RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5197
(564 letters)
>gnl|CDD|205150 pfam12925, APP_E2, E2 domain of amyloid precursor protein. The E2
domain is the largest of the conserved domains of the
amyloid precursor protein. The structure of E2 consists
of two coiled-coil sub-structures connected through a
continuous helix, and bears an unexpected resemblance to
the spectrin family of protein structures.E 2 can
reversibly dimerise in solution, and the dimerisation
occurs along the longest dimension of the molecule in an
antiparallel orientation, which enables the N-terminal
substructure of one monomer to pack against the
C-terminal substructure of a second monomer. The high
degree of conservation of residues at the putative dimer
interface suggests that the E2 dimer observed in the
crystal could be physiologically relevant. Heparin
sulfate proteoglycans, the putative ligands for the
precursor present in extracellular matrix, bind to E2 at
a conserved and positively charged site near the dimer
interface.
Length = 193
Score = 206 bits (527), Expect = 8e-64
Identities = 83/203 (40%), Positives = 129/203 (63%), Gaps = 12/203 (5%)
Query: 305 STTTPTSTATTKSHATTRVPTPDPYFTHFEPKDEHHAFKEALQRLEEMHREKVTKVMKDW 364
T +PTS A DPYF+ + +EH +KEA +RLEE HRE++T+VMK+W
Sbjct: 3 PTPSPTSDAV------------DPYFSEPKEDNEHERYKEAKKRLEEKHRERMTQVMKEW 50
Query: 365 SDLEERYQDMRSKSPGVAEDFKQKMTLRFQQTVQSLEEEGNAEKHQLIVMHQQRVAARIN 424
+ E +Y+++ P A+ ++++T RFQ+TVQ+LE+E AE+ QL+ HQQRV A +N
Sbjct: 51 EEAESQYKNLPKADPKAAQLMRKELTERFQETVQTLEQEAAAERQQLVETHQQRVEAHLN 110
Query: 425 QHKKDAMNCYIEALNDVSLNTHKVQKCLQKLLRALHKDRHHTIAHYKHLLATNLDFAVKE 484
+ ++ A+ Y+ AL N HK+ K L++ +RA KDR HT+ H++H+ T+ + A +
Sbjct: 111 ERRRAALENYLRALQAEPPNPHKILKALKRYIRAEQKDRQHTLRHFQHVRKTDPEKAAQM 170
Query: 485 KPMTLEHLVDIDHTINQSMTMLQ 507
+P LEHL ID +NQS+T+L
Sbjct: 171 RPQVLEHLRVIDERMNQSLTLLY 193
>gnl|CDD|128326 smart00006, A4_EXTRA, amyloid A4. amyloid A4 precursor of
Alzheimers disease.
Length = 165
Score = 185 bits (470), Expect = 8e-56
Identities = 61/113 (53%), Positives = 76/113 (67%), Gaps = 1/113 (0%)
Query: 1 IYPKHDITNIVESSNYVKITNWCKVGHSKCKHTD-WVKPYRCLEGPFQSDALLVPEHCVF 59
YP+ ITN+VE+S V I NWC+ G S+CK +V P+RCL G F SDALLVPE C F
Sbjct: 53 AYPELQITNVVEASQPVTIQNWCRRGRSQCKTHHHFVIPFRCLVGEFVSDALLVPEGCQF 112
Query: 60 DHIHNQSKCWEYERWNQTAAQSCLERDLSLRSFAMLLPCGISLFAGVEFVCCP 112
H +C ++RW+Q A ++C E+ + L SF MLLPCGI F GVEFVCCP
Sbjct: 113 LHQERMDQCETHQRWHQEAKEACSEKGMILHSFGMLLPCGIDKFRGVEFVCCP 165
>gnl|CDD|193397 pfam12924, APP_Cu_bd, Copper-binding of amyloid precursor, CuBD.
This short domain, part of the extra-cellular N-terminus
of the amyloid precursor protein, APP, can bind both
copper and zinc, CuBD. The structure of Cu2+-bound CuBD
reveals that the metal ligands are His147, His151,
Tyr168 and two water molecules, which are arranged in a
square pyramidal geometry. The structure of Cu+-bound
CuBD is almost identical to the Cu2+-bound structure
except for the loss of one of the water ligands. The
geometry of the site is unfavourable for Cu+, thus
providing a mechanism by which CuBD could readily
transfer Cu ions to other proteins.
