RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13403
(195 letters)
>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 80.3 bits (199), Expect = 3e-18
Identities = 32/89 (35%), Positives = 58/89 (65%), Gaps = 9/89 (10%)
Query: 4 AHAKMHLREHVSEDDVNMAIRMMLESFVDTQKYSVMKQMKQVTGSLPITIRHIESMIRMA 63
A+A+ +++ +S++ A ++ +V+ +K S GS+PIT+R +ES+IR++
Sbjct: 248 AYARENIKPKLSDE----AREKLVNWYVELRKESEGS-----RGSIPITVRQLESLIRLS 298
Query: 64 QAHAKMHLREHVSEDDVNMAIRMMLESFV 92
+AHA++ L E V+E+DV AIR++LES
Sbjct: 299 EAHARLRLSEEVTEEDVEEAIRLILESLK 327
Score = 50.6 bits (122), Expect = 8e-08
Identities = 15/31 (48%), Positives = 24/31 (77%)
Query: 1 MAQAHAKMHLREHVSEDDVNMAIRMMLESFV 31
+++AHA++ L E V+E+DV AIR++LES
Sbjct: 297 LSEAHARLRLSEEVTEEDVEEAIRLILESLK 327
>gnl|CDD|214631 smart00350, MCM, minichromosome maintenance proteins.
Length = 509
Score = 81.2 bits (201), Expect = 3e-18
Identities = 25/63 (39%), Positives = 41/63 (65%), Gaps = 3/63 (4%)
Query: 33 TQKYSVMKQM---KQVTGSLPITIRHIESMIRMAQAHAKMHLREHVSEDDVNMAIRMMLE 89
+ Y +++ + S+PIT+R +ES+IR+++AHAKM L + V E DV AIR++ E
Sbjct: 447 VKAYVDLRKEDSQTESRSSIPITVRQLESIIRLSEAHAKMRLSDVVEEADVEEAIRLLRE 506
Query: 90 SFV 92
S +
Sbjct: 507 SII 509
Score = 50.3 bits (121), Expect = 1e-07
Identities = 15/31 (48%), Positives = 22/31 (70%)
Query: 1 MAQAHAKMHLREHVSEDDVNMAIRMMLESFV 31
+++AHAKM L + V E DV AIR++ ES +
Sbjct: 479 LSEAHAKMRLSDVVEEADVEEAIRLLRESII 509
>gnl|CDD|224162 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 67.4 bits (165), Expect = 2e-13
Identities = 31/104 (29%), Positives = 54/104 (51%), Gaps = 7/104 (6%)
Query: 21 MAIRMMLESFVDTQKYSVMKQMKQVTGSLPITIRHIESMIRMAQAHAKMHLREHVSEDDV 80
A + + +V+ +K + + ++PIT R +ES+IR+A+AHAKM L + V E+DV
Sbjct: 529 EAREELEDYYVEMRK---KSALVEEKRTIPITARQLESIIRLAEAHAKMRLSDVVEEEDV 585
Query: 81 NMAIRMMLES----FVDTQKYSVMKQMKQTFQKYLSFKKDTTEL 120
+ AIR++ S VD +K + + + + K L
Sbjct: 586 DEAIRLVDFSLKTVAVDPEKGKIDIDIIEPGKSKSKRDKIEKVL 629
Score = 43.1 bits (102), Expect = 4e-05
Identities = 22/105 (20%), Positives = 47/105 (44%), Gaps = 18/105 (17%)
Query: 1 MAQAHAKMHLREHVSEDDVNMAIRMMLESFVDTQKYSVMKQMKQVTGSLPITIRH----- 55
+A+AHAKM L + V E+DV+ AIR++ S +V + ++ + +
Sbjct: 567 LAEAHAKMRLSDVVEEEDVDEAIRLVDFSLKT---VAVDPEKGKIDIDIIEPGKSKSKRD 623
Query: 56 --------IESMIRMAQAHAKMHLREH--VSEDDVNMAIRMMLES 90
I+ ++ ++ + + E +SE +V A+ + +
Sbjct: 624 KIEKVLDIIKELVERSEDPVEEIIEEAEGISEKEVEEALEKLKKK 668
>gnl|CDD|173403 PTZ00111, PTZ00111, DNA replication licensing factor MCM4;
Provisional.
