RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4906
(144 letters)
>gnl|CDD|217869 pfam04065, Not3, Not1 N-terminal domain, CCR4-Not complex
component.
Length = 233
Score = 195 bits (498), Expect = 2e-64
Identities = 84/132 (63%), Positives = 111/132 (84%)
Query: 9 QGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIA 68
Q EID+ LKKV+EG+E+F+ I++K+ NATN++QKEK E+DLK+EIKKLQRLRDQIK+W++
Sbjct: 7 QQEIDKLLKKVAEGLESFDSIYEKLENATNASQKEKLESDLKREIKKLQRLRDQIKTWLS 66
Query: 69 SAEIKDKSTLLDYRKLIETQMERFKVVERETKTKAYSKEGLGAVQKMDPAQKEKEEISTW 128
S++IKDK +LL+ RKLIET MERFK VE+E KTKA+SKEGL A K+DP +KEK E+ +
Sbjct: 67 SSDIKDKDSLLENRKLIETAMERFKAVEKEMKTKAFSKEGLSAASKLDPKEKEKAEVCDF 126
Query: 129 LVTSIDALNIQV 140
L +ID LN Q+
Sbjct: 127 LSNTIDELNKQI 138
>gnl|CDD|227952 COG5665, NOT5, CCR4-NOT transcriptional regulation complex, NOT5
subunit [Transcription].
Length = 548
Score = 126 bits (318), Expect = 4e-35
Identities = 60/128 (46%), Positives = 88/128 (68%)
Query: 13 DRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEI 72
D+ LKKV EG+E F+DI++K + NS+ +EK E+DLK+EIKKLQ+ RDQIK+W++ ++
Sbjct: 1 DKLLKKVKEGIEDFDDIYEKFQSTDNSSHREKLESDLKREIKKLQKHRDQIKTWLSKEDV 60
Query: 73 KDKSTLLDYRKLIETQMERFKVVERETKTKAYSKEGLGAVQKMDPAQKEKEEISTWLVTS 132
KDK L+ R+LIE MERFK VE+ KTK +SKE L +DP + +K + ++
Sbjct: 61 KDKQVLMTNRRLIENGMERFKSVEKLMKTKQFSKEALTNPDIIDPKELKKRDQVLFIHDC 120
Query: 133 IDALNIQV 140
+D L Q+
Sbjct: 121 LDELQKQL 128
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 30.8 bits (70), Expect = 0.21
Identities = 22/80 (27%), Positives = 32/80 (40%), Gaps = 9/80 (11%)
Query: 19 VSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTL 78
V EG TFE+I KV N T+S D+K + L IKS ++ S L
Sbjct: 338 VQEGNSTFEEIPSKVKNQTSSVVP-----DVKAALDS---LGTDIKSVAEDLPLQVLSVL 389
Query: 79 LDYRKLIETQMERFK-VVER 97
++ + VE+
Sbjct: 390 SQILNNTQSSSNPYLPYVEQ 409
>gnl|CDD|200321 TIGR03751, conj_TIGR03751, conjugative transfer region
lipoprotein, TIGR03751 family. Members of this protein
family are found occasionally on plasmids. Usually,
however, they are found on the bacterial main
chromosome in regions flanked by markers of conjugative
transfer and/or transposition [Mobile and
extrachromosomal element functions, Plasmid functions].
Length = 124
Score = 30.1 bits (68), Expect = 0.23
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 6/58 (10%)
Query: 21 EGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLR----DQIKSWIASAEIKD 74
EG T DIW ++S Q + Y L++ + + + + A EI
Sbjct: 21 EGGLTMLDIWNG--GGSSSRQLQDYRQTLRRPLSDPENYASLNEQESYTRTAENEISQ 76
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 29.5 bits (67), Expect = 0.69
Identities = 14/61 (22%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 49 LKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMERFKVVERETKT-KAYSKE 107
+K+E++++++ R+ + + K LL + +E ++ER + + + KT K ++ E
Sbjct: 220 IKEELEEIEKERESLLEELKELAKKYLEELLALYEYLEIELERAEALSKFLKTDKTFAIE 279
Query: 108 G 108
G
Sbjct: 280 G 280
>gnl|CDD|233137 TIGR00811, sit, silicon transporter. Marine diatoms such as
Cylindrotheca fusiformis encode at least six silicon
transport protein homologues which exhibit similar size
and topology. One characterized member of the family
(Sit1) functions in the energy-dependent uptake of
either Silicic acid [Si(OH)4] or Silicate [Si(OH)3O-] by
a Na+ symport mechanism. The system is found in marine
diatoms which make their "glass houses" out of silicon
[Transport and binding proteins, Other].
