RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6103
(125 letters)
>gnl|CDD|202668 pfam03493, BK_channel_a, Calcium-activated BK potassium channel
alpha subunit.
Length = 101
Score = 75.4 bits (186), Expect = 5e-19
Identities = 23/48 (47%), Positives = 29/48 (60%)
Query: 78 NIPSWDWKQGDDVICLAELKLGFIAQSCLAPGFSTMMANLFAMRSFKT 125
SW W D VIC+ ELKL +A+SCL PG ST++ NLF S +
Sbjct: 1 YENSWHWSFADQVICVEELKLALLAKSCLCPGISTLITNLFTSSSPQV 48
>gnl|CDD|218511 pfam05227, CHASE3, CHASE3 domain. CHASE3 is an extracellular
sensory domain, which is present in various classes of
transmembrane receptors that are parts of signal
transduction pathways in bacteria. Specifically, CHASE3
domains are found in histidine kinases, adenylate
cyclases, methyl-accepting chemotaxis proteins and
predicted diguanylate cyclases/phosphodiesterases.
Environmental factors that are recognised by CHASE3
domains are not known at this time.
Length = 138
Score = 30.0 bits (68), Expect = 0.21
Identities = 10/50 (20%), Positives = 22/50 (44%), Gaps = 4/50 (8%)
Query: 20 NSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQ 69
+ ++ E + + L ++ + A ++R K D+IR +I M
Sbjct: 80 DQRLEELEETIALR----REGGLDAALALVRSGEGKALMDEIRALIAEMI 125
>gnl|CDD|201403 pfam00701, DHDPS, Dihydrodipicolinate synthetase family. This
family has a TIM barrel structure.
Length = 289
Score = 30.0 bits (68), Expect = 0.24
Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 16/78 (20%)
Query: 46 ANIMRVISIKNYSDDIRVIIQLMQY-HNKAYLLNIPSWDWKQGDDVICLAELKLGFIAQS 104
A V+ +K+ D+ + + + +L+ GDD L+ L LG
Sbjct: 152 AECPNVVGVKDAVGDLERMENIRKRAGPDFTILS--------GDDETALSYLSLG----- 198
Query: 105 CLAPGFSTMMANLFAMRS 122
A G ++ +N+
Sbjct: 199 --ADGVISVTSNIAPKLM 214
>gnl|CDD|222434 pfam13884, Peptidase_S74, Chaperone of endosialidase. This is the
very C-terminal, chaperone, domain of the bacteriophage
protein endosialidase. It releases itself, via the
serine-lysine dyad at the N-terminus, from the remainder
of the end-tail-spike. Cleavage occurs after the
threonine which is the final residue of the
End-tail-spike family, pfam12219. The endosialidase
protein forms homotrimeric molecules in bacteriophages.
The catalytic dyad allows this portion of the molecule
to be cleaved from the more N-terminal region such that
the latter can fold and presumably bind to DNA.
Length = 54
Score = 27.2 bits (61), Expect = 0.53
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 72 NKAYLLNIPSWDWKQGDDVICLAELKLGFIAQ 103
+K L ++D+K+G+D A +G IAQ
Sbjct: 18 DKIKQLEPVTYDYKEGED---EARRHIGVIAQ 46
>gnl|CDD|178408 PLN02812, PLN02812, 5-formyltetrahydrofolate cyclo-ligase.
Length = 211
Score = 27.3 bits (61), Expect = 2.0
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 19 SNSKVHEADACLVLAN------KYCQDPDAEDAANIMRVISIKNYSDD 60
S +K+ E D +L+ K P ED + MR++ I + +DD
Sbjct: 54 SCAKLREVDTSKILSEILQNPDKRLYVPRVEDKNSNMRMLHITDMADD 101
>gnl|CDD|197322 cd09088, Ape2-like_AP-endo, Human Ape2-like subfamily of the ExoIII
family purinic/apyrimidinic (AP) endonucleases. This
subfamily includes human APE2, Saccharomyces cerevisiae
Apn2/Eth1, and related proteins. These are Escherichia
coli exonuclease III (ExoIII)-like AP endonucleases and
they belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different AP
endonuclease enzymes catalyze the different reactions
with different efficiences. Many organisms have two AP
endonucleases, usually one is the dominant AP
endonuclease, the other has weak AP endonuclease
activity. For examples, Ape1 and Ape2 in humans, and
Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are
both found in this subfamily, and have the weaker AP
endonuclease activity. Ape2 shows strong 3'-5'
exonuclease and 3'-phosphodiesterase activities; it can
reduce the mutagenic consequences of attack by reactive
oxygen species by removing 3'-end adenine opposite from
8-oxoG, in addition to repairing 3'-damaged termini.
