RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8245
(629 letters)
>gnl|CDD|216144 pfam00839, Cys_rich_FGFR, Cysteine rich repeat. This cysteine rich
repeat contains four cysteines. It is found in multiple
copies in a protein that binds to fibroblast growth
factors. The repeat is also found in MG160 and
E-selectin ligand (ESL-1).
Length = 58
Score = 64.0 bits (156), Expect = 4e-13
Identities = 23/56 (41%), Positives = 36/56 (64%)
Query: 66 DCRHQVLRLSELQSDDIKLDRVLYVACANDRYRLCSDVPQGSGQIYKCLMDHTGDK 121
+C+ V RL E +++D +LD VL AC +D + CSD+ +G GQ+ +CL +H D
Sbjct: 2 ECQQAVWRLQEEEAEDYRLDPVLQKACKDDIEKFCSDIEEGEGQVLECLKEHKDDL 57
Score = 52.4 bits (126), Expect = 5e-09
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 193 ECQAEMTSHRKMLLTDYRLSPEIVTRCSEDIVTYCRGLEAG-GKTIHCLMEHARRNR 248
ECQ + ++ DYRL P + C +DI +C +E G G+ + CL EH +
Sbjct: 2 ECQQAVWRLQEEEAEDYRLDPVLQKACKDDIEKFCSDIEEGEGQVLECLKEHKDDLK 58
Score = 47.8 bits (114), Expect = 2e-07
Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 2/58 (3%)
Query: 448 PDCAALVESLIKTADAGEDWRVDPVLKEACQPVVDIACRGIRGGDARVMSCLMDNLDN 505
P+C V L + ED+R+DPVL++AC+ ++ C I G+ +V+ CL ++ D+
Sbjct: 1 PECQQAVWRL--QEEEAEDYRLDPVLQKACKDDIEKFCSDIEEGEGQVLECLKEHKDD 56
Score = 47.0 bits (112), Expect = 4e-07
Identities = 21/58 (36%), Positives = 36/58 (62%), Gaps = 2/58 (3%)
Query: 255 PPCLRAVESLIKTADAGEDWRVDPVLKEACQPVVDIACRGIRGGDARVMSCLMDNLDN 312
P C +AV L + ED+R+DPVL++AC+ ++ C I G+ +V+ CL ++ D+
Sbjct: 1 PECQQAVWRL--QEEEAEDYRLDPVLQKACKDDIEKFCSDIEEGEGQVLECLKEHKDD 56
Score = 44.7 bits (106), Expect = 2e-06
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 125 DKCREQLLRRQMLIASDYQVSKRLARACKEDIRTHKCRRLVSDDREIRLAQILVCLENAV 184
+C++ + R Q A DY++ L +ACK+DI C D E Q+L CL+
Sbjct: 1 PECQQAVWRLQEEEAEDYRLDPVLQKACKDDIEKF-C-----SDIEEGEGQVLECLKEHK 54
Query: 185 HNGS 188
+
Sbjct: 55 DDLK 58
Score = 42.4 bits (100), Expect = 2e-05
Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 393 CGDEVRRVMRQRAESVRLLPEVEQACVDDLGMYCPE-RTGPGQEMDCLQE 441
C V R+ + AE RL P +++AC DD+ +C + G GQ ++CL+E
Sbjct: 3 CQQAVWRLQEEEAEDYRLDPVLQKACKDDIEKFCSDIEEGEGQVLECLKE 52
Score = 40.9 bits (96), Expect = 6e-05
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 10/64 (15%)
Query: 319 CESALIQIQYFIARDFELDPRLYRACYDEATRLCHAKKEWFKVKDLEPNNGPLVLPCLYR 378
C+ A+ ++Q A D+ LDP L +AC D+ + C +E VL CL
Sbjct: 3 CQQAVWRLQEEEAEDYRLDPVLQKACKDDIEKFCSDIEE----------GEGQVLECLKE 52
Query: 379 YLYH 382
+
Sbjct: 53 HKDD 56
Score = 40.9 bits (96), Expect = 6e-05
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 10/64 (15%)
Query: 512 CESALIQIQYFIARDFELDPRLYRACYDEATRLCHAKKEWFKVKDLEPNNGPLVLPCLYR 571
C+ A+ ++Q A D+ LDP L +AC D+ + C +E VL CL
Sbjct: 3 CQQAVWRLQEEEAEDYRLDPVLQKACKDDIEKFCSDIEE----------GEGQVLECLKE 52
Query: 572 YLYH 575
+
Sbjct: 53 HKDD 56
Score = 37.0 bits (86), Expect = 0.001
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 7/56 (12%)
Query: 9 VEWIAFSDFRLISQFTDVCKTFVQKFTCGRVETDKSTKFSQGKTLECLQMHIDKLD 64
++ D+RL CK ++KF C +E +G+ LECL+ H D L
Sbjct: 10 LQEEEAEDYRLDPVLQKACKDDIEKF-CSDIEEG------EGQVLECLKEHKDDLK 58
Score = 27.4 bits (61), Expect = 4.1
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 597 PDCAALVGNFTSAQVQDVRLNPLIMKYCGHVIH 629
P+C V + +D RL+P++ K C I
Sbjct: 1 PECQQAVWRLQEEEAEDYRLDPVLQKACKDDIE 33
>gnl|CDD|185370 PRK15473, cbiF, cobalt-precorrin-4 C(11)-methyltransferase;
Provisional.
