RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13391
(146 letters)
>gnl|CDD|214710 smart00533, MUTSd, DNA-binding domain of DNA mismatch repair MUTS
family.
Length = 308
Score = 82.0 bits (203), Expect = 1e-19
Identities = 44/146 (30%), Positives = 66/146 (45%), Gaps = 8/146 (5%)
Query: 2 KQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYR 61
QPL DL I ER AV LV N E R L + L+ +PD++ L RI R +A +D R
Sbjct: 25 LQPLLDLKEINERLDAVEELVENPELRQKLRQL-LKRIPDLERLLSRIERGRASPRDLLR 83
Query: 62 VYEGVSQLPKLISILESLVQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSE 121
+Y+ + L ++ +LESL + L IL L L + ++E D +
Sbjct: 84 LYDSLEGLKEIRQLLESLDGPLLGLLLKVILEPLLEL------LELLLELLNDDDPLEVN 137
Query: 122 REFFIRPSFDEDLQG-KAIKSNLKSR 146
I+ FD +L + L+
Sbjct: 138 DGGLIKDGFDPELDELREKLEELEEE 163
>gnl|CDD|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional.
Length = 854
Score = 70.1 bits (173), Expect = 7e-15
Identities = 37/133 (27%), Positives = 64/133 (48%), Gaps = 10/133 (7%)
Query: 3 QPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRV 62
+PL+D +AI R AV L+ + R +L E L+G+ D++ L RI +A +D +
Sbjct: 309 RPLRDREAIEARLDAVEELLEDPLLREDLREL-LKGVYDLERLLSRIALGRANPRDLAAL 367
Query: 63 YEGVSQLPKLISILESLVQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSER 122
+ + LP+L +L L ++ L + L L +LA +++E I E R
Sbjct: 368 RDSLEALPELKELLAEL----DSPLLAELAEQLDPLE-ELA---DLLERAIVEEPPLLIR 419
Query: 123 E-FFIRPSFDEDL 134
+ I +D +L
Sbjct: 420 DGGVIADGYDAEL 432
>gnl|CDD|218489 pfam05192, MutS_III, MutS domain III. This domain is found in
proteins of the MutS family (DNA mismatch repair
proteins) and is found associated with pfam00488,
pfam05188, pfam01624 and pfam05190. The MutS family of
proteins is named after the Salmonella typhimurium MutS
protein involved in mismatch repair; other members of
the family included the eukaryotic MSH 1,2,3, 4,5 and 6
proteins. These have various roles in DNA repair and
recombination. Human MSH has been implicated in
non-polyposis colorectal carcinoma (HNPCC) and is a
mismatch binding protein. The aligned region corresponds
with domain III, which is central to the structure of
Thermus aquaticus MutS as characterized in.
Length = 290
Score = 67.8 bits (166), Expect = 2e-14
Identities = 36/133 (27%), Positives = 59/133 (44%), Gaps = 15/133 (11%)
Query: 3 QPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRV 62
+PL DLD I R AV L+ + + L+G+PD++ L R+ +A +D +
Sbjct: 43 RPLTDLDEINARLDAVEELLEDLREELREA---LKGIPDLERLLSRLALGRASPRDLLAL 99
Query: 63 YEGVSQLPKLISILESLVQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSER 122
+ LP L +L S A L + L L + E++E ID + S R
Sbjct: 100 RSSLEALPALRKLLAS------APLLADLADQL-----PLPELLELLERAIDEDPPLSLR 148
Query: 123 E-FFIRPSFDEDL 134
+ I+ +D +L
Sbjct: 149 DGGVIKDGYDPEL 161
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 65.4 bits (160), Expect = 3e-13
Identities = 41/134 (30%), Positives = 74/134 (55%), Gaps = 5/134 (3%)
Query: 1 MKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCY 60
+ QPL D + I ER AV L +N E R L E L+ +PD++ L R+ +A +D
Sbjct: 305 LLQPLLDKEEIEERLDAVEELKDNPELREKLREM-LKKVPDLERLLSRLSLGRASPRDLL 363
Query: 61 RVYEGVSQLPKLISILESLVQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHS 120
R+ + + ++P++ +L SL S+L +L ++SL LA+ E++ET I+ + +
Sbjct: 364 RLRDSLEKIPEIFKLLSSL---KSESDLLLLLEDIESLDY-LAELLELLETAINEDPPLA 419
Query: 121 EREFFIRPSFDEDL 134
R+ I+ ++ +L
Sbjct: 420 VRDGIIKEGYNIEL 433
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and repair].
