RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12190
(105 letters)
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 80.9 bits (199), Expect = 3e-19
Identities = 35/101 (34%), Positives = 64/101 (63%)
Query: 1 YIRIDGSVGSEERKSVVDQFQYEDKFRVAVLSITAANSGITLTAANLVVFAELFWNPGIL 60
Y+R+DGS ++ R+ ++D+F +++ +V +LS+ A G+ LT A+ V+ + +WNP +
Sbjct: 738 YVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVE 797
Query: 61 TQAEDRAHRIGQQDSVLIQYLVAKQTADDYLWPLVMTKLDV 101
QA DRAHRIGQ+ V + L+ + T ++ + L K ++
Sbjct: 798 LQAIDRAHRIGQKRPVKVYRLITRGTIEEKILELQEKKQEL 838
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 72.1 bits (177), Expect = 3e-16
Identities = 35/78 (44%), Positives = 48/78 (61%), Gaps = 3/78 (3%)
Query: 1 YIRIDGSVGSEERKSVVDQFQYE--DKFRVAVLSITAANSGITLTAANLVVFAELFWNPG 58
Y RIDG+ G E+R + +D F +KF V +LS A GI L A++V+ + WNP
Sbjct: 514 YCRIDGNTGGEDRDASIDAFNKPGSEKF-VFLLSTRAGGLGINLATADIVILYDSDWNPQ 572
Query: 59 ILTQAEDRAHRIGQQDSV 76
+ QA+DRAHRIGQ+ V
Sbjct: 573 VDLQAQDRAHRIGQKKEV 590
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety
of helicases and helicase related proteins. It may be
that this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 66.4 bits (163), Expect = 5e-16
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 1 YIRIDGSVGSEERKSVVDQFQYEDKFRVAVLSITAANSGITLTAANLVVFAELFWNPGIL 60
R+ G + EER+ +++ F+ K +V +++ A GI L NLV+ +L WNP
Sbjct: 10 VARLHGGLSQEEREEILEDFR-NGKSKV-LVATDVAGRGIDLPDVNLVINYDLPWNPASY 67
Query: 61 TQAEDRAHRIG 71
Q RA R G
Sbjct: 68 IQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 62.6 bits (153), Expect = 2e-14
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 1 YIRIDGSVGSEERKSVVDQFQYEDKFRVAVLSITAANSGITLTAANLVVFAELFWNPGIL 60
R+ G + EER+ ++D+F K +V +++ A G+ L +LV+ +L W+P
Sbjct: 14 VARLHGGLSQEEREEILDKFN-NGKIKV-LVATDVAERGLDLPGVDLVIIYDLPWSPASY 71
Query: 61 TQAEDRAHRIG 71
Q RA R G
Sbjct: 72 IQRIGRAGRAG 82
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 51.9 bits (125), Expect = 8e-10
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 1 YIRIDGSVGSEERKSVVDQFQYEDKFRVAVLSITAANSGITLTAANLVVFAELFWNPGIL 60
+ DGS EER+ V+ F+ E + V +++ GI L ++V+ +L W+P
Sbjct: 57 ALHGDGSQ--EEREEVLKDFR-EGEIVV-LVATDVIARGIDLPNVSVVINYDLPWSPSSY 112
Query: 61 TQAEDRAHRIGQQ 73
Q RA R GQ+
Sbjct: 113 LQRIGRAGRAGQK 125
>gnl|CDD|226187 COG3661, AguA, Alpha-glucuronidase [Carbohydrate transport and
metabolism].
Length = 684
Score = 30.6 bits (69), Expect = 0.13
Identities = 23/92 (25%), Positives = 39/92 (42%), Gaps = 11/92 (11%)
Query: 14 KSVVD--QFQYEDKFRVAVLSITAAN--SGITLTAANLVVFAELFWNPGILTQ--AEDRA 67
K +VD + V ++ + +G L ANL VF L WNP T+ A++
Sbjct: 430 KKIVDGSLDDRKLTGMAGVSNVGSDRNWTGHQLAQANLYVFGRLAWNPEAGTEAIAQEWT 489
Query: 68 HRIGQQDSVLIQYLV-----AKQTADDYLWPL 94
D ++ +V +++ +DY PL
Sbjct: 490 RMTFGDDERVVTPVVSMLMGSREAYEDYTTPL 521
>gnl|CDD|135998 PRK06673, PRK06673, DNA polymerase III subunit beta; Validated.
