RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1623
(522 letters)
>gnl|CDD|215716 pfam00100, Zona_pellucida, Zona pellucida-like domain.
Length = 252
Score = 68.7 bits (168), Expect = 5e-13
Identities = 55/285 (19%), Positives = 85/285 (29%), Gaps = 66/285 (23%)
Query: 130 CSEDGMEFTLRTPEGFLGRIYTYGYYDR---CFYRGNGGTANVLRISGAQGYPDCGTQR- 185
C+ED M + F +Y + C T + R CGT R
Sbjct: 2 CTEDTMTVVVSKDLTFTPGLYLSSLHLGDPSCRPVETNSTHAIFRF----PLSSCGTTRQ 57
Query: 186 -------YGDTMTNIVVVQFSDYVQTSRDKRYNLTCLFRGPGEAVVTSSYMTANSGSPIP 238
Y + + + V + D+R ++C + V SS + P+
Sbjct: 58 RTGDGIVYENEIVSQPSVSVGPPITRDSDRRLPVSCSYTSRS--VSVSSVAVLPTVPPVS 115
Query: 239 IEYLPAENSLSSRVRLQ--ILFQGRPTNTIAVGDPLTFKLDSQDGYN------YVTDIFA 290
E SL+ +RL + TI +GDPL + ++ +A
Sbjct: 116 P-SPSGEGSLTFSLRLYTDDSYTSDYPVTIELGDPLYVEATVSVLPRSDPLVLFLDSCWA 174
Query: 291 TNVIARDPYSGRSVQLIDRYGYWIIESTFNHLPVNQCSPQRSFSALTVTIFSFRCPVDNF 350
T DP S LI+ CPVD
Sbjct: 175 TP--GPDPDSSPRYDLIEN----------------------------------GCPVDGD 198
Query: 351 VFPALDRSREGDGLEARF--NAFKIPE-SNFLVFEATVRTCRDGC 392
L G+ ARF AF+ P S+ + +V+ C
Sbjct: 199 STSTLSHPV-GESHTARFSFKAFRFPGDSSQVYIHCSVKVCDKSD 242
>gnl|CDD|238532 cd01099, PAN_AP_HGF, Subfamily of PAN/APPLE-like domains; present
in N-terminal (N) domains of plasminogen/hepatocyte
growth factor proteins, and various proteins found in
Bilateria, such as leech anti-platelet proteins.
PAN/APPLE domains fulfill diverse biological functions
by mediating protein-protein or protein-carbohydrate
interactions.
Length = 80
Score = 58.6 bits (142), Expect = 5e-11
Identities = 26/78 (33%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 31 RMRRQFIKKSTTAASLAACERECAESRDFICRSFNYRAVPYGGQRENCELSDRDARDLDM 90
++ +K T ASL C R+C E +F CRSFNY Y + C LSD D M
Sbjct: 12 KILVSEVKTEITVASLEECLRKCLEETEFTCRSFNYN---YKSK--ECILSDED----RM 62
Query: 91 NNPSYFEPTGDFDFYEKS 108
++ + D+YE
Sbjct: 63 SSGVKLLYDSNVDYYENK 80
>gnl|CDD|215662 pfam00024, PAN_1, PAN domain. The PAN domain contains a conserved
core of three disulphide bridges. In some members of the
family there is an additional fourth disulphide bridge
the links the N and C termini of the domain. The domain
is found in diverse proteins, in some they mediate
protein-protein interactions, in others they mediate
protein-carbohydrate interactions.
Length = 78
Score = 42.6 bits (100), Expect = 2e-05
Identities = 17/75 (22%), Positives = 22/75 (29%), Gaps = 9/75 (12%)
Query: 34 RQFIKKSTTAASLAACERECAESRDFICRSFNYRAVPYGGQRENCELSDRDARDLDMNNP 93
S C C +CRSF Y + + C L + L P
Sbjct: 12 SGTDVSVVDVPSAEECAALCTNEPR-VCRSFTYNP-----KSKECLLKSSSSGSL---PP 62
Query: 94 SYFEPTGDFDFYEKS 108
D+YEKS
Sbjct: 63 RLKRSDQGVDYYEKS 77
>gnl|CDD|214680 smart00473, PAN_AP, divergent subfamily of APPLE domains.
Apple-like domains present in Plasminogen, C. elegans
hypothetical ORFs and the extracellular portion of plant
receptor-like protein kinases. Predicted to possess
protein- and/or carbohydrate-binding functions.