Length = 545
Score = 29.2 bits (65), Expect = 0.83
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 7/50 (14%)
Query: 13 DRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQ 62
+R LK + E E NA + +K +EA L E+K L +L +
Sbjct: 485 ERMLKNIRELREMIN-------NAISDEEKTTFEAALAIEVKALDKLNAE 527
>gnl|CDD|227512 COG5185, HEC1, Protein involved in chromosome segregation,
interacts with SMC proteins [Cell division and
chromosome partitioning].
Length = 622
Score = 28.0 bits (62), Expect = 2.0
Identities = 22/98 (22%), Positives = 39/98 (39%)
Query: 43 EKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMERFKVVERETKTK 102
EK+ + +I L+ D + I A + K + + K K
Sbjct: 263 EKFVHIINTDIANLKTQNDNLYEKIQEAMKISQKIKTLREKWRALKSDSNKYENYVNAMK 322
Query: 103 AYSKEGLGAVQKMDPAQKEKEEISTWLVTSIDALNIQV 140
S+E G ++K+ + KEE L ++ID L+ Q+
Sbjct: 323 QKSQEWPGKLEKLKSEIELKEEEIKALQSNIDELHKQL 360
>gnl|CDD|131005 TIGR01950, SoxR, redox-sensitive transcriptional activator SoxR.
SoxR is a MerR-family homodimeric transcription factor
with a 2Fe-2S cluster in each monomer. The motif
CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur
cluster activates SoxR. The physiological role in E.
coli is response to oxidative stress. It is activated by
superoxide, singlet oxygen, nitric oxide (NO), and
hydrogen peroxide. In E. coli, SoxR increases expression
of transcription factor SoxS; different downstream
targets may exist in other species [Cellular processes,
Detoxification, Regulatory functions, DNA interactions].
Length = 142
Score = 27.1 bits (60), Expect = 2.3
Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 8/57 (14%)
Query: 11 EIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWI 67
I L + EG D W ++ ++ +L + I +L LRDQ+ I
Sbjct: 62 TIGEALAVLPEGRTPTADDWARL--------SSQWREELDERIDQLNALRDQLDGCI 110
>gnl|CDD|232887 TIGR00232, tktlase_bact, transketolase, bacterial and yeast. This
model is designed to capture orthologs of bacterial
transketolases. The group includes two from the yeast
Saccharomyces cerevisiae but excludes dihydroxyactetone
synthases (formaldehyde transketolases) from various
yeasts and the even more distant mammalian
transketolases. Among the family of thiamine
diphosphate-dependent enzymes that includes
transketolases, dihydroxyacetone synthases, pyruvate
dehydrogenase E1-beta subunits, and
deoxyxylulose-5-phosphate synthases, mammalian and
bacterial transketolases seem not to be orthologous
[Energy metabolism, Pentose phosphate pathway].
Length = 653
Score = 27.4 bits (61), Expect = 3.2
Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 10/76 (13%)
Query: 42 KEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMERFKVVERETKT 101
++++ KK L + ++ + + ++ FK + T
Sbjct: 302 EQEWNELFAAYKKKYPELAAEFTRRLSG----------ELPADWDKKLPEFKAKLQALAT 351
Query: 102 KAYSKEGLGAVQKMDP 117
+ YS+ L A+ + P
Sbjct: 352 RKYSQNVLNAIANVLP 367
>gnl|CDD|133383 cd01108, HTH_CueR, Helix-Turn-Helix DNA binding domain of CueR-like
transcription regulators. Helix-turn-helix (HTH)
transcription regulators CueR and ActP, copper efflux
regulators. In Bacillus subtilis, copper induced CueR
regulates the copZA operon, preventing copper toxicity.
In Rhizobium leguminosarum, ActP controls copper
homeostasis; it detects cytoplasmic copper stress and
activates transcription in response to increasing copper
concentrations. These proteins are comprised of two
distinct domains that harbor the regulatory
(effector-binding) site and the active (DNA-binding)
site. Their conserved N-terminal domains contain winged
HTH motifs that mediate DNA binding, while the
C-terminal domains have two conserved cysteines that
define a monovalent copper ion binding site. These
proteins share the N-terminal DNA binding domain with
other transcription regulators of the MerR superfamily
that promote transcription by reconfiguring the spacer
between the -35 and -10 promoter elements.