Length = 915
Score = 35.0 bits (80), Expect = 0.020
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 44 QVTGSLPITI--RHIESMIRMAQAHAKMHLREHVSEDDVNMAIRMM----LESFVD 93
Q +G+ I + R I S+IR++ + A+M L V+ D A++++ +S VD
Sbjct: 759 QSSGTRMIYVSSRMISSIIRISVSLARMRLSTVVTPADALQAVQIVKSSTFQSLVD 814
>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D. This
model represents one of two ATPase subunits of the
trimeric magnesium chelatase responsible for insertion
of magnesium ion into protoporphyrin IX. This is an
essential step in the biosynthesis of both chlorophyll
and bacteriochlorophyll. This subunit is found in green
plants, photosynthetic algae, cyanobacteria and other
photosynthetic bacteria. Unlike subunit I (TIGR02030),
this subunit is not found in archaea [Biosynthesis of
cofactors, prosthetic groups, and carriers, Chlorophyll
and bacteriochlorphyll].
Length = 589
Score = 33.6 bits (77), Expect = 0.060
Identities = 12/29 (41%), Positives = 22/29 (75%)
Query: 60 IRMAQAHAKMHLREHVSEDDVNMAIRMML 88
+R A+AHA +H R V+E+D+ +A+ ++L
Sbjct: 231 VRAAKAHAALHGRTEVTEEDLKLAVELVL 259
Score = 30.5 bits (69), Expect = 0.57
Identities = 11/26 (42%), Positives = 20/26 (76%)
Query: 2 AQAHAKMHLREHVSEDDVNMAIRMML 27
A+AHA +H R V+E+D+ +A+ ++L
Sbjct: 234 AKAHAALHGRTEVTEEDLKLAVELVL 259
>gnl|CDD|213866 TIGR03818, MotA1, flagellar motor stator protein MotA. The MotA
protein, along with its partner MotB, comprise the
stator complex of the bacterial flagellar motor. MotAB
span the cytoplasmic membrane and undergo conformational
changes powered by the translocation of protons. These
conformational changes in turn are communicated to the
rotor assembly, producing torque. This model represents
one family of MotA proteins which are often not
identified by the "transporter, MotA/TolQ/ExbB proton
channel family" model, pfam01618.
Length = 282
Score = 30.6 bits (70), Expect = 0.43
Identities = 27/93 (29%), Positives = 38/93 (40%), Gaps = 23/93 (24%)
Query: 99 VMKQMKQTFQKYLSFKK----DTTELLYYILRQ------MTLDQLIHIPFVSQTFQKYLS 148
+K + + F K + K D LLY +LR+ M ++ I P S F KY
Sbjct: 57 TLKGLPKVF-KGSKYGKADYLDLLSLLYELLRKARREGLMAIESHIENPEESSIFSKYPK 115
Query: 149 FKKDTTELLYYI---LRQMT--------LDQLM 170
KD L+ +I LR M L+ LM
Sbjct: 116 ILKD-HHLVEFICDYLRLMVMGNMNPHELEALM 147
>gnl|CDD|171532 PRK12482, PRK12482, flagellar motor protein MotA; Provisional.
Length = 287
Score = 29.7 bits (67), Expect = 0.84
Identities = 22/62 (35%), Positives = 28/62 (45%), Gaps = 13/62 (20%)
Query: 98 SVMKQMKQTFQKYLSFKKDTTE------LLYYILRQMT-------LDQLIHIPFVSQTFQ 144
SV+K+M + + K+ E LL Y L +M LDQ I IP S FQ
Sbjct: 52 SVLKEMWHQIKGVIRRKEYGVEFQRQLLLLLYELLEMVQEGGLKRLDQHIEIPEESSLFQ 111
Query: 145 KY 146
KY
Sbjct: 112 KY 113
>gnl|CDD|173963 cd07979, TAF9, TATA Binding Protein (TBP) Associated Factor 9
(TAF9) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 9 (TAF9) is one of several TAFs that bind TBP
and are involved in forming the TFIID complex. TFIID is
one of seven General Transcription Factors (GTF)
(TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are
involved in accurate initiation of transcription by RNA
polymerase II in eukaryotes. TFIID plays an important
role in the recognition of promoter DNA and assembly of
the pre-initiation complex. The TFIID complex is
composed of the TBP and at least 13 TAFs. TAFs from
various species were originally named by their
predicted molecular weight or their electrophoretic
mobility in polyacrylamide gels. A new, unified
nomenclature for the pol II TAFs has been suggested to
show the relationship between TAFs orthologs and
paralogs. Human TAF9 has a paralogue gene (TAF9L) which
has a redundant function. Several hypotheses are
proposed for TAF function such as serving as
activator-binding sites, in core-promoter recognition
or a role in essential catalytic activity. It has been
shown that TAF9 interacts directly with different
transcription factors such as p53, herpes simplex virus
activator vp16 and the basal transcription factor
TFIIB. Each TAF, with the help of a specific activator,
is required only for expression of subset of genes and
are not universally involved for transcription as are
GTFs. In yeast and human cells, TAFs have been found as
components of other complexes besides TFIID. TAF9 is a
component of TFIID in multiple organisms as well as
different TBP-free TAF complexes containing the
GCN5-type histone acetyltransferase. Several TAFs
interact via histone-fold (HFD) motifs; HFD is the
interaction motif involved in heterodimerization of the
core histones and their assembly into nucleosome
octamers. The minimal HFD contains three alpha-helices
linked by two loops and is found in core histones, TAFS
and many other transcription factors. TFIID has a
histone octamer-like substructure. TFIID has a histone
octamer-like substructure. TAF9 is a shared subunit of
both, histone acetyltransferase complex (SAGA) and
TFIID complexes. TAF9 domain interacts with TAF6 to
form a novel histone-like heterodimer that is
structurally related to the histone H3 and H4 oligomer.