Length = 78
Score = 37.9 bits (88), Expect = 9e-04
Identities = 22/72 (30%), Positives = 30/72 (41%), Gaps = 11/72 (15%)
Query: 36 FIKKSTTAASLAACERECAESRDFICRSFNYRAVPYGGQRENCELSDRDARDLDMNNPSY 95
F + + ASL C +C S + CRSF Y G + C L + +
Sbjct: 17 FSRIVISVASLEECASKCLNS-NCSCRSFTYN---NGTK--GCLLWSES----SLGDARL 66
Query: 96 FEPTGDFDFYEK 107
F P+G D YEK
Sbjct: 67 F-PSGGVDLYEK 77
>gnl|CDD|214579 smart00241, ZP, Zona pellucida (ZP) domain. ZP proteins are
responsible for sperm-adhesion fo the zona pellucida. ZP
domains are also present in multidomain transmembrane
proteins such as glycoprotein GP2, uromodulin and
TGF-beta receptor type III (betaglycan).
Length = 252
Score = 37.8 bits (88), Expect = 0.009
Identities = 55/280 (19%), Positives = 87/280 (31%), Gaps = 66/280 (23%)
Query: 130 CSEDGMEFTLRTPEGFLGRIYTYGYYD---RCFYRGNGGTANVLRISGAQGYPDCGT--Q 184
C ED M ++ T F G I G C + T+ + CGT Q
Sbjct: 2 CGEDQMVVSVSTDLLFPGGINVKGLTLGDPSCRPQFTDATSAFVSFEV--PLNGCGTRRQ 59
Query: 185 RYGDTMT--NIVVVQ-FSDYVQTSRDK-RYNLTCLFRGPGEAVVTSSYMTANSGSPIPIE 240
D + N +VV F T D+ Y+ C + V+ + S IP
Sbjct: 60 VNPDGIVYSNTLVVSPFHPGFITRDDRAAYHFQCFYPENE--KVSLNL----DVSTIPPT 113
Query: 241 YLPAENSLSSRVRLQIL-----FQGRPTNTIAVGDPLT--FKLDSQDGYNY---VTDIFA 290
L + + ++ + +GDP+ ++ D D V + +A
Sbjct: 114 ELSSVSEGPLTCSYRLYKDDSFGSPYQSADYVLGDPVYHEWECDGADDPPLGLLVDNCYA 173
Query: 291 TNVIARDPYSGRSVQLIDRYGYWIIESTFNHLPVNQCSPQRSFSALTVTIFSFRCPVDNF 350
T DP SG +ID CPVD +
Sbjct: 174 TPG--PDPSSGPKYFIIDN----------------------------------GCPVDGY 197
Query: 351 VFPALDRSREGDGLEARF--NAFKIPESNFLVFEATVRTC 388
+ + + ARF FK + + + F +R C
Sbjct: 198 LDSTIPYN-SNPLHRARFSVKVFKFADRSLVYFHCQIRLC 236
>gnl|CDD|238461 cd00919, Heme_Cu_Oxidase_I, Heme-copper oxidase subunit I.
Heme-copper oxidases are transmembrane protein complexes
in the respiratory chains of prokaryotes and
mitochondria which catalyze the reduction of O2 and
simultaneously pump protons across the membrane. The
superfamily is diverse in terms of electron donors,
subunit composition, and heme types. The number of
subunits varies from three to five in bacteria and up to
13 in mammalian mitochondria. It has been proposed that
Archaea acquired heme-copper oxidases through gene
transfer from Gram-positive bacteria. Membership in the
superfamily is defined by subunit I, which contains a
heme-copper binuclear center (the active site where O2
is reduced to water) formed by a high-spin heme and a
copper ion. It also contains a low-spin heme, believed
to participate in the transfer of electrons to the
binuclear center. Only subunit I is common to the
entire superfamily. For every reduction of an O2
molecule, eight protons are taken from the inside
aqueous compartment and four electrons are taken from
the electron donor on the opposite side of the membrane.
The four electrons and four of the protons are used in
the reduction of O2; the four remaining protons are
pumped across the membrane. This charge separation of
four charges contributes to the electrochemical gradient
used for ATP synthesis. Two proton channels, the
D-pathway and K-pathway, leading to the binuclear center
have been identified in subunit I of cytochrome c
oxidase (CcO) and ubiquinol oxidase. A well-defined
pathway for the transfer of pumped protons beyond the
binuclear center has not been identified. Electron
transfer occurs in two segments: from the electron
donor to the low-spin heme, and from the low-spin heme
to the binuclear center. The first segment can be a
multi-step process and varies among the different
families, while the second segment, a direct transfer,
is consistent throughout the superfamily.
