RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1552
(220 letters)
>gnl|CDD|233801 TIGR02251, HIF-SF_euk, Dullard-like phosphatase domain. This model
represents the putative phosphatase domain of a family
of eukaryotic proteins including "Dullard" , and the NLI
interacting factor (NIF)-like phosphatases. This domain
is a member of the haloacid dehalogenase (HAD)
superfamily by virtue of a conserved set of three
catalytic motifs and a conserved fold as predicted by
PSIPRED. The third motif in this family is distinctive
(hhhhDNxPxxa) and aparrently lacking the last aspartate.
This domain is classified as a "Class III" HAD, since
there is no large "cap" domain found between motifs 1
and 2 or motifs 2 and 3. This domain is related to
domains found in FCP1-like phosphatases (TIGR02250), and
together both are detected by the pfam03031.
Length = 162
Score = 161 bits (410), Expect = 1e-50
Identities = 69/161 (42%), Positives = 84/161 (52%), Gaps = 52/161 (32%)
Query: 73 KKCMVIDLDETLVHSSFK------------------------------------------ 90
KK +V+DLDETLVHS+FK
Sbjct: 1 KKTLVLDLDETLVHSTFKMPKVDADFKVPVLIDGKIIPVYVFKRPHVDEFLERVSKWYEL 60
Query: 91 ---------YADPVADLLDRW-GVFRARLFRESCVFHHGNYVKDLNKLGRDLHQVIIVDN 140
YADPV D+LDR V RL+RESCVF +G YVKDL+ +G+DL +VII+DN
Sbjct: 61 VIFTASLEEYADPVLDILDRGGKVISRRLYRESCVFTNGKYVKDLSLVGKDLSKVIIIDN 120
Query: 141 SPASYIFHPDNAVPVASWFDDMTDTELYDLVPFFERLSKMD 181
SP SY PDNA+P+ SWF D DTEL +L+PF E L D
Sbjct: 121 SPYSYSLQPDNAIPIKSWFGDPNDTELLNLIPFLEGLRFED 161
>gnl|CDD|217328 pfam03031, NIF, NLI interacting factor-like phosphatase. This
family contains a number of NLI interacting factor
isoforms and also an N-terminal regions of RNA
polymerase II CTC phosphatase and FCP1 serine
phosphatase. This region has been identified as the
minimal phosphatase domain.
Length = 153
Score = 137 bits (348), Expect = 2e-41
Identities = 63/156 (40%), Positives = 81/156 (51%), Gaps = 50/156 (32%)
Query: 74 KCMVIDLDETLVHSSFK------------------------------------------- 90
K +V+DLDETLVHSSF+
Sbjct: 1 KTLVLDLDETLVHSSFEPDLPFDFVLNFNHGVYVKKRPGLDEFLQELSKYYEIVIFTASS 60
Query: 91 --YADPVADLLDRWG-VFRARLFRESCVFHHGNYVKDLNKLGRDLHQVIIVDNSPASYIF 147
YADPV D LD F+ RL+RESC F YVKDL+ LGRDL +V+IVDNSP S++
Sbjct: 61 KEYADPVLDKLDPKKKYFKHRLYRESCTF----YVKDLSLLGRDLSRVVIVDNSPRSFLL 116
Query: 148 HPDNAVPVASWFDDMTDTELYDLVPFFERLSKMDSV 183
PDN +P+ ++ D DTEL L+PF + L+K+D V
Sbjct: 117 QPDNGIPIPPFYGDPDDTELLKLLPFLKELAKVDDV 152
>gnl|CDD|214729 smart00577, CPDc, catalytic domain of ctd-like phosphatases.
