RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4191
(443 letters)
>gnl|CDD|218940 pfam06209, COBRA1, Cofactor of BRCA1 (COBRA1). This family
consists of several cofactor of BRCA1 (COBRA1) like
proteins. It is thought that COBRA1 along with BRCA1 is
involved in chromatin unfolding. COBRA1 is recruited to
the chromosome site by the first BRCT repeat of BRCA1,
and is itself sufficient to induce chromatin unfolding.
BRCA1 mutations that enhance chromatin unfolding also
increase its affinity for, and recruitment of, COBRA1.
It is thought that that reorganisation of higher levels
of chromatin structure is an important regulated step in
BRCA1-mediated nuclear functions.
Length = 475
Score = 487 bits (1255), Expect = e-170
Identities = 201/423 (47%), Positives = 257/423 (60%), Gaps = 80/423 (18%)
Query: 11 VKQLRPVVMAILRNTTHIDDKYLRVLVRDRELYKDTDTEVKRQIWKDNQSLFGDEVSPLL 70
+ L+PVVM ++++ + +K L++++ D+ELYKD EVKRQIW+DNQ+LFGDEVSPLL
Sbjct: 1 MPSLQPVVMCVMKHLPKVPEKKLKIVMADKELYKDCAVEVKRQIWQDNQALFGDEVSPLL 60
Query: 71 SQYIREKENILFDHH-NLTNLFFFPTPKEFKEPKLDSQVVTKFVPALMSLMVDDQVRALN 129
QYI EKE LF ++ + FF P
Sbjct: 61 KQYIVEKEAALFSTDLSVLHNFFSP----------------------------------- 85
Query: 130 SKMPPDERESAITIIEHSGRFNRIGEVVQKLAHMIGSSVKLYDMVLQFLRTLFLRTHNVH 189
P R R GEVVQKL MIG +VKLYDMVLQFLRTLFLRT NVH
Sbjct: 86 ---SPKTR--------------RQGEVVQKLTQMIGKNVKLYDMVLQFLRTLFLRTRNVH 128
Query: 190 YCTLRAELLMALHDLEIQDIISVDPCHKFTWCLDACIREKNVDIKRSRELQGFLDSIKRG 249
YCTLRAELLM+LHDL++ +I SVDPCHKFTWCLDACIREK VD KR+RELQGFLD +K+G
Sbjct: 129 YCTLRAELLMSLHDLDVSEICSVDPCHKFTWCLDACIREKFVDGKRARELQGFLDGVKKG 188
Query: 250 HEQVLGDLSMTLCDPYAINFLATSAMKILHYLINNEALPRENTVLVLLLRMLALGLSAWV 309
EQVLGDLSM LCDP+AIN LA S ++ L LIN + LPR++ L+LLLRML+LG AW
Sbjct: 189 QEQVLGDLSMILCDPFAINTLALSTIRNLQELINQDTLPRDSPDLLLLLRMLSLGQGAWD 248
Query: 310 MIDTQGGNILIEIFRSCFKLYDMVLQFLRTLFL-----RTHNVHY--------------- 349
MID+Q +F+ ++V +FL L T N+
Sbjct: 249 MIDSQ-------VFKEPRLDDELVTKFLPALMSLMVDDSTFNLEQKLPEDEKESVLYSDP 301
Query: 350 WPVPDAVQAYVQESSVACIISMYYTLHTARSRDRVGLMRVLGVLATSESDRAFDDPFLHF 409
+PDA ++QE+ VAC + +YYTLH A+ R++ L+R+L L ++ +D AF D FLH
Sbjct: 302 TTLPDAFTRFLQENRVACELGLYYTLHIAKQRNKNALLRLLPALVSTYNDMAFGDIFLHL 361
Query: 410 LSS 412
L+
Sbjct: 362 LTG 364
>gnl|CDD|225455 COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid
transport and metabolism].
Length = 1592
Score = 31.6 bits (72), Expect = 1.1
Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 1/64 (1%)
Query: 143 IIEHSGRFNRIGEVVQKLAHMIGSSVKLYDMVLQFLRTLFLRTHNVHYCTLRAELLMALH 202
I+E+ G F I E +L H G V +YD L + + + A L +
Sbjct: 572 ILENLG-FRVIEERTFRLGHADGRPVWIYDFELSSISGIPDDLTALEIRFEEAFLAIWRG 630
Query: 203 DLEI 206
LE
Sbjct: 631 RLEN 634
>gnl|CDD|215607 PLN03158, PLN03158, methionine aminopeptidase; Provisional.
Length = 396
Score = 30.2 bits (68), Expect = 2.5
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 138 ESAITIIEHSGRFNRIGEVVQKLAHMIGSSV 168
E AI I++ R+ +GEV+ + A M G SV
Sbjct: 264 EKAIAIVKPGVRYREVGEVINRHATMSGLSV 294
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible oxidation
of CO to CO2. CODH contains a nickel-iron-sulfur cluster
(C-center) and an iron-sulfur cluster (B-center). CO
oxidation occurs at the C-center. Three accessory
proteins encoded by cooCTJ genes are involved in nickel
incorporation into a nickel site. CooC functions as a
nickel insertase that mobilizes nickel to apoCODH using
energy released from ATP hydrolysis. CooC is a homodimer
and has NTPase activities. Mutation at the P-loop
abolishs its function.
Length = 116
Score = 28.4 bits (64), Expect = 3.1
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 290 ENTVLVLLLRMLALGLSAWVMIDTQGG 316
EN +L LLR L L V++DT+ G
Sbjct: 71 ENALLNALLRHLVLTRDEQVVVDTEAG 97
>gnl|CDD|240376 PTZ00350, PTZ00350, adenylosuccinate synthetase; Provisional.