Length = 57
Score = 107 bits (270), Expect = 1e-28
Identities = 30/57 (52%), Positives = 37/57 (64%)
Query: 56 HCVFDHIHNQSKCWEYERWNQTAAQSCLERDLSLRSFAMLLPCGISLFAGVEFVCCP 112
C FDHIH C ++ W+ A ++C + + L SF MLLPCGI LF GVEFVCCP
Sbjct: 1 KCKFDHIHRMDVCESFQHWHTVAKEACSTKGMELHSFGMLLPCGIDLFTGVEFVCCP 57
>gnl|CDD|216917 pfam02177, APP_N, Amyloid A4 N-terminal heparin-binding. This
N-terminal domain of APP, amyloid precursor protein, is
the heparin-binding domain of the protein. this region
is also responsible for stimulation of neurite
outgrowth. The structure reveals both a highly charged
basic surface that may interact with glycosaminoglycans
in the brain and an abutting hydrophobic surface that is
proposed to play an important functional role such as in
dimerisation or ligand-binding. Structural similarities
with cysteine-rich growth factors, taken together with
its known growth-promoting properties, suggest the APP
N-terminal domain could function as a growth factor in
vivo.
Length = 102
Score = 103 bits (260), Expect = 9e-27
Identities = 38/56 (67%), Positives = 43/56 (76%), Gaps = 1/56 (1%)
Query: 1 IYPKHDITNIVESSNYVKITNWCKVGHSKCK-HTDWVKPYRCLEGPFQSDALLVPE 55
+YP+ DITN+VE+S V I+NWCK SKCK HT VKPYRCL G F SDALLVPE
Sbjct: 47 VYPELDITNVVEASQPVTISNWCKFNRSKCKSHTHTVKPYRCLVGEFVSDALLVPE 102
>gnl|CDD|151071 pfam10515, APP_amyloid, beta-amyloid precursor protein C-terminus.
This is the amyloid, C-terminal, protein of the
beta-Amyloid precursor protein (APP) which is a
conserved and ubiquitous transmembrane glycoprotein
strongly implicated in the pathogenesis of Alzheimer's
disease but whose normal biological function is unknown.
The C-terminal 100 residues are released and aggregate
into amyloid deposits which are strongly implicated in
the pathology of Alzheimer's disease plaque-formation.
The domain is associated with family A4_EXTRA,
pfam02177, further towards the N-terminus.
Length = 53
Score = 80.3 bits (198), Expect = 6e-19
Identities = 30/62 (48%), Positives = 39/62 (62%), Gaps = 9/62 (14%)
Query: 224 AAVFIAMTVLKRRSARSPQNLCNVFFYFQGFIEVDQAATPEERHVANMQINGYENPTYKY 283
+ +++ +L+RR + G +EVD A TPEERH+ANMQ NGYENPTYKY
Sbjct: 1 IVIVVSLAMLRRRPYGAIS---------HGVVEVDPALTPEERHLANMQNNGYENPTYKY 51
Query: 284 FE 285
FE
Sbjct: 52 FE 53
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 38.8 bits (91), Expect = 0.002
Identities = 20/101 (19%), Positives = 46/101 (45%), Gaps = 1/101 (0%)
Query: 337 DEHHAFKEALQRLEEMHREKVTKVMKDWSDLEERYQDMRSKSPGVAEDFKQKMTLRFQQT 396
E A K A ++LE+ ++ ++ K +L++ Q ++ ++ ++E+ ++ QQ
Sbjct: 28 SESPAGKAAQKQLEKEFKKLQAELQKKEKELQKEEQKLQKQAATLSEEARKAKQQELQQK 87
Query: 397 VQSLEEEGNAEKHQLIVMHQQRVAARINQHKKDAMNCYIEA 437
Q L+++ A Q + QQ + I A+ +
Sbjct: 88 QQELQQKQQA-AQQELQQKQQELLQPIYDKIDKAIKEVAKE 127
>gnl|CDD|115579 pfam06933, SSP160, Special lobe-specific silk protein SSP160. This
family consists of several special lobe-specific silk
protein SSP160 sequences which appear to be specific to
Chironomus (Midge) species.