Length = 148
Score = 116 bits (293), Expect = 3e-33
Identities = 54/147 (36%), Positives = 65/147 (44%), Gaps = 54/147 (36%)
Query: 73 KKCMVIDLDETLVH---------------------------------------------- 86
KK +V+DLDETLVH
Sbjct: 2 KKTLVLDLDETLVHSTHRSFKEWTNRDFIVPVLIDGHPHGVYVKKRPGVDEFLKRASELF 61
Query: 87 -------SSFKYADPVADLLDR-WGVFRARLFRESCVFHHGNYVKDLNKLGRDLHQVIIV 138
YADPV DLLD RLFR+ CVF G YVKDL+ L RDL +VII+
Sbjct: 62 ELVVFTAGLRMYADPVLDLLDPKKYFGYRRLFRDECVFVKGKYVKDLSLLNRDLSKVIII 121
Query: 139 DNSPASYIFHPDNAVPVASWFDDMTDT 165
D+SP S+ FHP+N +P+ WF D DT
Sbjct: 122 DDSPDSWPFHPENLIPIKPWFGDPDDT 148
>gnl|CDD|227517 COG5190, FCP1, TFIIF-interacting CTD phosphatases, including
NLI-interacting factor [Transcription].
Length = 390
Score = 115 bits (289), Expect = 2e-30
Identities = 70/171 (40%), Positives = 87/171 (50%), Gaps = 50/171 (29%)
Query: 62 LLPPIRHQDMHKKCMVIDLDETLVHSSFK------------------------------- 90
L PP+ KK +V+DLDETLVHSSF+
Sbjct: 201 LEPPVSKSTSPKKTLVLDLDETLVHSSFRYITLLDFLVKVEISLLQHLVYVSKRPELDYF 260
Query: 91 -------------------YADPVADLLDRWGVFRARLFRESCVFHHGNYVKDLNKLGRD 131
YADPV D+LD VF RLFRESCV + G Y+KD++K+GR
Sbjct: 261 LGKLSKIHELVYFTASVKRYADPVLDILDSDKVFSHRLFRESCVSYLGVYIKDISKIGRS 320
Query: 132 LHQVIIVDNSPASYIFHPDNAVPVASWFDDMTDTELYDLVPFFERLSKMDS 182
L +VII+DNSPASY FHP+NA+P+ W D D EL +L+PF E L D
Sbjct: 321 LDKVIIIDNSPASYEFHPENAIPIEKWISDEHDDELLNLLPFLEDLPDRDL 371
>gnl|CDD|216069 pfam00702, Hydrolase, haloacid dehalogenase-like hydrolase. This
family is structurally different from the alpha/beta
hydrolase family (pfam00561). This family includes
L-2-haloacid dehalogenase, epoxide hydrolases and
phosphatases. The structure of the family consists of
two domains. One is an inserted four helix bundle, which
is the least well conserved region of the alignment,
between residues 16 and 96 of Pseudomonas sp.
(S)-2-haloacid dehalogenase 1. The rest of the fold is
composed of the core alpha/beta domain. Those members
with the characteristic DxD triad at the N-terminus are
probably phosphatidylglycerolphosphate (PGP)
phosphatases involved in cardiolipin biosynthesis in the
mitochondria.
Length = 187
Score = 32.2 bits (73), Expect = 0.11
Identities = 16/110 (14%), Positives = 29/110 (26%), Gaps = 5/110 (4%)
Query: 74 KCMVIDLDETLVHSSFKYADPVA--DLLDRWGV-FRARLFRESCVFHHGNYVKDLNKLGR 130
K +V DLD TL + A + GV V+ L
Sbjct: 2 KAVVFDLDGTLTDGEPVVPEAEALLEAAAALGVAIVIAAGENLTKEGREELVRRLLLRAL 61
Query: 131 DLHQVIIVDNSPASYIFHPDNAVPVASWFDDMTDTELYDLVPFFERLSKM 180
+++ + + + V + TD + L +
Sbjct: 62 AGEELLEELLRAGATVVAVLDLVVLGLIAL--TDPLYPGAREALKELKEA 109
>gnl|CDD|226548 COG4062, MtrB, Tetrahydromethanopterin S-methyltransferase, subunit
B [Coenzyme metabolism].
