RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14580
(149 letters)
>gnl|CDD|189650 pfam00645, zf-PARP, Poly(ADP-ribose) polymerase and DNA-Ligase
Zn-finger region. Poly(ADP-ribose) polymerase is an
important regulatory component of the cellular response
to DNA damage. The amino-terminal region of
Poly(ADP-ribose) polymerase consists of two PARP-type
zinc fingers. This region acts as a DNA nick sensor.
Length = 81
Score = 92.0 bits (229), Expect = 2e-25
Identities = 38/83 (45%), Positives = 53/83 (63%), Gaps = 4/83 (4%)
Query: 20 AKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEV 79
AK+GR+ CKKCK+KI G +RI K+ +PF GKMK+W+H C E + R T E
Sbjct: 3 AKSGRASCKKCKEKIAKGELRIGKVVPSPFFDGKMKKWYHWGCFTEKRLRNRAT----ED 58
Query: 80 VDDMGGWDDLTPEDQEEVLSRFP 102
VDD+ G+++L PEDQE++
Sbjct: 59 VDDLDGFEELRPEDQEKIKKALE 81
>gnl|CDD|215590 PLN03123, PLN03123, poly [ADP-ribose] polymerase; Provisional.
Length = 981
Score = 73.3 bits (180), Expect = 6e-16
Identities = 39/122 (31%), Positives = 53/122 (43%), Gaps = 19/122 (15%)
Query: 20 AKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEV 79
AKT R+ C++C +KI G VRI+ K WHH C LE+
Sbjct: 112 AKTSRATCRRCSEKILKGEVRISSKPEGQ--GYKGLAWHHAKCFLEMSPSTP-------- 161
Query: 80 VDDMGGWDDLTPEDQEEVLS---RFPESLRESNKDRDVPE------RKIPSSSEKKSKTP 130
V+ + GWD L+ DQE VL + P +E + E RK +S + KSK
Sbjct: 162 VEKLSGWDTLSDSDQEAVLPLVKKSPSEAKEEKAEERKQESKKGAKRKKDASGDDKSKKA 221
Query: 131 KK 132
K
Sbjct: 222 KT 223
Score = 61.3 bits (149), Expect = 7e-12
Identities = 34/103 (33%), Positives = 50/103 (48%), Gaps = 8/103 (7%)
Query: 9 PEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFK 68
K + + AK+ RS CK CK ID +R+ KM + G M W+H CI K
Sbjct: 2 AAPPKPWKAEYAKSSRSSCKTCKSPIDKDELRLGKMVQSTQFDGFMPMWNHASCI---LK 58
Query: 69 KQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKD 111
K+ Q I+ +DD+ G D L EDQ++ + ++ ES
Sbjct: 59 KKNQ----IKSIDDVEGIDSLRWEDQQK-IRKYVESGGTGTGT 96
>gnl|CDD|236177 PRK08186, PRK08186, allophanate hydrolase; Provisional.
Length = 600
Score = 29.0 bits (66), Expect = 1.00
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 5/40 (12%)
Query: 71 RQTTAKIEVVDDMGGWDDLTPEDQ-----EEVLSRFPESL 105
A+I VDD W L PE + +R P +L
Sbjct: 28 AALYARIAAVDDPEVWIHLRPEADLLAQAAALEARDPAAL 67
>gnl|CDD|144013 pfam00268, Ribonuc_red_sm, Ribonucleotide reductase, small chain.
Length = 281
Score = 28.9 bits (65), Expect = 1.0
Identities = 11/46 (23%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 55 KQWHHIDC--ILEVFKK---QRQTTAKIEVVDDMGGWDDLTPEDQE 95
K+++ I I E++KK R ++++ D+ W+ L ++E
Sbjct: 9 KRFYPIQHPDIWELYKKAEANRWLAEEVDLSKDIPDWEKLNEAERE 54
>gnl|CDD|221138 pfam11573, Med23, Mediator complex subunit 23. Med23 is one of the
subunits of the Tail portion of the Mediator complex
that regulates RNA polymerase II activity. Med23 is
required for heat-shock-specific gene expression, and
has been shown to mediate transcriptional activation of
E1A in mice.