Length = 758
Score = 37.4 bits (86), Expect = 0.020
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 290 DSYENIVSPSS--GPASSTTTPTSTATTKSHATTRVPT 325
+Y+N +P S PA++ TT +ST TT + TT PT
Sbjct: 662 AAYQNCTAPGSVTVPAAANTTTSSTTTTTTTTTTAAPT 699
Score = 29.7 bits (66), Expect = 5.5
Identities = 20/65 (30%), Positives = 29/65 (44%)
Query: 294 NIVSPSSGPASSTTTPTSTATTKSHATTRVPTPDPYFTHFEPKDEHHAFKEALQRLEEMH 353
N S S+ ++STT ST TT S +T + T D F ALQ L+ +
Sbjct: 284 NSTSNSNSTSNSTTNSNSTTTTNSTTSTNSTSSSNSSTIAGCIDIAANFTIALQNLQALL 343
Query: 354 REKVT 358
++ T
Sbjct: 344 LQEAT 348
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 34.5 bits (80), Expect = 0.15
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 112 PMKDKERERFLEKQRKEVHKHEREELREEKARVKAAAEGRTYEPTGPSTPIPP 164
+ ER++ +KQRK K E+EE EKA K AE + GP
Sbjct: 405 NLSPAERKKLRKKQRKAEKKAEKEE--AEKAAAKKKAEAAAKKAKGPDGETKK 455
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 33.0 bits (76), Expect = 0.37
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 115 DKERERFLEKQRKEVHKHEREELREEKARVKAAAE 149
DK RE EK K + +EE +E+K K
Sbjct: 262 DKTREEEEEKILKAAEEERQEEAQEKKEEKKKEER 296
>gnl|CDD|219102 pfam06600, DUF1140, Protein of unknown function (DUF1140). This
family consists of several short, hypothetical phage and
bacterial proteins. The function of this family is
unknown.
Length = 107
Score = 30.7 bits (69), Expect = 0.51
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 4/80 (5%)
Query: 447 KVQKCLQKLLRALHKDRHHTIAHYKHLLATNLDFAVKEKPMTLEHLVDIDHTINQSMTML 506
+ +C +K+ + R T H+K NL+F ++EK L L+++D + S +
Sbjct: 31 RANRCREKIAESGLCVR--TSRHWKA--QENLEFYIREKSFLLHQLLELDRSYRWSEKLH 86
Query: 507 QRHPALAVKISELMQDYMQA 526
Q + K ++++Y Q
Sbjct: 87 QDRYSFVTKYVAVLEEYRQE 106
>gnl|CDD|225715 COG3174, COG3174, Predicted membrane protein [Function unknown].
Length = 371
Score = 32.7 bits (75), Expect = 0.55
Identities = 36/191 (18%), Positives = 60/191 (31%), Gaps = 40/191 (20%)
Query: 84 ERDLSLRS-FAMLLPCGISLFAGVEFVCCPMKDKERE------RFLEKQRKEVHKHER-- 134
+RDL + + A+L + AG M D E L ++ +H+ R
Sbjct: 43 DRDLGVTTPIALLATFALGALAG-------MGDLEAAAGGIVLALLLASKEPLHRFLRRL 95
Query: 135 --EELREEKARVKAAAEGRTYEPTGPSTPIPPGVDAHPPYSSQRHDTVQPAYAMSHDLSI 192
EELR A AA Y P P+ + P + ++ +I
Sbjct: 96 SWEELRS--ALELAALAAVVY-PVLPNGGVDPWGGPREVWL--------MVVLIA---AI 141
Query: 193 GEPSYLRHEVRPRGDSKGVYVTVVFAGLAVMAAVFIAMTVLKR------RSARSPQNLCN 246
Y+ VR G +G+ +T + G AV R + L
Sbjct: 142 SFAGYI--AVRILGGRRGLILTGLIGGFVSSTAVTATFAARVRIGEDVLPPEAAAALLAA 199
Query: 247 VFFYFQGFIEV 257
+ + +
Sbjct: 200 AVMLIRNLLLI 210
>gnl|CDD|163153 TIGR03142, cytochro_ccmI, cytochrome c-type biogenesis protein
CcmI. This TPR repeat-containing protein is the CcmI
protein (also called CycH) of c-type cytochrome
biogenesis. CcmI is thought to act as an apo-cytochrome
c chaperone. This model describes the N-terminal region
of the protein, Members of this protein family [Protein
fate, Protein folding and stabilization, Energy
metabolism, Electron transport].
Length = 117
Score = 31.1 bits (71), Expect = 0.55
Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 215 VVFAGLAVMAAVFIAMTVLKRRSARSPQNL--CNVFFYFQGFIEVD 258
+V A L ++A +F+ + +L+RR A + + N+ Y E++
Sbjct: 4 IVAALLTLVALLFLLLPLLRRRRAAATVDRDELNLAVYRDRLAELE 49
>gnl|CDD|236993 PRK11820, PRK11820, hypothetical protein; Provisional.
Length = 288
Score = 32.4 bits (75), Expect = 0.56
Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 10/70 (14%)
Query: 341 AFKEALQRLEEMHREKVTKVMKDWSDLEERYQDM-------RSKSPGVAEDFKQKMTLRF 393
A EAL L EM RE+ +K DL +R + + +P + E++++++ R
Sbjct: 134 ALDEALDDLIEM-REREGAALKA--DLLQRLDAIEALVAKIEALAPEILEEYRERLRERL 190
Query: 394 QQTVQSLEEE 403
++ + L+E
Sbjct: 191 EELLGELDEN 200
>gnl|CDD|218738 pfam05766, NinG, Bacteriophage Lambda NinG protein. NinG or Rap is
involved in recombination. Rap (recombination adept with
plasmid) increases lambda-by-plasmid recombination
catalyzed by Escherichia coli's RecBCD pathway.