Length = 117
Score = 28.7 bits (65), Expect = 0.93
Identities = 7/33 (21%), Positives = 19/33 (57%)
Query: 54 RHIESMIRMAQAHAKMHLREHVSEDDVNMAIRM 86
R+ ++ A+ +++ + ++ DDV +AI+
Sbjct: 33 RYTTDVLDDAKVYSEHAGKANIDADDVKLAIQS 65
>gnl|CDD|233870 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit.
Cobaltochelatase is responsible for the insertion of
cobalt into the corrin ring of coenzyme B12 during its
biosynthesis. Two versions have been well described.
CbiK/CbiX is a monomeric, anaerobic version which acts
early in the biosynthesis (pfam06180). CobNST is a
trimeric, ATP-dependent, aerobic version which acts late
in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A
number of genomes (actinobacteria, cyanobacteria,
betaproteobacteria and pseudomonads) which apparently
biosynthesize B12, encode a cobN gene but are
demonstrably lacking cobS and cobT. These genomes do,
however contain a homolog (modelled here) of the
magnesium chelatase subunits BchI/BchD family. Aside
from the cyanobacteria (which have a separate magnesium
chelatase trimer), these species do not make chlorins,
so do not have any use for a magnesium chelatase.
Furthermore, in nearly all cases the members of this
family are proximal to either CobN itself or other genes
involved in cobalt transport or B12 biosynthesis.
Length = 633
Score = 29.3 bits (66), Expect = 1.3
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 59 MIRMAQAHAKMHLREHVSEDDVNMAIRMML 88
M R A+A A + R V+ +DV A ++L
Sbjct: 276 MARAARALAALDGRRRVTAEDVREAAELVL 305
>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional.
Length = 584
Score = 29.2 bits (66), Expect = 1.7
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 60 IRMAQAHAKMHLREHVSEDDVNMAIRMML 88
+R A+A A + R V E+D+ +A R++L
Sbjct: 223 LRAARAAAALAGRTAVEEEDLALAARLVL 251
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 28.5 bits (64), Expect = 1.8
Identities = 25/81 (30%), Positives = 33/81 (40%), Gaps = 15/81 (18%)
Query: 93 DTQKYSVMKQMKQTFQKYLSFKKDTTELLYY----ILRQMTLDQLIH------IPFV--S 140
T K +V Q KY+ K + L+ + LRQ L+ + I FV S
Sbjct: 26 GTVKKTVTSQEPSAAYKYMLHKGFSFTLIDFPGHVKLRQKLLETIKDSSSLRGIVFVVDS 85
Query: 141 QTFQKYLSFKKDTTELLYYIL 161
F K + DT E LY IL
Sbjct: 86 TAFPKEV---TDTAEFLYEIL 103
>gnl|CDD|236101 PRK07803, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 626
Score = 27.7 bits (62), Expect = 4.6
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 11 REHVSEDDVNMAIRMMLESFVDTQK----YSVMKQMKQVTGSLPITIRHIESMIR 61
R VSE+ V+ A R L F Y++ +++Q L IR + + +
Sbjct: 453 RPAVSEEAVDAAAREALAPFERPAGAENPYTLHAELQQTMNDLVGIIRKEDEIEQ 507
>gnl|CDD|215530 PLN02980, PLN02980, 2-oxoglutarate decarboxylase/ hydro-lyase/
magnesium ion binding / thiamin pyrophosphate binding.
Length = 1655
Score = 27.9 bits (62), Expect = 4.7
Identities = 10/46 (21%), Positives = 21/46 (45%)
Query: 2 AQAHAKMHLREHVSEDDVNMAIRMMLESFVDTQKYSVMKQMKQVTG 47
AQ H KM + E + ++ + S+++ Q ++M + T
Sbjct: 1236 AQQHGKMAVISAAYESGLGLSAYIQFASYLEMQNAKASREMNKGTC 1281
>gnl|CDD|165411 PHA03139, PHA03139, helicase-primase primase subunit; Provisional.