Length = 1341
Score = 28.7 bits (64), Expect = 1.3
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 95 EEVLSRFPESLRESNKDRDVPERKIPSSSEKKS 127
E LS FP L E K +VP K P+ + KKS
Sbjct: 754 EHTLSCFPPWLNEYFKQHNVP--KEPNQALKKS 784
>gnl|CDD|182983 PRK11127, PRK11127, autonomous glycyl radical cofactor GrcA;
Provisional.
Length = 127
Score = 27.1 bits (60), Expect = 2.7
Identities = 11/18 (61%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 89 LTPEDQEEVLSR-FPESL 105
LTPE Q +V++R F ESL
Sbjct: 110 LTPEQQRDVIARTFTESL 127
>gnl|CDD|143457 cd07139, ALDH_AldA-Rv0768, Mycobacterium tuberculosis aldehyde
dehydrogenase AldA-like. The Mycobacterium
tuberculosis NAD+-dependent, aldehyde dehydrogenase PDB
structure, 3B4W, and the Mycobacterium tuberculosis
H37Rv aldehyde dehydrogenase AldA (locus Rv0768)
sequence, as well as the Rhodococcus rhodochrous ALDH
involved in haloalkane catabolism, and other similar
sequences, are included in this CD.
Length = 471
Score = 27.5 bits (62), Expect = 2.9
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 82 DMGGWDDLTPEDQEEVLSRFPESLRESNKD 111
D G W L+P ++ VL R ++L +
Sbjct: 50 DNGPWPRLSPAERAAVLRRLADALEARADE 79
>gnl|CDD|226332 COG3811, COG3811, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 85
Score = 25.5 bits (56), Expect = 5.6
Identities = 7/13 (53%), Positives = 8/13 (61%)
Query: 57 WHHIDCILEVFKK 69
W DC L VF+K
Sbjct: 41 WLLPDCTLAVFRK 53
>gnl|CDD|238928 cd01966, Nitrogenase_NifN_1, Nitrogenase_nifN1: A subgroup of the
NifN subunit of the NifEN complex: NifN forms an
alpha2beta2 tetramer with NifE. NifN and nifE are
structurally homologous to nitrogenase MoFe protein
beta and alpha subunits respectively. NifEN
participates in the synthesis of the iron-molybdenum
cofactor (FeMoco) of the MoFe protein. NifB-co (an
iron and sulfur containing precursor of the FeMoco)
from NifB is transferred to the NifEN complex where it
is further processed to FeMoco. The nifEN bound
precursor of FeMoco has been identified as a
molybdenum-free, iron- and sulfur- containing analog of
FeMoco. It has been suggested that this nifEN bound
precursor also acts as a cofactor precursor in
nitrogenase systems which require a cofactor other than
FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron
only cofactor (FeFeco).
Length = 417
Score = 26.4 bits (59), Expect = 6.6
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 72 QTTAKIEVVDDMGGWDDL 89
QTTA EV +GG ++L
Sbjct: 52 QTTAMDEVSTILGGGENL 69
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 26.5 bits (58), Expect = 7.6
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 5/39 (12%)
Query: 78 EVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPE 116
E+ DD+G D++ P+ QE PE N+D D+PE
Sbjct: 3958 EMSDDVGIDDEIQPDIQENNSQPPPE-----NEDLDLPE 3991
>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein. The YqfQ-like protein family
includes the B. subtilis YqfQ protein, also known as
VrrA, which is functionally uncharacterized. This family
of proteins is found in bacteria. Proteins in this
family are typically between 146 and 237 amino acids in
length. There are two conserved sequence motifs: QYGP
and PKLY.
