RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17638
(160 letters)
>gnl|CDD|238020 cd00063, FN3, Fibronectin type 3 domain; One of three types of
internal repeats found in the plasma protein
fibronectin. Its tenth fibronectin type III repeat
contains an RGD cell recognition sequence in a flexible
loop between 2 strands. Approximately 2% of all animal
proteins contain the FN3 repeat; including extracellular
and intracellular proteins, membrane spanning cytokine
receptors, growth hormone receptors, tyrosine
phosphatase receptors, and adhesion molecules. FN3-like
domains are also found in bacterial glycosyl hydrolases.
Length = 93
Score = 57.1 bits (138), Expect = 2e-11
Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 5/89 (5%)
Query: 18 PGTVQSLEAIPLGSSAFYLKWVKPEQPNGVLMGYKIKYQSVKGTKVGPLLERLPYISDPT 77
P +L + S++ L W PE G + GY ++Y+ + +
Sbjct: 1 PSPPTNLRVTDVTSTSVTLSWTPPEDDGGPITGYVVEYREKGSGDWKEVEVT-----PGS 55
Query: 78 TTSAKLAGLEPSTKYRIHLAGYTKAGDGA 106
TS L GL+P T+Y + G+
Sbjct: 56 ETSYTLTGLKPGTEYEFRVRAVNGGGESP 84
>gnl|CDD|200951 pfam00041, fn3, Fibronectin type III domain.
Length = 84
Score = 52.0 bits (125), Expect = 1e-09
Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 6/86 (6%)
Query: 21 VQSLEAIPLGSSAFYLKWVKPEQPNGVLMGYKIKYQSVKGTKVGPLLERLPYISDPTTTS 80
+L + S++ L W P NG + GY+++Y+ V G + E TTTS
Sbjct: 3 PTNLTVTDVTSTSLTLSWSPPP-GNGPITGYEVEYRPVNGGE-----EWKEITVPGTTTS 56
Query: 81 AKLAGLEPSTKYRIHLAGYTKAGDGA 106
L GL+P T+Y + + AG+G
Sbjct: 57 YTLTGLKPGTEYEVRVQAVNGAGEGP 82
>gnl|CDD|214495 smart00060, FN3, Fibronectin type 3 domain. One of three types of
internal repeat within the plasma protein, fibronectin.
The tenth fibronectin type III repeat contains a RGD
cell recognition sequence in a flexible loop between 2
strands. Type III modules are present in both
extracellular and intracellular proteins.
Length = 83
Score = 51.5 bits (123), Expect = 2e-09
Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 5/88 (5%)
Query: 18 PGTVQSLEAIPLGSSAFYLKWVKPEQPNGVLMGYKIKYQSVKGTKVGPLLERLPYISDPT 77
P +L + S++ L W P GY + Y+ + E P+
Sbjct: 1 PSPPSNLRVTDVTSTSVTLSWEPPPDDGIT--GYIVGYRVEYREEGSEWKE---VNVTPS 55
Query: 78 TTSAKLAGLEPSTKYRIHLAGYTKAGDG 105
+TS L GL+P T+Y + AG+G
Sbjct: 56 STSYTLTGLKPGTEYEFRVRAVNGAGEG 83
>gnl|CDD|225936 COG3401, COG3401, Fibronectin type 3 domain-containing protein
[General function prediction only].
Length = 343
Score = 39.9 bits (93), Expect = 2e-04
Identities = 25/111 (22%), Positives = 38/111 (34%), Gaps = 7/111 (6%)
Query: 49 MGYKIKYQSVKGTKVGPLLERLPYISDPTTTSAKLAGLEPSTKYRIHLAGYTKAGDGADY 108
Y I + TK L+R+ I + T GLE Y G TK D Y
Sbjct: 1 ANYDIDGFVLYRTKKDLKLKRIGTIKNKYQTHYYDEGLEGEESYPYQE-GTTK-VDKISY 58
Query: 109 FIEHRTRGTDNVAPGKPNFKLVRSGTENGYGAFKVIWEPNPERPGSHFFVK 159
E T + + F + + KV W P+P+ + ++
Sbjct: 59 DSERILVKTSFIERVRSVFASLERPK-----SVKVFWSPHPDVSVGKYIIQ 104
>gnl|CDD|221156 pfam11649, T4_neck-protein, Virus neck protein. This family of
protein represents gene product 14, a major component of
the neck in T4-like viruses along with gene product 13.
Gene product 14 is rich is beta-sheets. The formation of
the neck to the head of the bacteriophage is crucial for
the tail attachment.
Length = 247
Score = 32.8 bits (75), Expect = 0.045
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 27 IPLGSSAFYLKWVKPEQP---NGVLMGYKIKYQSV--KGTKVGPLLERLPYISDPTTTSA 81
PL +S F +KWV+PE P G KI + G ++ P ++ + I+ T
Sbjct: 138 FPLTNSLFEIKWVEPEDPFYQLGKNYVRKITAEKFEYSGEEIDPGVDEIDGINIETDFEL 197
Query: 82 KLA 84
LA
Sbjct: 198 DLA 200
>gnl|CDD|222872 PHA02555, 14, neck protein; Provisional.