Length = 257
Score = 31.6 bits (72), Expect = 0.87
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 8/73 (10%)
Query: 119 GDK-LMSDKCREQLLRRQMLIASDYQVSKRLARACKEDIRTHKCRRLVSDDREIRLAQIL 177
GDK L++ K L + Q++I + ++ L C H D E+ L QI+
Sbjct: 18 GDKELITLKGYRLLQQAQVVIYAGSLINTELLDYCPAQAECH-------DSAELHLEQII 70
Query: 178 VCLENAVHNGSKV 190
+E V G V
Sbjct: 71 DLMEAGVKAGKTV 83
>gnl|CDD|212550 cd11712, GINS_A_psf2, Alpha-helical domain of GINS complex protein
Psf2 (partner of Sld5 2). Psf2 is a component of GINS
tetrameric protein complex and has been found to play
important roles in normal eye development in Xenopus
laevis. GINS is a complex of four subunits (Sld5, Psf1,
Psf2 and Psf3) that is involved in both initiation and
elongation stages of eukaryotic chromosome replication.
Besides being essential for the maintenance of genomic
integrity, GINS plays a central role in coordinating DNA
replication with cell cycle checkpoints and is involved
in cell growth. The eukaryotic GINS subunits are
homologous and homologs are also found in the archaea;
the complex is not found in bacteria. The four subunits
of the complex consist of two domains each, termed the
alpha-helical (A) and beta-strand (B) domains. The A and
B domains of Sld5/Psf1 are permuted with respect to
Psf1/Psf3.
Length = 119
Score = 29.9 bits (68), Expect = 1.6
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 4/63 (6%)
Query: 144 VSKRLARACKEDIRT-HKCRRLVSDDREIRLAQILVCLENAVHNGS---KVSGECQAEMT 199
++K L +DI + R LV D R++R A++ LE + +G K+ E+
Sbjct: 40 IAKLLLEVASDDIPDADEIRSLVEDIRDVRQAKLRSGLEKLLGSGEVHAKLDNLTAMEIN 99
Query: 200 SHR 202
R
Sbjct: 100 EIR 102
>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 = 30.0 bits (67), Expect = 4.5
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 4/49 (8%)
Query: 74 LSELQSDDIKLDRVLYVACANDRYRLCSDVPQGSGQIYKCLMDHTGDKL 122
L +L++ DIK+D+ V+C N R SD+ + ++ D G K+
Sbjct: 312 LKDLEAQDIKIDKAYLVSCTNSR---ASDI-AAAADVFCEAADKNGGKI 356
>gnl|CDD|182732 PRK10789, PRK10789, putative multidrug transporter
membrane\ATP-binding components; Provisional.
Length = 569
Score = 30.1 bits (68), Expect = 4.6
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 36 CGRVETDKSTKFSQGKTLECLQMHIDKLDGDCRHQVLRLSELQSDD 81
CG + KST L +Q H D +GD R + L++LQ D
Sbjct: 347 CGPTGSGKST------LLSLIQRHFDVSEGDIRFHDIPLTKLQLDS 386
>gnl|CDD|132324 TIGR03281, methan_mark_12, putative methanogenesis marker protein
12. Members of this protein family, to date, are found
in a completed prokaryotic genome if and only if the
species is one of the archaeal methanogens. The exact
function is unknown, but likely is linked to
methanogenesis or a process closely connected to it
[Energy metabolism, Methanogenesis].
