RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7187
(214 letters)
>gnl|CDD|214631 smart00350, MCM, minichromosome maintenance proteins.
Length = 509
Score = 337 bits (867), Expect = e-115
Identities = 117/215 (54%), Positives = 150/215 (69%), Gaps = 2/215 (0%)
Query: 1 MEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSRCSVLAAA 60
+E GA+VLAD GV CIDEFDKM + DR AIHEAMEQQTISIAKAGITTTLN+RCSVLAAA
Sbjct: 291 LEAGALVLADNGVCCIDEFDKMDDSDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAA 350
Query: 61 NSVFGRWDDTKG-EQNIDFMPTILSRFDMIFIIKDEHDETRDITLAKHIMKVHMTAGQEI 119
N + GR+D E+NID ILSRFD++F++ DE DE RD LAKH++ +H + E
Sbjct: 351 NPIGGRYDPKLTPEENIDLPAPILSRFDLLFVVLDEVDEERDRELAKHVVDLHRYSHPEE 410
Query: 120 DVASDGELPLPVLKKYINYCRMRCGPRLTHEAGEKLKNRYVLMRNGSKEDGEKKLNIPIT 179
D A + L L+KYI Y R + P+L+ EA +KL YV +R E + +IPIT
Sbjct: 411 DEAFEPPLSQEKLRKYIAYAREKIKPKLSEEAADKLVKAYVDLRKED-SQTESRSSIPIT 469
Query: 180 VRQLEAIVRIAESMAKMQLEPFAIDSHVTEALRLF 214
VRQLE+I+R++E+ AKM+L ++ V EA+RL
Sbjct: 470 VRQLESIIRLSEAHAKMRLSDVVEEADVEEAIRLL 504
>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 316 bits (812), Expect = e-109
Identities = 117/215 (54%), Positives = 157/215 (73%), Gaps = 5/215 (2%)
Query: 1 MEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSRCSVLAAA 60
+E GA+VLADGGV CIDEFDKM E+DRVAIHEAMEQQTISIAKAGI TLN+RCSVLAAA
Sbjct: 112 LEAGALVLADGGVCCIDEFDKMNEEDRVAIHEAMEQQTISIAKAGIVATLNARCSVLAAA 171
Query: 61 NSVFGRWDDTKG-EQNIDFMPTILSRFDMIFIIKDEHDETRDITLAKHIMKVHMTAGQEI 119
N +FGR+D K +NI+ P +LSRFD+IF++ D+ DE RD LAKHI+ +H + +E
Sbjct: 172 NPIFGRYDPKKSVAENINLPPPLLSRFDLIFVLLDKPDEERDEELAKHIVDLHRASDEE- 230
Query: 120 DVASDGELPLPVLKKYINYCRMRCGPRLTHEAGEKLKNRYVLMRNGSKEDGEKKLNIPIT 179
++ ++ E+ +L+KYI Y R P+L+ EA EKL N YV +R KE + +IPIT
Sbjct: 231 EIETEDEIDPELLRKYIAYARENIKPKLSDEAREKLVNWYVELR---KESEGSRGSIPIT 287
Query: 180 VRQLEAIVRIAESMAKMQLEPFAIDSHVTEALRLF 214
VRQLE+++R++E+ A+++L + V EA+RL
Sbjct: 288 VRQLESLIRLSEAHARLRLSEEVTEEDVEEAIRLI 322
>gnl|CDD|224162 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 272 bits (698), Expect = 5e-88
Identities = 121/219 (55%), Positives = 152/219 (69%), Gaps = 7/219 (3%)
Query: 2 EGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSRCSVLAAAN 61
E GA+VLADGGV CIDEFDKM E+DRVAIHEAMEQQTISIAKAGIT TLN+RCSVLAAAN
Sbjct: 375 EAGALVLADGGVCCIDEFDKMNEEDRVAIHEAMEQQTISIAKAGITATLNARCSVLAAAN 434
Query: 62 SVFGRWDDTKGE-QNIDFMPTILSRFDMIFIIKDEHDETRDITLAKHIMKVHMTAGQEID 120
FGR+D K +NI+ +LSRFD+IF++KD+ DE +D +A+HI+ H E
Sbjct: 435 PKFGRYDPKKTVAENINLPAPLLSRFDLIFVLKDDPDEEKDEEIAEHILDKHRGEEPEET 494
Query: 121 VASDG-----ELPLPVLKKYINYCRMRCGPRLTHEAGEKLKNRYVLMRNGSKEDGEKKLN 175
++ DG E +L+KYI+Y R P LT EA E+L++ YV MR S EK+
Sbjct: 495 ISLDGVDEVEERDFELLRKYISYARKNVTPVLTEEAREELEDYYVEMRKKSALVEEKRT- 553
Query: 176 IPITVRQLEAIVRIAESMAKMQLEPFAIDSHVTEALRLF 214
IPIT RQLE+I+R+AE+ AKM+L + V EA+RL
Sbjct: 554 IPITARQLESIIRLAEAHAKMRLSDVVEEEDVDEAIRLV 592
>gnl|CDD|173403 PTZ00111, PTZ00111, DNA replication licensing factor MCM4;
Provisional.