Length = 108
Score = 30.1 bits (68), Expect = 0.34
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 6/59 (10%)
Query: 135 VIIVDNSPASYIFHPDNAVPVASWFDDMTDTELYDLVPFFERLSKMDSVYSFLRNSNHP 193
V I P P+ V VA F+D+ D+ P E++ K++++ L NS P
Sbjct: 4 VFIDPEIPLVM--DPETGV-VAEGFEDVI---FLDVDPIEEQIKKLETLVDDLENSLDP 56
>gnl|CDD|198082 smart01014, ARID, ARID/BRIGHT DNA binding domain. Members of the
recently discovered ARID (AT-rich interaction domain)
family of DNA-binding proteins are found in fungi and
invertebrate and vertebrate metazoans. ARID-encoding
genes are involved in a variety of biological processes
including embryonic development, cell lineage gene
regulation and cell cycle control. Although the specific
roles of this domain and of ARID-containing proteins in
transcriptional regulation are yet to be elucidated,
they include both positive and negative transcriptional
regulation and a likely involvement in the modification
of chromatin structure. The basic structure of the ARID
domain domain appears to be a series of six
alpha-helices separated by beta-strands, loops, or
turns, but the structured region may extend to an
additional helix at either or both ends of the basic
six. Based on primary sequence homology, they can be
partitioned into three structural classes: Minimal ARID
proteins that consist of a core domain formed by six
alpha helices; ARID proteins that supplement the core
domain with an N-terminal alpha-helix; and Extended-ARID
proteins, which contain the core domain and additional
alpha-helices at their N- and C-termini.
Length = 88
Score = 29.1 bits (66), Expect = 0.55
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 175 ERLSKMDSVYSFLRNSNHPYNMQPSLGG 202
ER +D + F+ P + P +GG
Sbjct: 2 ERELFLDRLRKFMEKRGTPLDKIPVIGG 29
>gnl|CDD|222906 PHA02606, 5.1, hypothetical protein; Provisional.
Length = 179
Score = 29.5 bits (66), Expect = 0.84
Identities = 18/79 (22%), Positives = 29/79 (36%), Gaps = 6/79 (7%)
Query: 140 NSPASYIFHPDNAVPVASWFD--DMTDTELYDLVPFFERLSKMDSVYSFLRNSNHPYNMQ 197
N Y D +SW D D + +LY F+ + +++ + Y
Sbjct: 67 NDALKYRLKDDEFKTASSWEDLPDPSTADLY----LFKAPQNLQKTFTYEVTLIYDYQEP 122
Query: 198 PSLGGGGSNNGSQDGGGLP 216
GG GS + S +G G
Sbjct: 123 SESGGSGSGSNSSEGAGET 141
>gnl|CDD|188441 TIGR03926, T7_EssB, type VII secretion protein EssB. Members of
this family are associated with type VII secretion of
WXG100 family targets in the Firmicutes, but not in the
Actinobacteria. This protein is designated YukC in
Bacillus subtilis and EssB is Staphylococcus aureus
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 377
Score = 30.0 bits (68), Expect = 0.90
Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 20/72 (27%)
Query: 127 KLGRDLHQVIIVDNSPASYIFHPDNAVPVASWFDDMTDTELYDLVPFFERLSKMDSVYSF 186
+L +L + NS ++I HP+N V F L P ++
Sbjct: 82 RLALNLADLEEHLNSRLTFILHPENLV-----FTK-------GLTPSI--------IHRG 121
Query: 187 LRNSNHPYNMQP 198
++ S PY +
Sbjct: 122 VKESLPPYELDE 133
>gnl|CDD|179187 PRK00965, PRK00965, tetrahydromethanopterin S-methyltransferase
subunit B; Provisional.
Length = 96
Score = 28.4 bits (64), Expect = 1.2
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 149 PDNAVPVASWFDDMTDTELYDLVPFFERLSKMDSVYSFLRNSNHPYN 195
PD + +A +D+ + D+ P E ++K++++ L NS P N
Sbjct: 16 PDTGL-IAEMREDII---VVDMDPIEEEINKLEALADDLENSLDPRN 58
>gnl|CDD|114180 pfam05440, MtrB, Tetrahydromethanopterin S-methyltransferase
subunit B. The N5-methyltetrahydromethanopterin:
coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is
a membrane-associated, corrinoid-containing protein that
uses a transmethylation reaction to drive an
energy-conserving sodium ion pump.