Length = 463
Score = 31.3 bits (72), Expect = 1.3
Identities = 11/42 (26%), Positives = 21/42 (50%)
Query: 478 LQTMQPAIPDSICMSNREYYSLLTTLFILLTFLIVVTAFAGF 519
L ++ A P S+ + + Y L+T +++ F V+ A G
Sbjct: 25 LIRLELATPGSLFLDPQLYNQLVTAHGVIMIFFFVMPAIFGG 66
>gnl|CDD|226344 COG3823, COG3823, Glutamine cyclotransferase [Posttranslational
modification, protein turnover, chaperones].
Length = 262
Score = 30.1 bits (68), Expect = 2.5
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 11/67 (16%)
Query: 243 PAENSLSSRVRLQILFQGRPTNTIAVGDPLTFKLDSQDGYNYVTDIFATNVIAR-DPYSG 301
P + V Q+ G P + + +L+ DG Y +++ T IAR DP SG
Sbjct: 157 PKTFAELDTV--QVTDDGVPVSKLN-------ELEWVDGELY-ANVWQTTRIARIDPDSG 206
Query: 302 RSVQLID 308
R V ID
Sbjct: 207 RVVAWID 213
>gnl|CDD|182123 PRK09866, PRK09866, hypothetical protein; Provisional.
Length = 741
Score = 30.6 bits (69), Expect = 2.5
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 429 RREIASVGDSEG--VVVNSEGKTKNGTDDEEQVREMI 463
R I +VG S V+VN + +DD +QVR +I
Sbjct: 280 REAILAVGQSVPLYVLVNKFDQQDRNSDDADQVRALI 316
>gnl|CDD|213989 cd07434, PHP_PolIIIA_DnaE2, Polymerase and Histidinol Phosphatase
domain of alpha-subunit of bacterial polymerase III at
DnaE2 gene. PolIIIA DnaE2 plays a role in SOS
mutagenesis/translesion synthesis and has dominant
effects in determining GC variability in the bacterial
genome. PolIIIAs that contain an N-terminal PHP domain
have been classified into four basic groups based on
genome composition, phylogenetic, and domain structural
analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also
called histidinol phosphatase-2/HIS2) domain is
associated with several types of DNA polymerases, such
as PolIIIA and family X DNA polymerases, stand alone
histidinol phosphate phosphatases (HisPPases), and a
number of uncharacterized protein families. DNA
polymerase III holoenzyme is one of the five eubacterial
DNA polymerases that are responsible for the replication
of the DNA duplex. PolIIIA core enzyme catalyzes the
reaction for polymerizing both DNA strands. PolC PHP is
located in a different location compared to dnaE1, 2,
and 3. dnaE1 is the longest compared to dnaE2 and dnaE3.
A unique motif was also identified in dnaE1 and dnaE3
genes. The PHP domain has four conserved sequence motifs
and contains an invariant histidine that is involved in
metal ion coordination. PHP domains found in DnaEs of
thermophilic origin exhibit 3'-5' exonuclease activity.
Length = 260
Score = 29.3 bits (67), Expect = 3.9
Identities = 13/38 (34%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 244 AENSLSSRVRLQILFQGRP---TNTIAVGDPLTFKLDS 278
AE L S L LF P T+ + TF LD
Sbjct: 217 AERHLRSPAELARLFLYPPEALAETLEIAARCTFSLDE 254
>gnl|CDD|72671 pfam09255, Antig_Caf1, Caf1 Capsule antigen. Members of this
family are predominantly found in the F1 capsule antigen
Caf1 synthesised by Yersinia bacteria. They adopt a
structure consisting of a seven strands arranged in two
beta-sheets, in a Greek-key topology, and mediate
targeting of the bacterium to sites of infection.
Length = 136
Score = 28.6 bits (63), Expect = 4.0
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 265 TIAVGDPLTFKLDSQDGYNYVTDIFATNVIARD 297
T A GDP+ SQDG N+ F T VI +D
Sbjct: 50 TDAAGDPMYLTFTSQDGNNHQ---FTTKVIGKD 79
>gnl|CDD|219574 pfam07782, DC_STAMP, DC-STAMP-like protein. This is a family of
sequences which are similar to a region of the dendritic
cell-specific transmembrane protein (DC-STAMP). This is
thought to be a novel receptor protein that shares no
identity with other multimembrane-spanning proteins. It
is thought to have seven putative transmembrane regions,
two of which are found in the region featured in this
family. DC-STAMP is also described as having potential
N-linked glycosylation sites and a potential
phosphorylation site for PKC, but these are not
conserved throughout the family.
