Score = 27.9 bits (62), Expect = 1.8
Identities = 19/52 (36%), Positives = 22/52 (42%), Gaps = 9/52 (17%)
Query: 7 PRCLHCPAGTFAGINQKTCTPCPRGFYQNNDRQGVCL-KCPMGTYTREEGSK 57
P C C G CT C GFY + G C+ +CP GTY EG
Sbjct: 4 PSCATC-----TGPGPDQCTSCRHGFYLDG---GTCVSECPEGTYADTEGGV 47
>gnl|CDD|227217 COG4880, COG4880, Secreted protein containing C-terminal
beta-propeller domain distantly related to WD-40 repeats
[General function prediction only].
Length = 603
Score = 31.0 bits (70), Expect = 2.5
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 8/68 (11%)
Query: 182 SDPGRP--VDGYQVATSYEQVRYD------DEQYGNFLDTRYQSSFFFGCQDTFKLAGQT 233
SD P V Y ++ ++ V YD D + F Y + F +D KL +
Sbjct: 503 SDLAAPKEVSNYTLSNAWSPVFYDHHAFLYDPEAEIFFLPAYLGGYIFFIEDGSKLRKRA 562
Query: 234 DKNDNVVR 241
++ N R
Sbjct: 563 ERKLNADR 570
>gnl|CDD|214601 smart00289, WR1, Worm-specific repeat type 1. Worm-specific
repeat type 1. Cysteine-rich domain apparently unique
(so far) to C. elegans. Often appears with KU domains.
About 3 dozen worm proteins contain this domain.
Length = 38
Score = 26.8 bits (59), Expect = 3.7
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 12 CPAGTFAGINQKTCTP---CPRGFYQNNDRQGVCLKCP 46
CP G+ G + C+P CP G+ N +QG+C CP
Sbjct: 3 CPNGSDLGGSPVRCSPNGSCPSGYSCQNSKQGIC--CP 38
>gnl|CDD|217481 pfam03303, WTF, WTF protein. This is a family of hypothetical
Schizosaccharomyces pombe proteins. Their function is
unknown.
Length = 240
Score = 29.5 bits (66), Expect = 4.2
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 42 CLKCPMG----TYTREEGSKAVQECVPVCGYGTYS 72
CL C + TY E +KAV+ V CG G +
Sbjct: 124 CLICTIALIFLTYFYETWTKAVKVTVIACGAGLRN 158
>gnl|CDD|214589 smart00261, FU, Furin-like repeats.
Length = 45
Score = 26.7 bits (59), Expect = 4.2
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 6/46 (13%)
Query: 8 RCLHCPAG--TFAGINQKTCTPCPRGFYQNNDRQGVCLK-CPMGTY 50
C C T G CT C GF+ + + C+ CP GTY
Sbjct: 3 ECKPCHPECATCTGPGPDDCTSCKHGFFLDGGK---CVSECPPGTY 45
>gnl|CDD|214972 smart01009, AlkA_N, AlkA N-terminal domain. This domain is found
at the N terminus of bacterial AlkA . AlkA
(3-methyladenine-DNA glycosylase II) is a base excision
repair glycosylase from Escherichia coli. It removes a
variety of alkylated bases from DNA, primarily by
removing alkylation damage from duplex and single
stranded DNA. AlkA flips a 1-azaribose abasic nucleotide
out of DNA. This produces a 66 degrees bend in the DNA
and a marked widening of the minor groove.
Length = 113
Score = 28.3 bits (64), Expect = 4.4
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 8/43 (18%)
Query: 588 IELVDKQDSYVMNFNETRRRVNVSDASGEVTVTFSPDRATILL 630
+E VD SY RR + + +G VTV PDR + +
Sbjct: 22 VERVD-DGSY-------RRTLRLGGGAGWVTVRHDPDRHQLRV 56
>gnl|CDD|234533 TIGR04285, nucleoid_noc, nucleoid occlusion protein. This model
describes nucleoid occlusion protein, a close homolog to
ParB chromosome partitioning proteins including Spo0J in
Bacillus subtilis. Its gene often is located near the
gene for the Spo0J ortholog. This protein bind a
specific DNA sequence and blocks cytokinesis from
happening until chromosome segregation is complete.
Length = 255
Score = 29.4 bits (67), Expect = 5.9
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 502 QPIIVRKGPNGIE 514
QPI+VRK + E
Sbjct: 40 QPIVVRKKDDKYE 52
>gnl|CDD|200963 pfam00056, Ldh_1_N, lactate/malate dehydrogenase, NAD binding
domain. L-lactate dehydrogenases are metabolic enzymes
which catalyze the conversion of L-lactate to pyruvate,
the last step in anaerobic glycolysis.
L-2-hydroxyisocaproate dehydrogenases are also members
of the family. Malate dehydrogenases catalyze the
interconversion of malate to oxaloacetate. The enzyme
participates in the citric acid cycle. L-lactate
dehydrogenase is also found as a lens crystallin in bird
and crocodile eyes. N-terminus (this family) is a
Rossmann NAD-binding fold. C-terminus is an unusual
alpha+beta fold.
Length = 142
Score = 28.3 bits (64), Expect = 6.1
Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 5/35 (14%)
Query: 501 QQPIIVRKGPNGI-----EPVNITEPVAVDNSGSI 530
P I + P+ I PV+I +A SG
Sbjct: 101 IVPAIAKSAPDAIVLVVSNPVDILTYIAWKVSGLP 135
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
0.321 0.139 0.440
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,396,279
Number of extensions: 3127477
Number of successful extensions: 1960
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1942
Number of HSP's successfully gapped: 39
Length of query: 642
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 539
Effective length of database: 6,369,140
Effective search space: 3432966460
Effective search space used: 3432966460
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: 62 (27.5 bits)