Length = 860
Score = 27.6 bits (61), Expect = 5.8
Identities = 11/73 (15%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 97 YSVMKQMKQTFQKYLSFKKDTTELLYYILRQMTLDQLIHIPFVSQTFQKYLSFKKDTTEL 156
+ V + + + + ++ + D LL++ ++ +++LI+ ++ LSF +
Sbjct: 656 FIVPEGYRNSCKTFIQMQMDLNNLLHHGTKKAPIEELIYSITDKGCPKENLSFMDLKSRQ 715
Query: 157 LYYILRQMTLDQL 169
L+ + + L
Sbjct: 716 LWN-KVNIATETL 727
>gnl|CDD|181580 PRK08912, PRK08912, hypothetical protein; Provisional.
Length = 387
Score = 27.2 bits (61), Expect = 6.2
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 39 MKQMKQVTGSLPITIRHIESMIRMAQAHAKMHL 71
MK V LP TI E M ++A+ H ++L
Sbjct: 1 MKMGNPVFADLPTTI--FEVMSQLAREHGAINL 31
>gnl|CDD|227634 COG5324, COG5324, Uncharacterized conserved protein [Function
unknown].
Length = 758
Score = 27.3 bits (60), Expect = 7.1
Identities = 21/91 (23%), Positives = 35/91 (38%), Gaps = 7/91 (7%)
Query: 111 LSFKKDTTELLYYILRQMTLD-QLIHIPFVSQTFQKY-----LSFKKDTTELLYYILRQM 164
L + K+ L + + LD I + FV + +K + KK+ L L
Sbjct: 193 LKYDKEHLGLYLHGENKNDLDFHTIDLEFVEKLAKKVGFSSVILTKKEELRRLKNFLYNF 252
Query: 165 TLDQLMYIRGVHGVVI-DTVEIHEKDFKEKY 194
+ + M + + G VI +E F KY
Sbjct: 253 SHEGTMSLEEIEGFVIRCHLEQSGLMFFFKY 283
>gnl|CDD|222290 pfam13654, AAA_32, AAA domain. This family includes a wide variety
of AAA domains including some that have lost essential
nucleotide binding residues in the P-loop.
Length = 509
Score = 27.0 bits (61), Expect = 7.4
Identities = 9/33 (27%), Positives = 14/33 (42%)
Query: 53 IRHIESMIRMAQAHAKMHLREHVSEDDVNMAIR 85
I ++R A A++ E V + V AI
Sbjct: 472 FGDIADLLREADYWARLAGAELVDAEHVERAIE 504
>gnl|CDD|236989 PRK11809, putA, trifunctional transcriptional regulator/proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1318
Score = 26.9 bits (60), Expect = 8.2
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 19 VNMAIRMMLESFV 31
V+MA+R+M E FV
Sbjct: 248 VDMAMRLMGEQFV 260
Score = 26.9 bits (60), Expect = 8.2
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 80 VNMAIRMMLESFV 92
V+MA+R+M E FV
Sbjct: 248 VDMAMRLMGEQFV 260
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative. This
family, found in archaea and eukaryotes, includes the
only archaeal proteins markedly similar to bacterial
TruB, the tRNA pseudouridine 55 synthase. However, among
two related yeast proteins, the archaeal set matches
yeast YLR175w far better than YNL292w. The first, termed
centromere/microtubule binding protein 5 (CBF5), is an
apparent rRNA pseudouridine synthase, while the second
is the exclusive tRNA pseudouridine 55 synthase for both
cytosolic and mitochondrial compartments. It is unclear
whether archaeal proteins found by this model modify
tRNA, rRNA, or both [Protein synthesis, tRNA and rRNA
base modification].
Length = 322
Score = 26.7 bits (59), Expect = 8.3
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 9/54 (16%)
Query: 44 QVTGSLPITIRHIESMIRMAQAHAK-----MHLREHVSEDDVNMAIRMMLESFV 92
+VTG LP+ I +++ Q K M L E+D I +L+ F
Sbjct: 72 KVTGVLPVCIERATRLVKSQQEAPKEYVCLMRLHRDAKEED----ILRVLKEFT 121
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
0.324 0.133 0.365
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,778,292
Number of extensions: 899103
Number of successful extensions: 1302
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1298
Number of HSP's successfully gapped: 57
Length of query: 195
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 103
Effective length of database: 6,857,034
Effective search space: 706274502
Effective search space used: 706274502
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.4 bits)