Length = 188
Score = 31.2 bits (71), Expect = 0.83
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 109 VCCP---MKDKERERFLEKQRKEVHKHEREELREEKARVKAAAE 149
VC P + K RE+ EK+RK + ER EL+ K ++K ++
Sbjct: 25 VCSPECALALK-REKAQEKKRKAEAQAERRELKARKEKLKTRSD 67
>gnl|CDD|224328 COG1410, MetH, Methionine synthase I, cobalamin-binding domain
[Amino acid transport and metabolism].
Length = 842
Score = 31.5 bits (72), Expect = 1.2
Identities = 14/66 (21%), Positives = 23/66 (34%), Gaps = 4/66 (6%)
Query: 103 FAGVEFVCCPMKDKERERFLEKQRKEVHK----HEREELREEKARVKAAAEGRTYEPTGP 158
V + M ++R + E RKE H + R ++AA +
Sbjct: 521 SRAVGVMDTLMSAEQRADYSEGFRKEYETVRTQHANRKARTRPLSIEAARDNAEAVWADY 580
Query: 159 STPIPP 164
P+PP
Sbjct: 581 EPPVPP 586
>gnl|CDD|139531 PRK13383, PRK13383, acyl-CoA synthetase; Provisional.
Length = 516
Score = 31.5 bits (71), Expect = 1.3
Identities = 25/102 (24%), Positives = 34/102 (33%), Gaps = 19/102 (18%)
Query: 138 REEKARVKAAAEGRTYEPTGPSTPIPPGVDAHPPYSSQRHDTVQPAYAMSHDLSIGEPSY 197
E R AA GR T +T P GV P S ++G
Sbjct: 164 EESGGRPAVAAPGRIVLLTSGTTGKPKGVPRAPQLRS----------------AVGVWVT 207
Query: 198 LRHEVRPRGDSKGVYVTVVFAGLA---VMAAVFIAMTVLKRR 236
+ R R S+ +F GL +M + + TVL R
Sbjct: 208 ILDRTRLRTGSRISVAMPMFHGLGLGMLMLTIALGGTVLTHR 249
>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex. This
entry is characterized by proteins with alternating
conserved and low-complexity regions. Bud13 together
with Snu17p and a newly identified factor,
Pml1p/Ylr016c, form a novel trimeric complex. called The
RES complex, pre-mRNA retention and splicing complex.
Subunits of this complex are not essential for viability
of yeasts but they are required for efficient splicing
in vitro and in vivo. Furthermore, inactivation of this
complex causes pre-mRNA leakage from the nucleus. Bud13
contains a unique, phylogenetically conserved C-terminal
region of unknown function.
Length = 141
Score = 30.0 bits (68), Expect = 1.6
Identities = 12/40 (30%), Positives = 19/40 (47%)
Query: 114 KDKERERFLEKQRKEVHKHEREELREEKARVKAAAEGRTY 153
K+++ E+ E + V K ERE+ EE + K R
Sbjct: 28 KERKEEKEKEWGKGLVQKEEREKRLEELEKAKNKPLARYA 67
>gnl|CDD|151642 pfam11200, DUF2981, Protein of unknown function (DUF2981). This
eukaryotic family of proteins has no known function.