Length = 840
Score = 48.2 bits (115), Expect = 2e-07
Identities = 34/135 (25%), Positives = 64/135 (47%), Gaps = 10/135 (7%)
Query: 1 MKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCY 60
+ +PL+D + + R V +L+ + R L L+ + D++ LA R+ A +D
Sbjct: 293 LHRPLRDREVLEARQDTVEVLLRHFFLREGLRPL-LKEVGDLERLAARVALGNARPRDLA 351
Query: 61 RVYEGVSQLPKLISILESLVQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHS 120
R+ + QLP+L ++LE L L +L + +D ++ E++E +
Sbjct: 352 RLRTSLEQLPELRALLEELEGPT--------LQALAAQIDDFSELLELLEAALIENPPLV 403
Query: 121 ERE-FFIRPSFDEDL 134
R+ IR +DE+L
Sbjct: 404 VRDGGLIREGYDEEL 418
>gnl|CDD|220899 pfam10899, DUF2743, Protein of unknown function (DUF2743). This is
a bacterial family of proteins with unknown function.
Length = 188
Score = 31.7 bits (72), Expect = 0.087
Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 10/76 (13%)
Query: 71 KLISILESLVQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIE---------RFHSE 121
L+ L L+++++ S + + L +L I+ F+ E
Sbjct: 77 PLLKSLRELLKDLD-SPNSFKEDTHSKLLENLRLSLIYIKPFDGSMYGNKKYVNKDFYDE 135
Query: 122 REFFIRPSFDEDLQGK 137
RE+ P+FDE L K
Sbjct: 136 REWRYIPNFDEILGPK 151
>gnl|CDD|215357 PLN02665, PLN02665, pectinesterase family protein.
Length = 366
Score = 31.2 bits (71), Expect = 0.17
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 11 IVERH--AAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDC 59
IVE A NI++ N+ R + Q++AMRI KA +C
Sbjct: 150 IVESDYFMAANIIIKNSAPRPD------GKRKGAQAVAMRISGDKAAFYNC 194
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 28.8 bits (65), Expect = 1.0
Identities = 16/67 (23%), Positives = 23/67 (34%), Gaps = 2/67 (2%)
Query: 79 LVQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSEREFFIRPSFDEDLQGKA 138
LVQ+ + I S + S L++ Q I T + R + I S D G
Sbjct: 889 LVQSNNFLDSTNIYSKAEIQSQSLSQNQGTIRTL--LNRNKESQSLLILSSSDCFRIGPF 946
Query: 139 IKSNLKS 145
K
Sbjct: 947 NGKKSKY 953
>gnl|CDD|236116 PRK07856, PRK07856, short chain dehydrogenase; Provisional.
Length = 252
Score = 28.0 bits (63), Expect = 1.7
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 8 LDAIVERHAAVNILVNN 24
+DAIVERH +++LVNN
Sbjct: 66 VDAIVERHGRLDVLVNN 82
>gnl|CDD|191958 pfam08167, RIX1, rRNA processing/ribosome biogenesis. Rix1 is a
nucleoplasmic particle involved in rRNA
processing/ribosome assembly. It associates with two
other proteins, Ipi1 and Ipi3, to form the RIX1 complex
that allows Rea1 - the AAA ATPase - to associate with
the 60S ribosomal subunit. More than 170 assembly
factors are involved in the construction and maturation
of yeast ribosomes, and after these factors have
completed their function they need to be released from
the pre-ribosomes. Rea1 induces the release of the
assembly protein complex in a mechanical fashion. This
family is usually associated with NUC202, pfam08166.