Length = 915
Score = 158 bits (400), Expect = 1e-44
Identities = 79/256 (30%), Positives = 140/256 (54%), Gaps = 43/256 (16%)
Query: 1 MEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSRCSVLAAA 60
++ GA+VLA+GGV CIDE DK + R++++E MEQQT++IAKAGI TL + ++LA+
Sbjct: 548 IQPGAVVLANGGVCCIDELDKCHNESRLSLYEVMEQQTVTIAKAGIVATLKAETAILASC 607
Query: 61 NSVFGRWDDTKGE-QNIDFMPTILSRFDMIFIIKDEHDETRD----ITLAKHIMKVHMT- 114
N + R++ K +NI+ P++ +RFD+I+++ D D+ D +++AK + HMT
Sbjct: 608 NPINSRYNKNKAVIENINISPSLFTRFDLIYLVLDHIDQDTDQLISLSIAKDFLLPHMTG 667
Query: 115 AGQEID---------VASDGELP--------LPVLKKYINYCRMRCGPRLTHEAGEKLKN 157
+G + D V + L +L+ YI + ++ C P+L+ EA + +
Sbjct: 668 SGNDEDTYDRSNTMHVEDESLRSEKDYNKNDLDMLRMYIKFSKLHCFPKLSDEAKKVITR 727
Query: 158 RYVLMRNG------------SKEDGEKKL--------NIPITVRQLEAIVRIAESMAKMQ 197
YV MR G ++ED + L I ++ R + +I+RI+ S+A+M+
Sbjct: 728 EYVKMRQGNFQTSNLDELEHAQEDDDDDLYYQSSGTRMIYVSSRMISSIIRISVSLARMR 787
Query: 198 LEPFAIDSHVTEALRL 213
L + +A+++
Sbjct: 788 LSTVVTPADALQAVQI 803
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 31.3 bits (71), Expect = 0.15
Identities = 16/89 (17%), Positives = 25/89 (28%), Gaps = 17/89 (19%)
Query: 4 GAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSRCSVLAAANSV 63
A GV+ IDE D + + A+ +E V+ A N
Sbjct: 78 ELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLN-------DLRIDRENVRVIGATNRP 130
Query: 64 FGRWDDTKGEQNIDFMPTILSRFDMIFII 92
D + R D+ +I
Sbjct: 131 L----------LGDLDRALYDRLDIRIVI 149
>gnl|CDD|129245 TIGR00139, h_aconitase, homoaconitase. Homoaconitase is known only
as a fungal enzyme from two species, where it is part of
an unusual lysine biosynthesis pathway. Because This
model is based on just two sequences from a narrow
taxonomic range, it may not recognize distant orthologs,
should any exist. Homoaconitase, aconitase, and
3-isopropylmalate dehydratase have similar overall
structures, but 3-isopropylmalate dehydratase is split
into large (leuC) and small (leuD) chains in eubacteria.
Several pairs of archaeal proteins resemble leuC and
leuD over their lengths but are even closer to the
respective domains of homoaconitase, and their identity
is uncertain [Amino acid biosynthesis, Aspartate
family].
Length = 712
Score = 30.8 bits (69), Expect = 0.59
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 34 MEQQTISIAKAGITTTLNSRCSVLAAANSVF 64
+E Q I I KA + + NSR S +AAA VF
Sbjct: 315 LEAQDIKIDKAYLVSCTNSRASDIAAAADVF 345
>gnl|CDD|153132 cd01582, Homoaconitase, Homoaconitase and other uncharacterized
proteins of the Aconitase family. Homoaconitase
catalytic domain. Homoaconitase and other
uncharacterized proteins of the Aconitase family.
Homoaconitase is part of an unusual lysine biosynthesis
pathway found only in filamentous fungi, in which lysine
is synthesized via the alpha-aminoadipate pathway. In
this pathway, homoaconitase catalyzes the conversion of
cis-homoaconitic acid into homoisocitric acid. The
reaction mechanism is believed to be similar to that of
other aconitases.
Length = 363
Score = 29.9 bits (67), Expect = 1.1
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 34 MEQQTISIAKAGITTTLNSRCSVLAAANSVF 64
+E Q I I KA + + NSR S +AAA V
Sbjct: 228 LEAQNIKINKAYLVSCTNSRASDIAAAADVV 258
>gnl|CDD|216389 pfam01251, Ribosomal_S7e, Ribosomal protein S7e.