Length = 319
Score = 31.0 bits (69), Expect = 1.6
Identities = 15/60 (25%), Positives = 24/60 (40%)
Query: 274 NGYENPTYKYFEIKDYDSYENIVSPSSGPASSTTTPTSTATTKSHATTRVPTPDPYFTHF 333
N Y+NP K KD +S S ++ P S T + + A + D ++ H
Sbjct: 196 NAYDNPDGKVGAAKDLNSGNTANSVNNTPNSVDNTAKPSDNGSNSAGEKKKEDDSFYDHL 255
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 31.2 bits (71), Expect = 2.1
Identities = 36/226 (15%), Positives = 70/226 (30%), Gaps = 36/226 (15%)
Query: 322 RVPTPDPYFTHFEPKDEHHAFKEALQRLEEMHREKVTKVMKDWSDLEERYQDMRSKSPGV 381
R+ PD E ++ +EALQ ++ EE+ ++
Sbjct: 592 RLDVPDYAANETELRERLQQAEEALQSAVAKQKQ-----------AEEQLVQANAE---- 636
Query: 382 AEDFKQKMTLRFQQTVQSLEEEGNAEKHQLIVMHQQRVAARINQHKKDAMNCYIEALNDV 441
E+ K+ + Q + QQ + ++ + L
Sbjct: 637 LEEQKRAEAEART------ALKQARLDLQRLQNEQQSLKDKLELAIAERKQQAETQLRQ- 689
Query: 442 SLNTHKVQKCLQKLLRALHKDRHHTIAHYKHLLATNLDFAVKEKPMTLEHLVDIDHTINQ 501
L L+ L + + + K K +E ++D+ + Q
Sbjct: 690 ----------LDAQLKQLLEQQQAFLEALKDDFRELR-TERLAKWQVVEG--ELDNQLAQ 736
Query: 502 -SMTMLQRHPALAVKISELMQDYMQALRSKDETPGSLLSLTREAEE 546
S + ++ EL + Y + L S D P ++ L R+ EE
Sbjct: 737 LSAAIEAARTQAKARLKELKKQYDRELASLDVDPNTVKELKRQIEE 782
>gnl|CDD|216513 pfam01456, Mucin, Mucin-like glycoprotein. This family of
trypanosomal proteins resemble vertebrate mucins. The
protein consists of three regions. The N and C terminii
are conserved between all members of the family, whereas
the central region is not well conserved and contains a
large number of threonine residues which can be
glycosylated. Indirect evidence suggested that these
genes might encode the core protein of parasite mucins,
glycoproteins that were proposed to be involved in the
interaction with, and invasion of, mammalian host cells.
This family contains an N-terminal signal peptide.
Length = 143
Score = 29.8 bits (66), Expect = 2.2
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 284 FEIKDYDSYENIVSPSSGPASSTTTPTSTATTKSHATTRVPT 325
E + S + ++ P ++TTT T+T TT + TT+ T
Sbjct: 36 VEAAEGQSQTTTTTTTTTPPTTTTTTTTTTTTITTTTTKTTT 77
Score = 29.1 bits (64), Expect = 3.9
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 297 SPSSGPASSTTTPTSTATTKSHATTRVPTP 326
S ++ ++TT PT+T TT + TT T
Sbjct: 43 SQTTTTTTTTTPPTTTTTTTTTTTTITTTT 72
>gnl|CDD|215964 pfam00513, Late_protein_L2, Late Protein L2.
Length = 466
Score = 30.3 bits (69), Expect = 2.6
Identities = 15/54 (27%), Positives = 18/54 (33%), Gaps = 12/54 (22%)
Query: 289 YDSYENI--------VSPSSGPASSTTTPTSTATTK----SHATTRVPTPDPYF 330
SYE I + P SST P + S A +V DP F
Sbjct: 188 THSYEEIPMDTFAVSEGTTPPPISSTPIPGVRRVARLRLYSRALQQVKVTDPAF 241
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
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 = 378
Score = 30.2 bits (68), Expect = 2.8
Identities = 9/74 (12%), Positives = 24/74 (32%), Gaps = 7/74 (9%)
Query: 296 VSPSSGPASSTTTPTSTATTKSHATTRVPTPDPYFTHFEPKDEH-----HAFKEALQRLE 350
+ A ++ + + +S T +P + ++ +
Sbjct: 105 PASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSERETTIEEIM 164
Query: 351 EM--HREKVTKVMK 362
EM RE+V + ++
Sbjct: 165 EMGYEREEVERALR 178
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 30.5 bits (69), Expect = 2.8
Identities = 39/244 (15%), Positives = 94/244 (38%), Gaps = 28/244 (11%)
Query: 336 KDEHHAFKEALQRLEEMHREKVTKVM---KDWSDLEERYQDMRSKSPGVAEDFKQKMTLR 392
+ E +E L RLEE E ++ K+ +L+ +++R + + Q+ L
Sbjct: 238 RKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREE-----LEELQEELLE 292
Query: 393 FQQTVQSLEEEGNAEKHQL------IVMHQQRVAARINQHKKDAMN-----CYIEALNDV 441
++ ++ LE E + + +L + ++R+ + + +E L +
Sbjct: 293 LKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQL 352
Query: 442 SLNTHKVQKCLQKLLRALHKDRHHTIAHYKHLLATNLDFAVKEKPMTLEHLVDIDHTINQ 501
+ ++ L++ L AL ++ + L E L ++ I
Sbjct: 353 LAELEEAKEELEEKLSALLEELEELFEALR----EELAELEAELAEIRNELEELKREIES 408
Query: 502 SMTMLQRHPALAVKISELMQDYMQALRSKDETPGSLLSLTREAE--EAILDKYKAQVIAM 559
L+R L+ ++ +L ++ + +E L L E E E L++ + ++ +
Sbjct: 409 LEERLER---LSERLEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKEL 465
Query: 560 QEDF 563
+ +
Sbjct: 466 EREL 469
>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria
with the myosin-like domain [Function unknown].