Length = 376
Score = 28.5 bits (63), Expect = 0.58
Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 25 KFRVAVLS---ITAANSGITLTAANLVVFAELF 54
K + +LS ITA SGITL A+N +F E F
Sbjct: 24 KAIIPILSGIKITADQSGITLIASNSNIFIEKF 56
>gnl|CDD|223182 COG0104, PurA, Adenylosuccinate synthase [Nucleotide transport and
metabolism].
Length = 430
Score = 28.0 bits (63), Expect = 0.91
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 66 RAHRIGQQDSVLIQYLVAKQTADDYLWPLVMTKLDV 101
R R G D+VL++Y V L +TKLDV
Sbjct: 304 RPRRCGWFDAVLLRYAVRINGITG----LAITKLDV 335
>gnl|CDD|239382 cd03108, AdSS, Adenylosuccinate synthetase (AdSS) catalyzes the
first step in the de novo biosynthesis of AMP. IMP and
L-aspartate are conjugated in a two-step reaction
accompanied by the hydrolysis of GTP to GDP in the
presence of Mg2+. In the first step, the r-phosphate
group of GTP is transferred to the 6-oxygen atom of IMP.
An aspartate then displaces this 6-phosphate group to
form the product adenylosuccinate. Because of its
critical role in purine biosynthesis, AdSS is a target
of antibiotics, herbicides and antitumor drugs.
Length = 363
Score = 27.1 bits (61), Expect = 1.8
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 66 RAHRIGQQDSVLIQYLVAKQTADDYLWPLVMTKLDV 101
R R G D V ++Y V + L +TKLDV
Sbjct: 250 RPRRCGWLDLVALKYAVRINGVTE----LALTKLDV 281
>gnl|CDD|233046 TIGR00603, rad25, DNA repair helicase rad25. All proteins in this
family for which functions are known are DNA-DNA
helicases used for the initiation of nucleotide excision
repair and transacription as part of the TFIIH
complex.This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 732
Score = 26.7 bits (59), Expect = 2.5
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 4 IDGSVGSEERKSVVDQFQYEDKFRVAVLSITAANSGITLTAANLVV 49
I G +ER ++ FQ+ K LS S I L AN+++
Sbjct: 521 IYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTS-IDLPEANVLI 565
>gnl|CDD|184326 PRK13788, PRK13788, adenylosuccinate synthetase; Provisional.
Length = 404
Score = 26.7 bits (59), Expect = 2.5
Identities = 17/38 (44%), Positives = 21/38 (55%), Gaps = 4/38 (10%)
Query: 66 RAHRIGQQDSVLIQYLVAKQTADDYLWPLVMTKLDVPS 103
RA R+G D VL++Y D LV+TKLDV S
Sbjct: 296 RARRVGWLDLVLLKYACEVNGFDG----LVLTKLDVLS 329
>gnl|CDD|216073 pfam00709, Adenylsucc_synt, Adenylosuccinate synthetase.
Length = 420
Score = 26.3 bits (59), Expect = 3.3
Identities = 12/36 (33%), Positives = 15/36 (41%), Gaps = 4/36 (11%)
Query: 66 RAHRIGQQDSVLIQYLVAKQTADDYLWPLVMTKLDV 101
R R G D V ++Y L +TKLDV
Sbjct: 301 RPRRCGWLDLVALRYAARINGVTS----LALTKLDV 332
>gnl|CDD|197875 smart00788, Adenylsucc_synt, Adenylosuccinate synthetase.
Adenylosuccinate synthetase plays an important role in
purine biosynthesis, by catalyzing the GTP-dependent
conversion of IMP and aspartic acid to AMP.
Adenylosuccinate synthetase has been characterized from
various sources ranging from Escherichia coli (gene
purA) to vertebrate tissues. In vertebrates, two
isozymes are present - one involved in purine
biosynthesis and the other in the purine nucleotide
cycle. The crystal structure of adenylosuccinate
synthetase from E. coli reveals that the dominant
structural element of each monomer of the homodimer is a
central beta-sheet of 10 strands. The first nine strands
of the sheet are mutually parallel with right-handed
crossover connections between the strands. The 10th
strand is antiparallel with respect to the first nine
strands. In addition, the enzyme has two antiparallel
beta-sheets, comprised of two strands and three strands
each, 11 alpha-helices and two short 3/10-helices.