Length = 155
Score = 25.9 bits (57), Expect = 7.8
Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 87 DDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKTPKKKAV 135
++ T E ++E +E K R+VP+ K K K +
Sbjct: 103 EESTDETEQEDPPETKTESKEKKK-REVPKPKTEKEKPKTEPKKPKPSK 150
>gnl|CDD|184244 PRK13687, PRK13687, hypothetical protein; Provisional.
Length = 85
Score = 24.9 bits (55), Expect = 8.5
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 57 WHHIDCILEVFKKQRQ 72
W DC L VFKK ++
Sbjct: 41 WLLADCTLAVFKKLKR 56
>gnl|CDD|236067 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated.
Length = 415
Score = 26.0 bits (57), Expect = 9.0
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 7/62 (11%)
Query: 59 HIDCILEVFKK-QR---QTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLR---ESNKD 111
HI L KK QR Q + ++D+ ++TP EVL R P S+ + KD
Sbjct: 256 HITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKD 315
Query: 112 RD 113
+D
Sbjct: 316 KD 317
>gnl|CDD|213978 TIGR04365, spare_glycyl, autonomous glycyl radical cofactor GrcA.
This small protein, previously designated YfiD in E.
coli, is closely homologous to pyruvate formate_lyase
(PFL) in a region surrounding the stable glycyl radical
that is prepared by the action of pyruvate formate-lyase
activase, a radical SAM enzyme. When damage at the site
of this radical breaks the main chain of PFL, this
protein acts as a spare part that reintroduces the
needed stable glycyl radical. Cutoffs for this model are
set to exclude a set of closely related phage proteins
that appear to have a corresponding function.
Length = 124
Score = 25.5 bits (56), Expect = 9.2
Identities = 11/18 (61%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 89 LTPEDQEEVLSR-FPESL 105
LTPE Q +V++R F ESL
Sbjct: 107 LTPEQQRDVITRTFTESL 124
>gnl|CDD|188726 cd09340, LIM1_Testin_like, The first LIM domain of Testin-like
family. The first LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion
events. Prickles have been implicated in roles of
regulating tissue polarity or planar cell polarity
(PCP). Dyxin involves in lung and heart development by
interaction with GATA6 and blocking GATA6 activated
target genes. LIMPETin might be the recombinant product
of genes coding testin and four and half LIM proteins
and its function is not well understood. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 58
Score = 24.5 bits (54), Expect = 9.2
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 9/34 (26%)
Query: 27 CKKCKQKIDTG--TVRIAKMGYNPFGSGKMKQWH 58
C+KCK+ I+ G V + G + WH
Sbjct: 1 CEKCKEPINPGEVAVFAERAGED-------ACWH 27
>gnl|CDD|236555 PRK09537, pylS, pyrolysyl-tRNA synthetase; Reviewed.
Length = 417
Score = 26.0 bits (57), Expect = 9.5
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 95 EEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKTPKKKAV 135
+E ++RF L ++ +D+ + K+ S+ KK K K V
Sbjct: 76 DEDINRF---LTKTFEDKTQVKVKVVSAPTKKKKAMPKSVV 113
>gnl|CDD|217645 pfam03629, DUF303, Domain of unknown function (DUF303).
Distribution of this domain seems limited to prokaryotes
and viruses.
Length = 257
Score = 25.8 bits (57), Expect = 9.9
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 5/37 (13%)
Query: 70 QRQTTAKIE-----VVDDMGGWDDLTPEDQEEVLSRF 101
Q + ++ V D+G DD+ P+++ EV R
Sbjct: 214 QAKALKELPNTGMVVTIDLGDEDDIHPKNKREVGERL 250
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
0.315 0.133 0.406
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,513,550
Number of extensions: 656045
Number of successful extensions: 624
Number of sequences better than 10.0: 1
Number of HSP's gapped: 619
Number of HSP's successfully gapped: 33
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
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: 42 (22.0 bits)
S2: 54 (24.7 bits)