Length = 216
Score = 30.4 bits (69), Expect = 0.28
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 27 IPLGSSAFYLKWVKPEQP---NGVLMGYKI---KYQSVKGTKVGPLLERLPYISDPTTTS 80
P+ +S F +KWV+PE P G KI K+ G ++ P ++ + I+ S
Sbjct: 116 FPMDNSLFEIKWVEPEDPFYQLGKNYVRKITCEKFI-YSGEEIDPGVQEIDGINITGFES 174
Query: 81 AKLAGLE 87
L +
Sbjct: 175 LDLWPVR 181
>gnl|CDD|214448 MTH00173, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 231
Score = 27.5 bits (62), Expect = 2.8
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 3 LSPPLWLTLNLEALVPGTVQSLEAI-PLGSSAFY 35
L+ PLWL+L L L +SL + P G+ A
Sbjct: 107 LALPLWLSLILSGLFYNPSKSLAGLVPAGAPAGL 140
>gnl|CDD|238040 cd00087, FReD, Fibrinogen-related domains (FReDs); C terminal
globular domain of fibrinogen. Fibrinogen is involved in
blood clotting, being activated by thrombin to assemble
into fibrin clots. The N-termini of 2 times 3 chains
come together to form a globular arrangement called the
disulfide knot. The C termini of fibrinogen chains end
in globular domains, which are not completely
equivalent. C terminal globular domains of the gamma
chains (C-gamma) dimerize and bind to the GPR motif of
the N-terminal domain of the alpha chain, while the GHR
motif of N-terminal domain of the beta chain binds to
the C terminal globular domains of another beta chain
(C-beta), which leads to lattice formation.
Length = 215
Score = 27.6 bits (62), Expect = 3.0
Identities = 9/24 (37%), Positives = 11/24 (45%), Gaps = 2/24 (8%)
Query: 89 STKYRIHLAGYTKAGDGADYFIEH 112
S YR+ L GY+ G D H
Sbjct: 118 SEGYRLTLGGYS--GTAGDALSYH 139
>gnl|CDD|220743 pfam10420, IL12p40_C, Cytokine interleukin-12p40 C-terminus.
IL12p40_C is the largely beta stranded C-terminal, D3,
domain of interleukin-12p40 or interleukin-12B. This
interleukin is produced on stimulation by
macrophage-engulfed micro-organisms and other stimuli,
when it dimerises with interleukin-12p35 to form a
heterodimer which then binds to receptors on natural
killer cells to activate them to destroy the
micro-organisms. This domain contains two disulfide
bridges, one of which serves to bind p40 to p35 and the
other to hold the beta strands within the domain
together. The cupped shape of the p35 binding interface
matches the elbow-like bend between D2 and D3 in p40.
The domain is often associated with family fn3,
pfam00041.
Length = 82
Score = 26.2 bits (58), Expect = 3.1
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 134 TENGYGAFKVIWEPNPERPGSHFFVK 159
+N G F W + R G F +K
Sbjct: 9 AKNYSGRFTCSWTWHSIRTGLVFSIK 34
>gnl|CDD|188401 TIGR03886, lyase_spl_fam, spore photoproduct lyase family
protein. This uncharacterized radical SAM domain
protein occurs rarely and sporadically in species that
include select Alphaproteobacteria and Actinobacteria,
and in Deinococcus deserti VCD115. It is a distant but
full-length homolog to the Bacillus subtilis spore
photoproduct lyase (spl), which monomerizes thymine
dimers created as DNA damage by uv radiation.
Length = 346
Score = 27.0 bits (60), Expect = 4.4
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 8 WLTLNLEALVPGTVQSLEAIPLGSSAFYLKWVKPEQPNGVLM 49
W+ + E LV G ++L A P G SA ++ P NG M
Sbjct: 50 WVRIKRETLVLGVKKTLTARPNGRSA---DFIAPSTANGCAM 88
>gnl|CDD|240407 PTZ00412, PTZ00412, leucyl aminopeptidase; Provisional.
Length = 569
Score = 26.5 bits (58), Expect = 8.9
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 13/65 (20%)
Query: 30 GSSAFYLKWVKPE-QPNG-----VLMGYKIK-------YQSVKGTKVGPLLERLPYISDP 76
G FY +W+K E P G VL G +++ Y KG++ P L YI +P
Sbjct: 229 GVPQFYAEWIKKELAPLGIKVRKVLRGEQLEGAGLNLMYNVGKGSRHEPYLVVFEYIGNP 288
Query: 77 TTTSA 81
+++A
Sbjct: 289 RSSAA 293
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
0.316 0.137 0.423
Gapped
Lambda K H
0.267 0.0591 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,347,112
Number of extensions: 736119
Number of successful extensions: 544
Number of sequences better than 10.0: 1
Number of HSP's gapped: 541
Number of HSP's successfully gapped: 18
Length of query: 160
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 71
Effective length of database: 6,990,096
Effective search space: 496296816
Effective search space used: 496296816
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: 41 (21.6 bits)
S2: 55 (25.3 bits)