Length = 163
Score = 27.2 bits (61), Expect = 2.4
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 70 PKLISILESLVQNVEASNLNTILSSLQSL 98
PKL +I+ SL+ + + T+LSSL L
Sbjct: 111 PKLPTIITSLLNLLSSFLPETVLSSLSKL 139
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 27.1 bits (61), Expect = 2.9
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 7/34 (20%)
Query: 8 LDAIVERHAAVNILVNN---TE----ARMNLHEY 34
+ A VER ++ILVNN E A M+ E+
Sbjct: 75 VAAAVERFGRIDILVNNAGIFEDKPLADMSDDEW 108
>gnl|CDD|235702 PRK06124, PRK06124, gluconate 5-dehydrogenase; Provisional.
Length = 256
Score = 27.4 bits (61), Expect = 3.0
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 8 LDAIVERHAAVNILVNNTEAR 28
I H ++ILVNN AR
Sbjct: 79 FARIDAEHGRLDILVNNVGAR 99
>gnl|CDD|224175 COG1255, COG1255, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 129
Score = 26.6 bits (59), Expect = 3.6
Identities = 11/50 (22%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 11 IVERHA--AVNILVNN-TEARMNLHE-----YALRGLPDMQSLAMRIGRK 52
I E+ A + +V++ T ++++E Y++R P++QS + + +
Sbjct: 44 INEKTAPEGLRFVVDDITNPNISIYEGADLIYSIRPPPELQSAILDVAKA 93
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 27.0 bits (61), Expect = 3.7
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 8 LDAIVERHAAVNILVNN 24
++A VE A++ILVNN
Sbjct: 73 IEAAVEAFGALDILVNN 89
>gnl|CDD|213357 cd12823, Mrs2_Mfm1p-like, Saccharomyces cerevisiae inner
mitochondrial membrane Mg2+ transporters Mfm1p and
Mrs2p-like family. A eukaryotic subfamily belonging to
the Escherichia coli CorA-Salmonella typhimurium
ZntB_like family (EcCorA_ZntB-like) family of the MIT
superfamily of essential membrane proteins involved in
transporting divalent cations (uptake or efflux) across
membranes. This functionally diverse subfamily includes
the inner mitochondrial membrane Mg2+ transporters
Saccharomyces cerevisiae Mfm1p/Lpe10p, Mrs2p, and human
MRS2/ MRS2L. It also includes a family of Arabidopsis
thaliana proteins (AtMGTs) some of which are localized
to distinct tissues, and not all of which can transport
Mg2+. Structures of the intracellular domain of two
EcCorA_ZntB-like family transporters: Vibrio
parahaemolyticus and Salmonella typhimurium ZntB form
funnel-shaped homopentamers, the tip of the funnel is
formed from two C-terminal transmembrane (TM) helices
from each monomer, and the large opening of the funnel
from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport through Salmonella typhimurium CorA, and
Mrs2p. Natural variants such as GVN and GIN, as in some
ZntB family proteins, may be associated with the
transport of different divalent cations, such as zinc
and cadmium. The functional diversity of MIT
transporters may also be due to minor structural
differences regulating gating, substrate selection, and
transport.
Length = 323
Score = 26.8 bits (60), Expect = 4.2
Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 70 PKLISILESLVQNVEASNLNTIL---SSLQSLSNDLAKFQEMIETTID 114
P+ + +L+ L + SNL +L L L + K ++ +E +D
Sbjct: 135 PEALPLLDELTDKISTSNLERLLPLKRRLVELETRVQKVRDALEELLD 182
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 26.9 bits (60), Expect = 4.4
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 80 VQNVEASNLNTILSSLQSLSNDLAKF-QEMIETTIDIERFHS 120
N+ L+ I+ SL +DL F +E+I+ +DI+
Sbjct: 54 ASNIVRDRLDKIVERFPSL-DDLHPFYRELIDVLVDIDHLKI 94
>gnl|CDD|150843 pfam10232, Med8, Mediator of RNA polymerase II transcription
complex subunit 8. Arc32, or Med8, is one of the
subunits of the Mediator complex of RNA polymerase II.