Length = 499
Score = 30.4 bits (68), Expect = 2.8
Identities = 14/90 (15%), Positives = 38/90 (42%), Gaps = 1/90 (1%)
Query: 343 KEALQRLEEMHREKVTKVMKDWSDLEERYQDMRSKSPGVAEDFKQKMTLRFQQTVQSLEE 402
+ Q L + K ++ + L ++ QD++++ +AE +Q +
Sbjct: 119 EAVRQELAAARQNL-AKAQQELARLTKQAQDLQTRLKTLAEQRRQLEAQAQSLQASQKQL 177
Query: 403 EGNAEKHQLIVMHQQRVAARINQHKKDAMN 432
+ +A + + V+ + +A+I Q ++
Sbjct: 178 QASATQLKSQVLDLKLRSAQIEQEAQNLAT 207
>gnl|CDD|224477 COG1561, COG1561, Uncharacterized stress-induced protein [Function
unknown].
Length = 290
Score = 29.9 bits (68), Expect = 3.0
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 10/70 (14%)
Query: 341 AFKEALQRLEEMHREKVTKVMKDWSDLEERYQDM-------RSKSPGVAEDFKQKMTLRF 393
A +EAL L EM RE+ +K +DL +R + S P + E +++++ R
Sbjct: 136 ALEEALDDLIEM-REREGAALK--ADLLQRLDAIEELVEKVESLMPEILEWYRERLVARL 192
Query: 394 QQTVQSLEEE 403
+ L+E+
Sbjct: 193 NEAQDQLDED 202
>gnl|CDD|225252 COG2377, COG2377, Predicted molecular chaperone distantly related
to HSP70-fold metalloproteases [Posttranslational
modification, protein turnover, chaperones].
Length = 371
Score = 30.3 bits (69), Expect = 3.0
Identities = 13/63 (20%), Positives = 21/63 (33%), Gaps = 2/63 (3%)
Query: 371 YQDMRSKSPGVAEDFKQKMTLRFQQTVQSLEEEGNAEKHQL--IVMHQQRVAARINQHKK 428
R+ + + + + L Q V +L E + I H Q V R H
Sbjct: 53 LCAARADTLAELAELDRALALLHAQAVAALLAEQGLLPRDIRAIGCHGQTVLHRPPGHAP 112
Query: 429 DAM 431
D +
Sbjct: 113 DTV 115
>gnl|CDD|143653 cd07912, Tweety_N, N-terminal domain of the protein encoded by the
Drosophila tweety gene and related proteins, a family of
chloride ion channels. The protein product of the
Drosophila tweety (tty) gene is thought to form a
trans-membrane protein with five membrane-spanning
regions and a cytoplasmic C-terminus. This N-terminal
domain contains the putative transmembrane spanning
regions. Tweety has been suggested as a candidate for a
large conductance chloride channel, both in vertebrate
and insect cells. Three human homologs have been
identified and designated TTYH1-3. TTYH2 has been
associated with the progression of cancer, and
Drosophila melanogaster tweety has been assumed to play
a role in development. TTYH2, and TTYH3 bind to and are
ubiquinated by Nedd4-2, a HECT type E3 ubiquitin ligase,
which most likely plays a role in controlling the
cellular levels of tweety family proteins.
Length = 418
Score = 30.0 bits (68), Expect = 3.4
Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 462 DRHHTIAHYKHLLATNLDFAVKEKPMTLEHLVDIDHTINQSMTMLQRHPALAVKISELMQ 521
+ + + + + L AV E P ++L+ + +N + L + AL + L +
Sbjct: 310 ESQRALTNMQSQVQGLLREAVFEFPTAEDNLLSLQGDLNSTEINLHQLTAL-LDCRGLHK 368
Query: 522 DYMQALRS 529
DY++ALR
Sbjct: 369 DYVEALRG 376
>gnl|CDD|219546 pfam07739, TipAS, TipAS antibiotic-recognition domain. This domain
is found at the C-terminus of some MerR family
transcription factors. The domain has an alpha-helical
globin-like fold. The family includes Mta a central
regulator of multidrug resistance in Bacillus subtilis.