Length = 189
Score = 29.2 bits (66), Expect = 1.4
Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 10/70 (14%)
Query: 98 ETRDITLAKHIMKVHMTAGQEIDVASDGE-----LPLPVLKKYINYCRMRCGPRLTHEAG 152
E+ L + + +T+ +EI+V + +P+P LK Y + RL E
Sbjct: 26 ESNSPDLKAELRDLQITSAKEIEVGGGKKAVVIFVPVPQLKAY-----RKIQQRLVRELE 80
Query: 153 EKLKNRYVLM 162
+K ++V+
Sbjct: 81 KKFSGKHVVF 90
>gnl|CDD|173869 cd08504, PBP2_OppA, The substrate-binding component of an ABC-type
oligopetide import system contains the type 2
periplasmic binding fold. This family represents the
periplasmic substrate-binding component of an
ATP-binding cassette (ABC)-type oligopeptide transport
system comprised of 5 subunits. The transport system
OppABCDEF contains two homologous integral membrane
proteins OppB and OppF that form the translocation pore;
two homologous nucleotide-binding domains OppD and OppF
that drive the transport process through binding and
hydrolysis of ATP; and the substrate-binding protein or
receptor OppA that determines the substrate specificity
of the transport system. The dipeptide (DppA) and
oligopeptide (OppA) binding proteins differ in several
ways. The DppA binds dipeptides and some tripeptides and
is involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 498
Score = 29.1 bits (66), Expect = 1.8
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 161 LMRNGSKEDGEKKLNIPITVRQLEAIVRIAESMAKM 196
L+ E G+ L + + E +IAE++ +M
Sbjct: 331 LLAEAGYELGKNPLKLTLLYNTSENHKKIAEAIQQM 366
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 28.7 bits (65), Expect = 2.1
Identities = 19/58 (32%), Positives = 31/58 (53%)
Query: 4 GAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSRCSVLAAAN 61
G + LA GV+ +DE + + A+ E +E I I++AG T +R ++AA N
Sbjct: 277 GEISLAHNGVLFLDELPEFKRSILEALREPLENGKIIISRAGSKVTYPARFQLVAAMN 334
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling inter-
mediates into the (bacterio)chlorophyll branch in
response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 27.9 bits (63), Expect = 3.4
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 10/63 (15%)
Query: 4 GAMVLADGGVVCIDE---FDKMREDDRV--AIHEAMEQQTISIAKAGITTTLNSRCSVLA 58
G + LA GV+ +DE F + RV ++ + +E I+I++A T +R ++A
Sbjct: 100 GEISLAHNGVLFLDELPEFSR-----RVLESLRQPLEDGEITISRARAKVTFPARFQLVA 154
Query: 59 AAN 61
A N
Sbjct: 155 AMN 157
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 27.8 bits (62), Expect = 4.6
Identities = 7/27 (25%), Positives = 16/27 (59%)
Query: 9 ADGGVVCIDEFDKMREDDRVAIHEAME 35
A ++ +DE ++ + + A+ EA+E
Sbjct: 111 AVRVILLLDEINRAPPEVQNALLEALE 137
>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
Length = 675
Score = 27.6 bits (62), Expect = 5.6
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 10/47 (21%)
Query: 83 LSRFDMIFIIKD--EHDETRDITLA---KHIMKVH----MTAGQEID 120
L + + II + EHD+ DI +A KHI K+ MTA E D
Sbjct: 289 LFDYGTV-IIDEVHEHDQIGDIIIAVARKHIDKIRSLFLMTATLEDD 334
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 27.5 bits (61), Expect = 6.0
Identities = 18/58 (31%), Positives = 31/58 (53%)
Query: 4 GAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSRCSVLAAAN 61
G + LA GV+ +DE + + A+ E +E +ISI++A +R ++AA N
Sbjct: 289 GEISLAHNGVLFLDELPEFKRSVLDALREPIEDGSISISRASAKIFYPARFQLVAAMN 346
>gnl|CDD|227283 COG4947, COG4947, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 227
Score = 27.1 bits (60), Expect = 6.0
Identities = 30/106 (28%), Positives = 39/106 (36%), Gaps = 36/106 (33%)
Query: 26 DRVAIHEAMEQQTISIAKAGITTTLNSRCSV--LAAANSVF-------------GRWD-- 68
DR H A E+ I A G +T+ S CS+ AAN VF G +D
Sbjct: 82 DRAERHRAYERYVIEEALPG--STIVSGCSMGAYHAANFVFRHPHLFTKVIALSGVYDAR 139
Query: 69 ---------DTKGEQNIDFMPTI--------LSRFDMIFIIKDEHD 97
D D++P + L R DM+F I DE
Sbjct: 140 DFFGGYYDDDVYYNSPSDYLPGLADPFRLERLRRIDMVFCIGDEDP 185
>gnl|CDD|216820 pfam01974, tRNA_int_endo, tRNA intron endonuclease, catalytic
C-terminal domain. Members of this family cleave pre
tRNA at the 5' and 3' splice sites to release the intron
EC:3.1.27.9.
Length = 85
Score = 25.7 bits (57), Expect = 7.0
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 175 NIPITVRQLEAIVRIAESMAK 195
+ I+ L VR+A S+ K
Sbjct: 50 DEEISWLDLLRAVRLAHSVKK 70
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
0.321 0.136 0.388
Gapped
Lambda K H
0.267 0.0754 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,004,132
Number of extensions: 1027368
Number of successful extensions: 937
Number of sequences better than 10.0: 1
Number of HSP's gapped: 927
Number of HSP's successfully gapped: 25
Length of query: 214
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 121
Effective length of database: 6,812,680
Effective search space: 824334280
Effective search space used: 824334280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.7 bits)