The region conserved contains two alpha helices
putatively necessary for binding to other subunits
within the core of the Mediator complex. The N-terminus
of Med8 binds to the essential core Head part of
Mediator and the C-terminus hinges to Med18 on the
non-essential part of the Head that also includes Med20.
Length = 226
Score = 26.8 bits (59), Expect = 4.7
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 86 SNLNTILSSLQSLSNDLAKFQEMIETT 112
+ S L SL+ LA ++++ T
Sbjct: 48 DQFAILSSQLVSLTKILAHEKDLLRNT 74
>gnl|CDD|146895 pfam04486, SchA_CurD, SchA/CurD like domain. Members of this
family have only been identified in species of the
Streptomyces genus. Two family members are known to be
part of gene clusters involved in the synthesis of
polyketide-based spore pigments, homologous to clusters
involved in the synthesis of polyketide antibiotics. The
function of this protein is unknown, but it has been
speculated to contain a NAD(P) binding site. Many of
these proteins contain two copies of this presumed
domain.
Length = 114
Score = 26.3 bits (58), Expect = 4.8
Identities = 13/45 (28%), Positives = 16/45 (35%), Gaps = 1/45 (2%)
Query: 7 DLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGR 51
D DA RH A V E + + R L D + L R
Sbjct: 58 DPDAAA-RHMARQPGVREVEPALAPYLEGPRDLADPERLLDFFHR 101
>gnl|CDD|221291 pfam11887, DUF3407, Protein of unknown function (DUF3407). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 360 to 454 amino acids in
length. This protein is found associated with pfam02470.
Length = 270
Score = 26.5 bits (59), Expect = 6.1
Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 7/57 (12%)
Query: 54 AGLKDCYRVYEGVSQLPKLISILESLVQ-----NVEASNLNTILSSLQSLSNDLAKF 105
L D Y + P L++ L++ + +L+ +L + LSN
Sbjct: 59 RSLADVSDTYADAA--PDLLTTLDNASTTSRTIVDQQDDLDALLLAATGLSNTGTDV 113
>gnl|CDD|237219 PRK12827, PRK12827, short chain dehydrogenase; Provisional.
Length = 249
Score = 26.2 bits (58), Expect = 6.4
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 8 LDAIVERHAAVNILVNN 24
LDA VE ++ILVNN
Sbjct: 78 LDAGVEEFGRLDILVNN 94
>gnl|CDD|235631 PRK05866, PRK05866, short chain dehydrogenase; Provisional.
Length = 293
Score = 26.2 bits (58), Expect = 7.6
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 7/27 (25%)
Query: 5 LKDLDAI-------VERHAAVNILVNN 24
L DLDA+ +R V+IL+NN
Sbjct: 98 LSDLDAVDALVADVEKRIGGVDILINN 124
>gnl|CDD|222563 pfam14131, DUF4298, Domain of unknown function (DUF4298). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and eukaryotes.
Proteins in this family are typically between 94 and 105
amino acids in length. There are two completely
conserved residues (Y and D) that may be functionally
important.
Length = 90
Score = 24.9 bits (55), Expect = 7.8
Identities = 6/40 (15%), Positives = 14/40 (35%)
Query: 86 SNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSEREFF 125
N L L L + +E E ++ ++ ++
Sbjct: 7 EIYNRFSELLAKLEEALEQLKEAQEDYRELRAYYGSEQWM 46
>gnl|CDD|235975 PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 251
Score = 25.9 bits (58), Expect = 8.0
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 8 LDAIVERHAAVNILVNNT 25
+ A +ER +V+ILVNN
Sbjct: 72 VAAALERFGSVDILVNNA 89
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
0.318 0.133 0.356
Gapped
Lambda K H
0.267 0.0700 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,175,410
Number of extensions: 630526
Number of successful extensions: 799
Number of sequences better than 10.0: 1
Number of HSP's gapped: 792
Number of HSP's successfully gapped: 61
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
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 (21.7 bits)
S2: 54 (24.6 bits)