Length = 118
Score = 28.8 bits (65), Expect = 3.4
Identities = 15/106 (14%), Positives = 40/106 (37%), Gaps = 10/106 (9%)
Query: 339 HHAFKEALQRLEEMHREKVTKVMKDWSDLEERYQDMRSKSPGVAEDFKQKMTLRFQQTVQ 398
A++E+ ++ + + +E ++ ++W +L + + Q++ R + +
Sbjct: 12 DEAYQESEEKTKNLSKEDWEEIQEEWDELFAELAAAMDEGVDPDSEEVQELAERHRDWLS 71
Query: 399 SLEEEGNAEKH-QLIVMHQQ--RVAARINQHKK-------DAMNCY 434
+ E L M+ R A +++ DA+ Y
Sbjct: 72 ESFTPCDPEALAGLGEMYVADPRFTANYDKYGPGLAEFLRDAIEAY 117
>gnl|CDD|234347 TIGR03759, conj_TIGR03759, integrating conjugative element protein,
PFL_4693 family. Members of this protein family, such
as model protein PFL_4693 from Pseudomonas fluorescens
Pf-5, belong to extended genomic regions that appear to
be spread by conjugative transfer. Most members have a
predicted N-terminal signal sequence. The function is
unknown [Mobile and extrachromosomal element functions,
Plasmid functions].
Length = 200
Score = 29.6 bits (67), Expect = 3.6
Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 3/66 (4%)
Query: 115 DKERERFLEKQRKEVHKHEREELREEKARVKAAAEGRTYEPTGPSTPIPPGVDAHPPYSS 174
D+ER R+ E K+ + +EL ++A A R Y P + A P +
Sbjct: 50 DEERRRYAELWVKQEAQRVEKELAFQRAYDAAWQ--RLY-PNVLPVNLFDPSGAAGPIAL 106
Query: 175 QRHDTV 180
Q +
Sbjct: 107 QGGGRL 112
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 30.3 bits (69), Expect = 3.9
Identities = 22/113 (19%), Positives = 45/113 (39%), Gaps = 16/113 (14%)
Query: 334 EPKDEHHAFKEALQRLEE--MHREKVTKVMKDWSDLEERYQD------------MRSKSP 379
+ +E L+RL E E++ ++ S+LE+R + R
Sbjct: 490 SRSEAWDVARELLRRLREQRHLAEQLQQLRMRLSELEQRLRQQQRAERLLAEFCKRLGKN 549
Query: 380 GVAEDFKQKMTLRFQQTVQSLEEEGNAEKHQLIVMHQQR--VAARINQHKKDA 430
ED +++ + ++SL E + + + + + QQ + ARI + A
Sbjct: 550 LDDEDELEQLQEELEARLESLSESVSEARERRMALRQQLEQLQARIQRLAARA 602
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 29.9 bits (68), Expect = 4.2
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 115 DKERERFLEKQRKEVHKHEREELREEKARVKAAAEGR 151
++ + RF +Q + ERE+ +AR K AAE R
Sbjct: 449 EEAKARFEARQARL----EREKA-AREARHKKAAEAR 480
>gnl|CDD|215243 PLN02444, PLN02444, HMP-P synthase.
Length = 642
Score = 29.9 bits (67), Expect = 4.5
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 4/68 (5%)
Query: 290 DSYENIVSPSSGPASSTTTPTSTATTKSHATTRVPTPDPYFTHFEPKDEHHAFKEALQRL 349
S + S+ ++ T T ++ T+ PT DP F P +F+E +
Sbjct: 38 VSAARLKKESTATRATLTFDPPTGNSEKAKQTK-PTVDPSAPDFLP---IPSFEECFPKS 93
Query: 350 EEMHREKV 357
+ ++E V
Sbjct: 94 TKEYKEVV 101
>gnl|CDD|184349 PRK13824, PRK13824, replication initiation protein RepC;
Provisional.
Length = 404
Score = 29.8 bits (68), Expect = 4.5
Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 17/85 (20%)
Query: 341 AFKEALQRLEE---MHREKVTK---------VMKDWSDLEERYQDM-----RSKSPGVAE 383
A ++AL+RL E + R + K V DW +E+R++ + R + E
Sbjct: 160 AERKALRRLRERLTLCRRDIAKLIEAAIEEGVPGDWEGVEQRFRAIVARLPRRATLAELE 219
Query: 384 DFKQKMTLRFQQTVQSLEEEGNAEK 408
++ ++ V LE +E
Sbjct: 220 PILDELEALREEVVNLLESHLKSEN 244
>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal
domain. This domain is found in a number of different
types of plant proteins including NAM-like proteins.
Length = 147
Score = 28.5 bits (64), Expect = 4.8
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 111 CPMKDKERERFLEKQRKEVHKHEREELREEKARVK 145
K+KE+E K E K ER EL ++KA K
Sbjct: 83 EAEKEKEKEERFMKALAEAEK-ERAELEKKKAEAK 116
>gnl|CDD|224250 COG1331, COG1331, Highly conserved protein containing a thioredoxin
domain [Posttranslational modification, protein
turnover, chaperones].