Apn2/Eth1 exhibits AP endonuclease activity, but has
30-40 fold more active 3'-phosphodiesterase and 3'-5'
exonuclease activities. Class II AP endonucleases have
been classified into two families, designated ExoIII and
EndoIV, based on their homology to the Escherichia coli
enzymes exonuclease III (ExoIII) and endonuclease IV
(EndoIV). This subfamily belongs to the ExoIII family;
the EndoIV family belongs to a different superfamily.
Length = 309
Score = 26.9 bits (60), Expect = 2.6
Identities = 9/26 (34%), Positives = 12/26 (46%), Gaps = 3/26 (11%)
Query: 89 DVICLAELKL---GFIAQSCLAPGFS 111
D+ICL E KL S + G+
Sbjct: 35 DIICLQETKLTRDELDEPSAIVEGYD 60
>gnl|CDD|238749 cd01472, vWA_collagen, von Willebrand factor (vWF) type A domain;
equivalent to the I-domain of integrins. This domain
has a variety of functions including: intermolecular
adhesion, cell migration, signalling, transcription,
and DNA repair. In integrins these domains form
heterodimers while in vWF it forms homodimers and
multimers. There are different interaction surfaces of
this domain as seen by its complexes with collagen with
either integrin or human vWFA. In integrins collagen
binding occurs via the metal ion-dependent adhesion
site (MIDAS) and involves three surface loops located
on the upper surface of the molecule. In human vWFA,
collagen binding is thought to occur on the bottom of
the molecule and does not involve the vestigial MIDAS
motif.
Length = 164
Score = 26.8 bits (60), Expect = 2.9
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 57 YSDDIRVIIQLMQYHNKAYLL 77
YSDD R L Y +K +L
Sbjct: 46 YSDDPRTEFYLNTYRSKDDVL 66
>gnl|CDD|183939 PRK13275, mtrF, tetrahydromethanopterin S-methyltransferase
subunit F; Provisional.
Length = 67
Score = 24.9 bits (55), Expect = 4.4
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 45 AANIMRVISIKNYSDDIRVIIQLMQYHNK 73
+N + +I N +DIR QL+ + K
Sbjct: 4 MSNKPNMSAIDNVVEDIRYKAQLIARNQK 32
>gnl|CDD|240358 PTZ00321, PTZ00321, ribosomal protein L11; Provisional.
Length = 342
Score = 26.5 bits (58), Expect = 4.8
Identities = 10/31 (32%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 56 NYSDDIRVIIQLMQYHNKAYLLNI--PSWDW 84
++ DD+ +I+++ Y +K+YL I P W
Sbjct: 93 HFKDDVELIVRIQVYFDKSYLFTIEPPPTAW 123
>gnl|CDD|183567 PRK12515, PRK12515, RNA polymerase sigma factor; Provisional.
Length = 189
Score = 25.5 bits (56), Expect = 8.0
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 6/45 (13%)
Query: 41 DAEDAANIMRVISIKNYSDDIRVIIQLMQYHNK-----AYLLNIP 80
D + +R + S R II L+ YH K ++ IP
Sbjct: 117 QKSDTSAALRA-CLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIP 160
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 0.132 0.405
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: 6,102,981
Number of extensions: 512223
Number of successful extensions: 387
Number of sequences better than 10.0: 1
Number of HSP's gapped: 387
Number of HSP's successfully gapped: 17
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
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 (21.9 bits)
S2: 53 (24.1 bits)