Length = 326
Score = 29.3 bits (66), Expect = 5.5
Identities = 21/79 (26%), Positives = 29/79 (36%), Gaps = 5/79 (6%)
Query: 256 PCLRAVESLIKTADAGEDWRVDPV-LKEACQPVVDIACRGIRGGDARVMSCLMDNLDNDV 314
P A++SL + A E + + KEA VV G + L V
Sbjct: 237 PGRLALDSLAMSV-AMEIASLGLLDCKEA--GVVLAGSGGTLREPINFSGKIKRVLSCKV 293
Query: 315 MTAPCESALIQIQYFIARD 333
+ ESA I + IA D
Sbjct: 294 LVLDSESAAIGLAL-IAED 311
>gnl|CDD|153374 cd07362, HPCD_like, Class III extradiol dioxygenases with
similarity to homoprotocatechuate 2,3-dioxygenase, which
catalyzes the key ring cleavage step in the metabolism
of homoprotocatechuate. This subfamily of class III
extradiol dioxygenases consists of two types of
proteins with known enzymatic activities;
3,4-dihydroxyphenylacetate (homoprotocatechuate)
2,3-dioxygenase (HPCD) and 2-amino-5-chlorophenol
1,6-dioxygenase. HPCD catalyzes the key ring cleavage
step in the metabolism of homoprotocatechuate (hpca), a
central intermediate in the bacterial degradation of
aromatic compounds. The enzyme incorporates both atoms
of molecular oxygen into hpca, resulting in aromatic
ring-opening to yield the product
alpha-hydroxy-delta-carboxymethyl cis-muconic
semialdehyde. 2-amino-5-chlorophenol 1,6-dioxygenase
catalyzes the oxidization and subsequent ring-opening of
2-amino-5-chlorophenol, which is an intermediate during
p-chloronitrobenzene degradation. The enzyme is probably
a heterotetramer composed of two alpha and two beta
subunits. Alpha and beta subunits share significant
sequence similarity and both belong to this family. Like
all Class III extradiol dioxygenases, these enzymes use
a non-heme Fe(II) to cleave aromatic rings between a
hydroxylated carbon and an adjacent non-hydroxylated
carbon.
Length = 272
Score = 29.0 bits (65), Expect = 6.2
Identities = 19/108 (17%), Positives = 36/108 (33%), Gaps = 16/108 (14%)
Query: 438 CLQERLPELKPDCAALVESLIKTADAGEDWRVDPVLKEACQPVVDIACRGIRGGDARVMS 497
C +E PE + ++ + + E+ + D +L +C + R
Sbjct: 13 CHEENPPENQGCLVGAIKGMKEIRKRIEELKPDVILVISCHWMSSSFHH-FVDATPR--- 68
Query: 498 CLMDNLDNDVMTA-PCESALIQIQYFIARDFELDPRLYRACYDEATRL 544
+ +TA C + + Y D+ DP L R +E
Sbjct: 69 -------HGGLTAVECPDLISDVPY----DYPGDPELGRLLVEEGQEA 105
>gnl|CDD|181199 PRK08020, ubiF, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
hydroxylase; Reviewed.
Length = 391
Score = 29.2 bits (66), Expect = 6.4
Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 9/53 (16%)
Query: 449 DCAALVESLIKTADAGEDWRVDPVLKEACQPVVDIACRGIRGGDARVMSCLMD 501
D AL++ L+ GE W + VLK R R D +M MD
Sbjct: 307 DVDALLDVLVNARSYGEAWASEAVLKR-------YQRR--RMADNLLMQSGMD 350
>gnl|CDD|181057 PRK07608, PRK07608, ubiquinone biosynthesis hydroxylase family
protein; Provisional.
Length = 388
Score = 29.2 bits (66), Expect = 7.4
Identities = 9/23 (39%), Positives = 10/23 (43%), Gaps = 2/23 (8%)
Query: 391 RSCGDEV--RRVMRQRAESVRLL 411
R GD RR R R E + L
Sbjct: 321 RDLGDLRLLRRYERARREDILAL 343
>gnl|CDD|221663 pfam12612, TFCD_C, Tubulin folding cofactor D C terminal. This
domain family is found in eukaryotes, and is typically
between 182 and 199 amino acids in length. The family is
found in association with pfam02985. There is a single
completely conserved residue R that may be functionally
important. Tubulin folding cofactor D does not
co-polymerise with microtubules either in vivo or in
vitro, but instead modulates microtubule dynamics by
sequestering beta-tubulin from GTP-bound
alphabeta-heterodimers in microtubules.
Length = 194
Score = 28.4 bits (64), Expect = 9.2
Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 211 LSPEIVTRCSEDIVTYCRGLEAG----GKTIHCLMEHARRNRKKERISPPCLRAVESLI 265
L+ +V ++ Y R LE + + L+ + N K +R+ P L+ ++ L+
Sbjct: 100 LTESLVKSSRSALLEYLRELEESTSALRQLLDDLLSILKENLKNDRVVVPTLKTLDFLL 158
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
0.323 0.138 0.432
Gapped
Lambda K H
0.267 0.0736 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,593,912
Number of extensions: 3064627
Number of successful extensions: 2122
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2118
Number of HSP's successfully gapped: 21
Length of query: 629
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 526
Effective length of database: 6,369,140
Effective search space: 3350167640
Effective search space used: 3350167640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 62 (27.6 bits)