Length = 127
Score = 26.8 bits (60), Expect = 3.2
Identities = 7/23 (30%), Positives = 15/23 (65%)
Query: 47 ADLKKEIKKLQRLRDQIKSWIAS 69
A+L+++I +LQ +R ++ S
Sbjct: 89 AELERKIAELQAMRRTLQQLADS 111
>gnl|CDD|131099 TIGR02044, CueR, Cu(I)-responsive transcriptional regulator. This
model represents the copper-, silver- and gold- (I)
responsive transcriptional activator of the gamma
proteobacterial copper efflux system. This protein is a
member of the MerR family of transcriptional activators
(pfam00376) and contains a distinctive pattern of
cysteine residues in its metal binding loop, Cys-X7-Cys.
This family also lacks a conserved cysteine at the
N-terminal end of the dimerization helix which is
required for the binding of divalent metals such as
zinc; here it is replaced by a serine residue
[Regulatory functions, DNA interactions].
Length = 127
Score = 26.6 bits (59), Expect = 3.4
Identities = 8/30 (26%), Positives = 19/30 (63%)
Query: 47 ADLKKEIKKLQRLRDQIKSWIASAEIKDKS 76
A+++++I +LQ +RDQ+++ + D
Sbjct: 89 AEIERKISELQSMRDQLEALAQACPGDDSP 118
>gnl|CDD|223759 COG0687, PotD, Spermidine/putrescine-binding periplasmic protein
[Amino acid transport and metabolism].
Length = 363
Score = 27.0 bits (60), Expect = 3.4
Identities = 7/35 (20%), Positives = 12/35 (34%)
Query: 40 NQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKD 74
+ DLKK L +L+ W ++
Sbjct: 194 SPNTTDPEDLKKAFDLLDKLKPVNVYWFDGSQYVQ 228
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 26.8 bits (60), Expect = 4.8
Identities = 21/92 (22%), Positives = 39/92 (42%), Gaps = 5/92 (5%)
Query: 10 GEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIAS 69
E + V G E F + + A + EK L+KEI ++++ + ++A
Sbjct: 787 EEPPVEVTAVVGGAELFLPLAGLIDLAAELARLEKELEKLEKEIDRIEKKLSN-EGFVAK 845
Query: 70 AE----IKDKSTLLDYRKLIETQMERFKVVER 97
A K+K L +Y+ + ER V++
Sbjct: 846 APEEVVEKEKEKLAEYQVKLAKLEERLAVLKA 877
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination, and
repair].
Length = 1187
Score = 27.0 bits (60), Expect = 5.1
Identities = 22/91 (24%), Positives = 43/91 (47%), Gaps = 10/91 (10%)
Query: 18 KVSEGVETFEDIWQKVHNATNSNQKEKYEADLK-KEIKKLQRLRDQIKSWIASAEIKDK- 75
++ VE ED + V+ + EK + EI+K+ ++ + + E+K++
Sbjct: 1042 ELEALVEILEDGFALVYPTRVLPELEKGTLKVTEVEIRKVSKVYLYTQGEVVE-EMKERG 1100
Query: 76 ----STLLDYRKLIETQMERFKVVERETKTK 102
ST Y K++ET + R V+E + + K
Sbjct: 1101 IGRPST---YAKIVETLLRRGYVIESKGRKK 1128
>gnl|CDD|234792 PRK00558, uvrC, excinuclease ABC subunit C; Validated.
Length = 598
Score = 26.6 bits (60), Expect = 5.4
Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 20/78 (25%)
Query: 3 RTYPGRQGEIDRCL----KKVSEGVETFEDIWQKVHNATN--SNQKEKYEADLKKEIKKL 56
R P +I RCL +S+ E+ + V A S + ++ +L++++++
Sbjct: 160 RKRPCLLYQIGRCLAPCVGLISK-----EEYAELVDEAKLFLSGKTDEVLKELEEKMEEA 214
Query: 57 ---------QRLRDQIKS 65
R RDQI++
Sbjct: 215 SENLEFERAARYRDQIQA 232
>gnl|CDD|216597 pfam01601, Corona_S2, Coronavirus S2 glycoprotein. The coronavirus
spike glycoprotein forms the characteristic 'corona'
after which the group is named. The Spike glycoprotein
is translated as a large polypeptide that is
subsequently cleaved to S1 pfam01600 and S2.
Length = 609
Score = 26.5 bits (59), Expect = 6.1
Identities = 7/45 (15%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 24 ETFEDIWQKVHNATNSNQKEKYEA---DLKKEIKKLQRLRDQIKS 65
+ + ++ +++ +K+ A +L EI +LQ + +
Sbjct: 484 KELDKWFKNLNSTVPDLDLDKFNATILNLTGEIDRLQEVIKNLND 528
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 26.8 bits (59), Expect = 6.3
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 46 EADLKKEIKKLQRLRDQIKSWIASAEIKD--KSTLL 79
E DL++ IK++ R++++ S ++KD KS L+
Sbjct: 549 EVDLEELIKEIDEDREKVRLGKISRKVKDLVKSALM 584
>gnl|CDD|221451 pfam12167, DUF3596, Domain of unknown function (DUF3596). This
presumed domain is functionally uncharacterized.This
domain family is found in bacteria and viruses, and is
approximately 90 amino acids in length. The family is
found in association with pfam00589.