Length = 97
Score = 28.2 bits (63), Expect = 1.2
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 6/59 (10%)
Query: 135 VIIVDNSPASYIFHPDNAVPVASWFDDMTDTELYDLVPFFERLSKMDSVYSFLRNSNHP 193
V I P+ V VA +D+ + P FE++ K++++ L NS P
Sbjct: 3 VRIAPEINLVM--DPETGV-VAEEREDVI---FLSMDPIFEQIDKLEAIADDLENSLDP 55
>gnl|CDD|184985 PRK15025, PRK15025, ureidoglycolate dehydrogenase; Provisional.
Length = 349
Score = 29.3 bits (66), Expect = 1.5
Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 23/93 (24%)
Query: 68 HQDMHKKCMVIDLDETLVHSSFKYADPVADLLDRWGVFRARLFRESCVFH-HGN-----Y 121
HQ + K L ++A VA++L ++ ++ H HG Y
Sbjct: 9 HQLIKNKLCKAGLKR-------EHAATVAEVL---------VYADARGIHSHGAVRVEYY 52
Query: 122 VKDLNKLGRDLHQVIIVDNS-PASYIFHPDNAV 153
+ ++K G + + + P S I H DNA
Sbjct: 53 AERISKGGTNREPEFRFEETGPCSAILHADNAA 85
>gnl|CDD|227038 COG4694, COG4694, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 758
Score = 28.7 bits (64), Expect = 2.6
Identities = 8/34 (23%), Positives = 16/34 (47%)
Query: 61 RLLPPIRHQDMHKKCMVIDLDETLVHSSFKYADP 94
R L P + D + +++E V+S +A+
Sbjct: 679 RFLGPFKRNDSSLSECIENIEEARVNSFISWAND 712
>gnl|CDD|226489 COG3981, COG3981, Predicted acetyltransferase [General function
prediction only].
Length = 174
Score = 27.7 bits (62), Expect = 3.3
Identities = 13/31 (41%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 19 KKARK-GIFRSLLCCFRGNHSSSNVSKASGG 48
+KAR+ GI + L+ C + N +S V +A+GG
Sbjct: 124 EKARELGIKKVLVTCDKDNIASRKVIEANGG 154
>gnl|CDD|133017 cd02526, GT2_RfbF_like, RfbF is a putative dTDP-rhamnosyl
transferase. Shigella flexneri RfbF protein is a
putative dTDP-rhamnosyl transferase. dTDP rhamnosyl
transferases of Shigella flexneri add rhamnose sugars
to N-acetyl-glucosamine in the O-antigen tetrasaccharide
repeat. Lipopolysaccharide O antigens are important
virulence determinants for many bacteria. The variations
of sugar composition, the sequence of the sugars and the
linkages in the O antigen provide structural diversity
of the O antigen.
Length = 237
Score = 27.6 bits (62), Expect = 4.6
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 125 LNKLGRDLHQVIIVDNSPASYIF 147
L L + +V++VDNS + I
Sbjct: 17 LAALAEQVDKVVVVDNSSGNDIE 39
>gnl|CDD|118668 pfam10140, YukC, WXG100 protein secretion system (Wss), protein
YukC. Members of this family of proteins include
predicted membrane proteins homologous to YukC in B.
subtilis. The YukC protein family would participate to
the formation of a translocon required for the secretion
of WXG100 proteins (pfam06013) in monoderm bacteria, the
WXG100 protein secretion system (Wss). This family
includes EssB in Staphylococcus aureus.
Length = 359
Score = 27.6 bits (62), Expect = 5.7
Identities = 15/72 (20%), Positives = 27/72 (37%), Gaps = 20/72 (27%)
Query: 127 KLGRDLHQVIIVDNSPASYIFHPDNAVPVASWFDDMTDTELYDLVPFFERLSKMDSVYSF 186
+L ++ + N ++I HP+N V FD L P F ++
Sbjct: 63 RLALNVAALEEHLNKRLTFILHPENLV-----FDK-------GLTPKF--------IHRG 102
Query: 187 LRNSNHPYNMQP 198
++ S PY +
Sbjct: 103 VKESLPPYELDE 114
>gnl|CDD|237326 PRK13271, treA, trehalase; Provisional.