Length = 436
Score = 29.6 bits (67), Expect = 3.3
Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 22 LRNTTHIDDKYLRVLVRDRELYK--DTDTEVKRQIWKDNQSLFGDEV---SPLLSQYIRE 76
L N + KY +++ + +E Y + D E + + +K D + +++ I+E
Sbjct: 164 LLNFETFEKKYRKLVEKLQEQYNIEEYDAEEELERYKGYAEKLKDMIVDTVYFMNKAIKE 223
Query: 77 KENILFDHHNLTNL 90
+ +L + N T L
Sbjct: 224 GKRVLVEGANATML 237
>gnl|CDD|182539 PRK10549, PRK10549, signal transduction histidine-protein kinase
BaeS; Provisional.
Length = 466
Score = 29.6 bits (67), Expect = 3.4
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 240 QGFLDSIKRGHEQVLGDLSMTLCDPYA 266
+GF+D IK G+EQ L LS L + Y
Sbjct: 37 RGFIDYIKHGNEQRLQMLSDALGEQYQ 63
>gnl|CDD|224543 COG1628, COG1628, Endonuclease V homolog [Replication,
recombination, and repair].
Length = 185
Score = 28.8 bits (65), Expect = 3.6
Identities = 18/86 (20%), Positives = 32/86 (37%), Gaps = 22/86 (25%)
Query: 99 FKEPKLDSQVVTKFVPALMSLMVDDQVR--ALNSKMPPD--------------ERESAIT 142
K+P ++ + AL D + R + S + E A
Sbjct: 104 RKKPDIE-----RIESALRKHFDDAEERIRIIESAGEIEKVITGPIYIQAAGIEPSEAER 158
Query: 143 IIEHSGRFNRIGEVVQKLAHMIGSSV 168
II + +I E + ++AH+I S+V
Sbjct: 159 IIRKTTIRGKIPEPL-RVAHLIASAV 183
>gnl|CDD|107385 cd06390, PBP1_iGluR_AMPA_GluR1, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR1 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR1 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 364
Score = 29.1 bits (65), Expect = 4.2
Identities = 19/63 (30%), Positives = 37/63 (58%), Gaps = 4/63 (6%)
Query: 40 RELYKDTDTEVKRQIWKDNQSLFGDEVSPLLSQYIREKENILFDHHNLTNLFFFPTP-KE 98
R+L++D D + +R I D +S + ++ +L+Q I+ ++N + H+ L NL F +
Sbjct: 161 RKLFQDLDKKKERLIVVDCES---ERLNAILNQIIKLEKNGIGYHYILANLGFMDIDLTK 217
Query: 99 FKE 101
F+E
Sbjct: 218 FRE 220
>gnl|CDD|153087 cd01678, PFL1, Pyruvate formate lyase 1. Pyruvate formate lyase
catalyzes a key step in anaerobic glycolysis, the
conversion of pyruvate and CoenzymeA to formate and
acetylCoA. The PFL mechanism involves an unusual radical
cleavage of pyruvate in which two cysteines and one
glycine form radicals that are required for catalysis.
PFL has a ten-stranded alpha/beta barrel domain that is
structurally similar to those of all three
ribonucleotide reductase (RNR) classes as well as
benzylsuccinate synthase and B12-independent glycerol
dehydratase.
Length = 738
Score = 28.9 bits (65), Expect = 6.2
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 171 YDMVLQFLRTLFLRTHNV-HYCTLR---AELLMALHDLEIQ 207
YD + +L ++ N+ HY + L MALHD +++
Sbjct: 466 YDKSMDWLADTYVNALNIIHYMHDKYAYEALQMALHDTDVR 506
>gnl|CDD|227565 COG5240, SEC21, Vesicle coat complex COPI, gamma subunit
[Intracellular trafficking and secretion].
Length = 898
Score = 28.8 bits (64), Expect = 8.0
Identities = 28/146 (19%), Positives = 45/146 (30%), Gaps = 19/146 (13%)
Query: 36 LVRDRELYKDTDTEVKRQIWKDNQSL---FGDEVSPLLSQYIREKENILFDHHNLTNLFF 92
L EL E++ + S F ++ + N+ T
Sbjct: 562 LFSSDELGDIPSLELELIGYISEDSFATAFDVNQVRKFTEDEMKAINLKRKKSETTLDTT 621
Query: 93 FPTPKEFKEPKLDSQVVTKFVPALMSLMVDDQVRALNSKMPPDERESAITIIEHSGRFNR 152
PKE K D + TK+ L+S + + I + E F
Sbjct: 622 ESVPKEDANSKADPNIKTKYADELLS------IEQIKPFGQLVNSSREIILTEPEAEF-- 673
Query: 153 IGEVVQKLAHMIGSSVKLYDMVLQFL 178
VV+ + H+ + VLQFL
Sbjct: 674 ---VVKVVKHVFKDRL-----VLQFL 691
>gnl|CDD|137204 PRK09310, aroDE, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase protein; Reviewed.
Length = 477
Score = 28.2 bits (63), Expect = 9.7
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 176 QFLRTLFLRTHNVHYCTLRAELLMALHDLEIQDIISVDPCHKFTW 220
Q LR+L V LR +LL++L DLE++ +I + P TW
Sbjct: 17 QILRSL----KLVDCIELRVDLLLSLSDLELKKLIELAPIPILTW 57
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
0.326 0.139 0.420
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,808,787
Number of extensions: 2249201
Number of successful extensions: 2592
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2590
Number of HSP's successfully gapped: 32
Length of query: 443
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 343
Effective length of database: 6,502,202
Effective search space: 2230255286
Effective search space used: 2230255286
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 61 (27.3 bits)