Length = 667
Score = 29.6 bits (67), Expect = 5.1
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 6/38 (15%)
Query: 325 TPD--PYF--THFEPKDEHHA--FKEALQRLEEMHREK 356
TPD P+F T+F +D + FK+ L+ + E RE
Sbjct: 116 TPDGKPFFAGTYFPKEDRYGRPGFKQLLEAIRETWRED 153
>gnl|CDD|224556 COG1641, COG1641, Uncharacterized conserved protein [Function
unknown].
Length = 387
Score = 29.2 bits (66), Expect = 5.4
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 6/64 (9%)
Query: 435 IEALN-DVSLNTHKVQKCLQKLLRALHKDRHHTIAHYKH----LLATNLDFAVKEKPMTL 489
+EAL +V L +VQK + + + D H H + A +L VK+ + +
Sbjct: 34 VEALGPEVDLRVEEVQKRGIRATK-VEVDAEHHHRHLPEIVELIKAADLPDRVKQVALAI 92
Query: 490 EHLV 493
L+
Sbjct: 93 FELL 96
>gnl|CDD|218421 pfam05086, Dicty_REP, Dictyostelium (Slime Mold) REP protein. This
family consists of REP proteins from Dictyostelium
(Slime molds). REP protein is likely involved in
transcription regulation and control of DNA replication,
specifically amplification of plasmid at low copy
numbers. The formation of homomultimers may be required
for their regulatory activity.
Length = 910
Score = 29.8 bits (67), Expect = 5.5
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 297 SPSSGPASSTTTPTSTATTKSHATTR 322
PS P ++TTT T+T TT TR
Sbjct: 247 QPSKRPNNTTTTTTTTTTTTFQPRTR 272
>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
component YidC; Validated.
Length = 429
Score = 29.0 bits (65), Expect = 7.6
Identities = 14/69 (20%), Positives = 24/69 (34%)
Query: 114 KDKERERFLEKQRKEVHKHEREELREEKARVKAAAEGRTYEPTGPSTPIPPGVDAHPPYS 173
K + ER + ++ ++ R +A VKA +G TP P
Sbjct: 353 KRRAAEREINREARQERAAAMARARARRAAVKAKKKGLIDASPNEDTPSENEESKGSPPQ 412
Query: 174 SQRHDTVQP 182
+ T +P
Sbjct: 413 VEATTTAEP 421
>gnl|CDD|222023 pfam13281, DUF4071, Domain of unknown function (DUF4071). This
domain is found at the N-terminus of many
serine-threonine kinase-like proteins.
Length = 365
Score = 28.5 bits (64), Expect = 9.3
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 109 VCCPMKDKERERFLEKQRKEVHKHEREELREEKARVKA 146
V +RE+FL RK K +ELR+E ++A
Sbjct: 85 VPIQSSAHKREKFLSDLRKAREKLSGKELRKELRELRA 122
>gnl|CDD|132218 TIGR03174, cas_Csc3, CRISPR type I-D/CYANO-associated protein
Csc3/Cas10d. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family is a CRISPR-associated (Cas) family strictly
associated with the Cyano subtype of CRISPR/Cas locus,
found in several species of Cyanobacteria and several
archaeal species. This family is designated Csc3 for
CRISPR/Cas Subtype Cyano protein 3, as it is often the
third gene upstream of the core cas genes,
cas3-cas4-cas1-cas2 [Mobile and extrachromosomal element
functions, Other].
Length = 953
Score = 28.7 bits (64), Expect = 9.5
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 500 NQSMTMLQRHPALAVKISELMQDYMQALRSKDETPGSLLSLTREAEEAILDK 551
N +T + L ++ EL + + + SK+ P ++L REA EAIL K
Sbjct: 815 NIVLTEKLENSNLTKRLVELYRRFYRVALSKNPKPHAVLKPFREAVEAILSK 866
>gnl|CDD|225500 COG2949, SanA, Uncharacterized membrane protein [Function unknown].
Length = 235
Score = 28.1 bits (63), Expect = 9.6
Identities = 20/48 (41%), Positives = 21/48 (43%), Gaps = 9/48 (18%)
Query: 128 EVHKHEREELREEKARVKAAAE----GRTYEPT--GPSTPIPPGVDAH 169
E LRE ARVKA + R EP GP PIPP DA
Sbjct: 185 EGRSGLSVRLREFLARVKAVLDLYILKR--EPKFLGPPVPIPPF-DAQ 229
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
0.318 0.131 0.391
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,532,182
Number of extensions: 2771925
Number of successful extensions: 4385
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4349
Number of HSP's successfully gapped: 82
Length of query: 564
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 462
Effective length of database: 6,413,494
Effective search space: 2963034228
Effective search space used: 2963034228
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.5 bits)