Further, it has been suggested that the similarities in
the GTP-binding domains of the synthetase and the p21ras
protein are an example of convergent evolution of two
distinct families of GTP-binding proteins. Structures of
adenylosuccinate synthetase from Triticum aestivum and
Arabidopsis thaliana when compared with the known
structures from E. coli reveals that the overall fold is
very similar to that of the E. coli protein.
Length = 417
Score = 26.3 bits (59), Expect = 3.8
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 66 RAHRIGQQDSVLIQYLVAKQTADDYLWPLVMTKLDV 101
R R G D+VL++Y V L +TKLDV
Sbjct: 297 RPRRCGWFDAVLLRYAVRINGITG----LALTKLDV 328
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 26.1 bits (57), Expect = 4.1
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 10/70 (14%)
Query: 4 IDGSVGSEERKSVVDQFQYEDKFRVAVLSIT-AANSGITLTAANLVVFAELFWNPGILTQ 62
+ G V ++R+S++++FQ K ++ +L T A G+ + V +N +
Sbjct: 287 LSGDVPQKKRESLLNRFQ---KGQLEILVATDVAARGLHIDGVKYV------YNYDLPFD 337
Query: 63 AEDRAHRIGQ 72
AED HRIG+
Sbjct: 338 AEDYVHRIGR 347
>gnl|CDD|212054 cd11485, SLC-NCS1sbd_YbbW-like, uncharacterized
nucleobase-cation-symport-1 (NCS1) transporter
subfamily, YbbW-like; solute-binding domain. NCS1s are
essential components of salvage pathways for nucleobases
and related metabolites; their known substrates include
allantoin, uracil, thiamine, and nicotinamide riboside.
This subfamily includes the putative allantoin
transporter Escherichia coli YbbW (also known as GlxB2).
NCS1s belong to a superfamily which also contains the
solute carrier 5 family sodium/glucose transporters
(SLC5s), and solute carrier 6 family neurotransmitter
transporters (SLC6s).
Length = 459
Score = 25.6 bits (57), Expect = 5.7
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 39 GITLTAANLVVFAELFWNPGIL 60
G+ +T+A +V+F E W+P L
Sbjct: 266 GVAVTSATVVIFGEAIWDPVDL 287
>gnl|CDD|238988 cd02030, NDUO42, NADH:Ubiquinone oxioreductase, 42 kDa (NDUO42) is
a family of proteins that are highly similar to
deoxyribonucleoside kinases (dNK). Members of this
family have been identified as one of the subunits of
NADH:Ubiquinone oxioreductase (complex I), a
multi-protein complex located in the inner mitochondrial
membrane. The main function of the complex is to
transport electrons from NADH to ubiquinone, which is
accompanied by the translocation of protons from the
mitochondrial matrix to the inter membrane space.
Length = 219
Score = 25.4 bits (56), Expect = 7.0
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 80 YLVAKQTADDYLWPLVMTKLDVPSP 104
V T + L P ++ LDVP P
Sbjct: 130 NEVKGNTIPELLPPHLVIYLDVPVP 154
>gnl|CDD|178693 PLN03148, PLN03148, Blue copper-like protein; Provisional.
Length = 167
Score = 25.2 bits (55), Expect = 7.8
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 27 RVAVLSITAANSGITLTAANLVVFAELFWNPGI 59
+ + A S TA + +V A WNPGI
Sbjct: 3 HLLLFCFFALFSASATTATDHIVGANKGWNPGI 35
>gnl|CDD|235956 PRK07192, flgL, flagellar hook-associated protein FlgL; Reviewed.
Length = 305
Score = 25.0 bits (55), Expect = 9.7
Identities = 9/38 (23%), Positives = 15/38 (39%), Gaps = 5/38 (13%)
Query: 59 ILTQAED-----RAHRIGQQDSVLIQYLVAKQTADDYL 91
ILT ++D R + ++ S QY + L
Sbjct: 36 ILTPSDDPIASARLLELSREQSNNSQYADNIANLSNSL 73
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
0.320 0.135 0.388
Gapped
Lambda K H
0.267 0.0847 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,082,352
Number of extensions: 416536
Number of successful extensions: 342
Number of sequences better than 10.0: 1
Number of HSP's gapped: 339
Number of HSP's successfully gapped: 27
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
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 (21.8 bits)
S2: 53 (24.0 bits)