Length = 191
Score = 29.2 bits (66), Expect = 4.3
Identities = 18/67 (26%), Positives = 21/67 (31%), Gaps = 7/67 (10%)
Query: 368 FNAFKIPESNFLVFEATVRTCRDGCQPVTLLPQGVVKLSLLCVDAYCTGHSGRNEPSLGR 427
AF S F + R C QP V L LL + A E R
Sbjct: 117 VGAFNP--SEKSSFSLSNRECLP--QPSPPDYTVYVALGLLLLLAVFL---VLLEAYALR 169
Query: 428 KRREIAS 434
RR I +
Sbjct: 170 LRRLICA 176
>gnl|CDD|149509 pfam08482, HrpB_C, ATP-dependent helicase C-terminal. This domain
is found near the C-terminus of bacterial ATP-dependent
helicases such as HrpB.
Length = 133
Score = 28.6 bits (65), Expect = 4.3
Identities = 24/54 (44%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 227 SYMTANSGSPIPIEYLPAEN-SLSSRVRLQILFQGRPTNTIAVGD-PLTFKLDS 278
++ T SGS +PI+Y L+ VRLQ LF T TIA G PLT L S
Sbjct: 42 THFTVPSGSRVPIDYSGDGGPVLA--VRLQELFGLTETPTIAGGRVPLTLHLLS 93
>gnl|CDD|177870 PLN02225, PLN02225, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 701
Score = 29.7 bits (66), Expect = 5.0
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 326 QCSPQRSFSALTVTI---FSFRCPVDNFVFPALDRSREGDGLEARFNAFKIPESN 377
Q S SF+A+ +T+ + FR PVDN ++ A++++ L R++A + N
Sbjct: 116 QKSMNPSFAAIELTLALHYVFRAPVDNILWDAVEQTYAHKVLTRRWSAIPSRQKN 170
>gnl|CDD|173329 PTZ00031, PTZ00031, ribosomal protein L2; Provisional.
Length = 317
Score = 29.0 bits (65), Expect = 5.3
Identities = 29/108 (26%), Positives = 48/108 (44%), Gaps = 14/108 (12%)
Query: 192 NIVVVQFSDYVQTSRDKRYNLTCLFRGPGEAVVTSSYMTANSGSPIPIEYLPAENSLSSR 251
+I ++Q+ D V + Y L L PG+ ++ S Y N G+ +P+ +P S+
Sbjct: 121 HIALLQYEDGVLS-----YILAPLLLRPGDKIIASKYANINPGNSLPLRNIPV-GSIVHN 174
Query: 252 VRL------QILFQGRPTNTIAVGDPL--TFKLDSQDGYNYVTDIFAT 291
V + QI+ G T+ D T KL S + + D +AT
Sbjct: 175 VEMRPGAGGQIIRAGGTYATVVSKDEQFATLKLKSTEIRKFPLDCWAT 222
>gnl|CDD|213205 cd03238, ABC_UvrA, ATP-binding cassette domain of the excision
repair protein UvrA. Nucleotide excision repair in
eubacteria is a process that repairs DNA damage by the
removal of a 12-13-mer oligonucleotide containing the
lesion. Recognition and cleavage of the damaged DNA is a
multistep ATP-dependent reaction that requires the UvrA,
UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases,
with UvrA having two ATP binding sites, which have the
characteristic signature of the family of ABC proteins,
and UvrB having one ATP binding site that is
structurally related to that of helicases.
Length = 176
Score = 28.1 bits (63), Expect = 7.4
Identities = 22/91 (24%), Positives = 32/91 (35%), Gaps = 19/91 (20%)
Query: 239 IEYLPAENSLSS-------RVRLQILFQGRPTNTIAVGDPLTFKLDSQDGYNYVTDIFAT 291
+ YL LS+ RV+L P T+ + D + L QD +
Sbjct: 76 LGYLTLGQKLSTLSGGELQRVKLASELFSEPPGTLFILDEPSTGLHQQDINQLL------ 129
Query: 292 NVIARDPYSGRSVQLID------RYGYWIIE 316
VI G +V LI+ WII+
Sbjct: 130 EVIKGLIDLGNTVILIEHNLDVLSSADWIID 160
>gnl|CDD|222657 pfam14295, PAN_4, PAN domain.
Length = 48
Score = 25.7 bits (57), Expect = 9.5
Identities = 12/39 (30%), Positives = 15/39 (38%), Gaps = 5/39 (12%)
Query: 42 TAASLAACERECAESRDFICRSFNYRAVPYGGQRENCEL 80
+ S AC CA CR++ Y GG C L
Sbjct: 14 SVDSPEACCAACAADSG--CRAWTYVDPASGGT---CWL 47
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
0.322 0.138 0.415
Gapped
Lambda K H
0.267 0.0605 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,577,402
Number of extensions: 2549058
Number of successful extensions: 2142
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2137
Number of HSP's successfully gapped: 21
Length of query: 522
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 421
Effective length of database: 6,457,848
Effective search space: 2718754008
Effective search space used: 2718754008
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: 61 (27.5 bits)