Length = 569
Score = 27.6 bits (61), Expect = 6.6
Identities = 16/46 (34%), Positives = 19/46 (41%), Gaps = 11/46 (23%)
Query: 180 MDSVYSFLRNSNHPYNMQPSL-----------GGGGSNNGSQDGGG 214
MD + FL N H Y+ + L GGGG QDG G
Sbjct: 478 MDVTWRFLTNVQHTYDREKKLVEKYDVSSTGTGGGGGEYPLQDGFG 523
>gnl|CDD|225090 COG2179, COG2179, Predicted hydrolase of the HAD superfamily
[General function prediction only].
Length = 175
Score = 26.9 bits (60), Expect = 7.4
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 63 LPPIRHQDMHKKCMVIDLDETLV 85
+ P + K +++DLD TLV
Sbjct: 18 ITPDILKAHGIKGVILDLDNTLV 40
>gnl|CDD|197267 cd09170, PLDc_Nuc, Catalytic domain of EDTA-resistant nuclease Nuc
from Salmonella typhimurium and similar proteins.
Catalytic domain of an EDTA-resistant nuclease Nuc from
Salmonella typhimurium and similar proteins. Nuc is an
endonuclease cleaving both single- and double-stranded
DNA. It is the smallest known member of the
phospholipase D (PLD, EC 3.1.4.4) superfamily that
includes a diverse group of proteins with various
catalytic functions. Most members of this superfamily
have two copies of the conserved HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue) in a single polypeptide chain and both are
required for catalytic activity. However, Nuc only has
one copy of the HKD motif per subunit but form a
functionally active homodimer (it is most likely also
active in solution as a multimeric protein), which has a
single active site at the dimer interface containing the
HKD motifs from both subunits. Due to the lack of a
distinct domain for DNA binding, Nuc cuts DNA
non-specifically. It utilizes a two-step mechanism to
cleave phosphodiester bonds: Upon substrate binding, the
bond is first attacked by a histidine residue from one
HKD motif to form a covalent phosphohistidine
intermediate, which is then hydrolyzed by water with the
aid of a second histidine residue from the other HKD
motif in the opposite subunit.
Length = 142
Score = 26.3 bits (59), Expect = 8.7
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 59 PVRLLPPIRHQDMHKKCMVIDLDETLVHSSFKYAD 93
PVR+ + MH K MVID +T++ SF +
Sbjct: 78 PVRIDD--NYAIMHNKVMVID-GKTVITGSFNFTA 109
>gnl|CDD|219082 pfam06547, DUF1117, Protein of unknown function (DUF1117). This
family represents the C-terminus of a number of
hypothetical plant proteins.
Length = 115
Score = 26.0 bits (57), Expect = 8.8
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 13 TSESVGKKARKG----IFRSLLCCFRGNHSSSNVSKAS 46
S + R G IFR++ CF HSS + S +S
Sbjct: 53 GSRGNRSRERGGIIRRIFRNMFSCFGRVHSSRSSSSSS 90
>gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated.
Length = 351
Score = 26.9 bits (60), Expect = 9.4
Identities = 11/25 (44%), Positives = 12/25 (48%), Gaps = 5/25 (20%)
Query: 57 HSPVRLLPPIRHQDMHKKCMVIDLD 81
HS RLLP IR +C I L
Sbjct: 179 HSSGRLLPTIR-----SRCQPISLK 198
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 0.136 0.422
Gapped
Lambda K H
0.267 0.0771 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,190,856
Number of extensions: 1028988
Number of successful extensions: 909
Number of sequences better than 10.0: 1
Number of HSP's gapped: 904
Number of HSP's successfully gapped: 36
Length of query: 220
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 127
Effective length of database: 6,812,680
Effective search space: 865210360
Effective search space used: 865210360
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: 57 (25.7 bits)