Length = 88
Score = 25.3 bits (56), Expect = 7.1
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 47 ADLKKEIKKLQRLRDQIKSWIA 68
D KK +RL +I++ IA
Sbjct: 29 PDTPANRKKAERLLARIEAEIA 50
>gnl|CDD|180685 PRK06767, PRK06767, methionine gamma-lyase; Provisional.
Length = 386
Score = 26.3 bits (58), Expect = 7.4
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 8 RQGEIDRCLKKVSEGVETFEDIWQKVHNATNS 39
++ I L ++S G+E++EDI + A
Sbjct: 354 QEMGIYDNLIRLSVGLESWEDIVSDLEQALKK 385
>gnl|CDD|237136 PRK12557, PRK12557, H(2)-dependent methylenetetrahydromethanopterin
dehydrogenase-related protein; Provisional.
Length = 342
Score = 26.2 bits (58), Expect = 7.7
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 48 DLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIE 86
DL ++ L+ L + + I AEIK +TL+ + L++
Sbjct: 280 DLDAALEILENLDEDLLKEIEEAEIK-PTTLVAAQALVK 317
>gnl|CDD|227584 COG5259, RSC8, RSC chromatin remodeling complex subunit RSC8
[Chromatin structure and dynamics / Transcription].
Length = 531
Score = 26.0 bits (57), Expect = 8.6
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 16 LKKVSEGVETFEDIWQKVHNATNSNQKE 43
L + EG+E + D W KV + KE
Sbjct: 287 LLLLLEGIEMYGDDWDKVARHVGTKTKE 314
>gnl|CDD|215018 smart01087, COG6, Conserved oligomeric complex COG6. COG6 is a
component of the conserved oligomeric golgi complex,
which is composed of eight different subunits and is
required for normal golgi morphology and localisation.
Length = 598
Score = 26.1 bits (58), Expect = 9.2
Identities = 12/60 (20%), Positives = 26/60 (43%), Gaps = 10/60 (16%)
Query: 10 GEIDRCLKKVSEGVE----TFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKS 65
+ L+++SE V+ + + + +++ A N Q DL E +LQ ++
Sbjct: 28 KPVAEQLQRLSEDVQKLNNSCDSMKDQLNTAKNQTQ------DLISEASELQEELALLEL 81
>gnl|CDD|189013 cd09606, M3B_PepF_1, Peptidase family M3B Oligopeptidase F
(PepF). Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7
and 17 amino acids with fairly broad specificity. The
PepF gene is duplicated in L. lactis on the plasmid
that bears it, while a shortened second copy is found
in Bacillus subtilis. Most bacterial PepFs are
cytoplasmic endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 546
Score = 26.0 bits (58), Expect = 9.4
Identities = 9/49 (18%), Positives = 21/49 (42%)
Query: 25 TFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIK 73
FE + ++ + + K +L+ +K+ LR ++ A I+
Sbjct: 5 DFEALKERFIDLIAKLKNAKSAEELEAWLKEWSELRRELDEMATLAYIR 53
>gnl|CDD|226126 COG3598, RepA, RecA-family ATPase [DNA replication, recombination,
and repair].
Length = 402
Score = 26.0 bits (57), Expect = 10.0
Identities = 21/86 (24%), Positives = 33/86 (38%), Gaps = 12/86 (13%)
Query: 40 NQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDK-----------STLLDYRKLIETQ 88
N+ KYE L K LQ RD + ++ K L+ +I
Sbjct: 309 NEFAKYEPILHKFEPILQHDRDIEYGFKTDELLRLKGPKHKRTVLAHLNKLESMAIIRWA 368
Query: 89 MERFKVVERETKTKAYSKEGLGAVQK 114
ER K + E+ ++ Y G G+ +K
Sbjct: 369 HERLK-AKEESISERYKAIGKGSTRK 393
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
0.311 0.126 0.345
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,070,547
Number of extensions: 614390
Number of successful extensions: 1068
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1049
Number of HSP's successfully gapped: 199
Length of query: 144
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 56
Effective length of database: 7,034,450
Effective search space: 393929200
Effective search space used: 393929200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (24.6 bits)