RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17995
(120 letters)
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). 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 = 309
Score = 209 bits (533), Expect = 5e-69
Identities = 87/120 (72%), Positives = 104/120 (86%)
Query: 1 MDDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRV 60
MDDQ CPRCKTTKYR P+LKLMVN+CGH LCE CVDLLF++G+G+C EC+ PLR+ NFRV
Sbjct: 1 MDDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRV 60
Query: 61 QLFDDSSVEKEVEIRKKLLKDYNKVEEDFNSLAEYNDYLEEIEEIVFNLCNNIDILETNK 120
QLF+D +VEKEV+IRK++LK YNK EEDF SL EYNDYLEE+E+IV+NL NNID+ T K
Sbjct: 61 QLFEDPTVEKEVDIRKRVLKIYNKREEDFPSLREYNDYLEEVEDIVYNLTNNIDLENTKK 120
>gnl|CDD|227545 COG5220, TFB3, Cdk activating kinase (CAK)/RNA polymerase II
transcription initiation/nucleotide excision repair
factor TFIIH, subunit TFB3 [Cell division and chromosome
partitioning / Transcription / DNA replication,
recombination, and repair].
Length = 314
Score = 115 bits (289), Expect = 2e-32
Identities = 58/122 (47%), Positives = 83/122 (68%), Gaps = 4/122 (3%)
Query: 1 MDDQECPRCKTTKYRKPTLKLMVN-ICGHPLCEGCVDLLFLKGTGNC--YECNQPLRRGN 57
M+D+ CP CK+ +Y P +K+++N C H +CE CVD +F +G C C + LR+
Sbjct: 8 MEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIK 67
Query: 58 FRVQLFDDSSVEKEVEIRKKLLKDYNKVEEDFN-SLAEYNDYLEEIEEIVFNLCNNIDIL 116
F Q F+D +VEKEV++RK+LL+ +NK EE+F LA+YNDYLEE+EE+VF L ID+
Sbjct: 68 FIKQTFEDITVEKEVDVRKRLLRAFNKEEEEFGGDLAKYNDYLEEVEELVFELLELIDVS 127
Query: 117 ET 118
T
Sbjct: 128 LT 129
>gnl|CDD|115072 pfam06391, MAT1, CDK-activating kinase assembly factor MAT1. MAT1
is an assembly/targeting factor for cyclin-dependent
kinase-activating kinase (CAK), which interacts with the
transcription factor TFIIH. The domain found to the
N-terminal side of this domain is a C3HC4 RING finger.
Length = 200
Score = 104 bits (260), Expect = 3e-29
Identities = 45/68 (66%), Positives = 57/68 (83%)
Query: 53 LRRGNFRVQLFDDSSVEKEVEIRKKLLKDYNKVEEDFNSLAEYNDYLEEIEEIVFNLCNN 112
LR+ NFRVQ+F+D ++EKEV+IRK++LK +NK EEDF SL EYNDYLEE+E IVFNL N
Sbjct: 1 LRKNNFRVQIFEDPTIEKEVDIRKRILKIFNKREEDFPSLREYNDYLEEVETIVFNLTNG 60
Query: 113 IDILETNK 120
ID+ ET +
Sbjct: 61 IDVEETEE 68
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain,
a specialized type of Zn-finger of 40 to 60 residues
that binds two atoms of zinc; defined by the
'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified
in a proteins with a wide range of functions such as
viral replication, signal transduction, and
development; has two variants, the C3HC4-type and a
C3H2C3-type (RING-H2 finger), which have different
cysteine/histidine pattern; a subset of RINGs are
associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 31.6 bits (72), Expect = 0.012
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPL 53
ECP C +R+P ++ CGH C C+D G C C P+
Sbjct: 1 ECPICLEE-FREPV---VLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|215494 PLN02915, PLN02915, cellulose synthase A [UDP-forming], catalytic
subunit.
Length = 1044
Score = 33.4 bits (76), Expect = 0.019
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 25 ICGHPLCEGCVDLLFLKGTGNCYECNQPLRR--GNFRVQLFDDSSVEK---EVEIRKKLL 79
+CG P+C+ C + +G C +CN +R G RV+ D+ + E E + K
Sbjct: 39 VCGFPVCKPCYEYERSEGNQCCPQCNTRYKRHKGCPRVEGDDEEGNDMDDFEDEFQIKSP 98
Query: 80 KDYNKVEEDFNSLAEYNDYLEE 101
+D+ V ++ + +E DY +
Sbjct: 99 QDHEPVHQNVFAGSENGDYNAQ 120
>gnl|CDD|215121 PLN02189, PLN02189, cellulose synthase.
Length = 1040
Score = 33.1 bits (75), Expect = 0.023
Identities = 27/94 (28%), Positives = 39/94 (41%), Gaps = 17/94 (18%)
Query: 1 MDDQECPRCKTTKYRKPTLKLMV--NICGHPLCEGCVDLLFLKGTGNCYECNQPLRR--G 56
+D Q C C L V N CG P+C C + +GT NC +C +R G
Sbjct: 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYKRLKG 91
Query: 57 NFRVQLFDDSSVEKEVEIRKKLLKDYNKVEEDFN 90
+ RV+ DD +D + +E +FN
Sbjct: 92 SPRVEGDDDE-------------EDIDDIEHEFN 112
>gnl|CDD|215124 PLN02195, PLN02195, cellulose synthase A.
Length = 977
Score = 32.2 bits (73), Expect = 0.048
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 10/48 (20%)
Query: 26 CGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRVQLFDDSSVEKEVE 73
C +PLC+ C++ +G C C P +D +V +VE
Sbjct: 31 CSYPLCKACLEYEIKEGRKVCLRCGGP----------YDAENVFDDVE 68
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 29.9 bits (68), Expect = 0.31
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 67 SVEKEVEIRKKLLKDYNKVEEDFNSLAEYNDYLEEIEEIVFNLCNNIDILE 117
SV+ E+ K + ++ K+E++ L E + E+E + L I+ LE
Sbjct: 80 SVKSLEELIKDVEEELEKIEKEIKELEE---EISELENEIKELEQEIERLE 127
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 29.8 bits (67), Expect = 0.33
Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 53 LRRGNF-RVQLFDDSSVEKEVEIRKKLLKDYNKV---EEDFNSLAEYNDYL--EEIEEIV 106
LR G F R+ +E+ +EI K L+D + D LAE + +I +V
Sbjct: 396 LRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALV 455
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 29.7 bits (66), Expect = 0.35
Identities = 22/86 (25%), Positives = 31/86 (36%), Gaps = 7/86 (8%)
Query: 6 CPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRVQLFDD 65
CP C R P + CGH C+ C+ L C C+ R+ L D
Sbjct: 277 CPLCHCL-LRNP---MKTPCCGHTFCDECIGTALLDSDFKCPNCS---RKDVLLDGLTPD 329
Query: 66 SSVEKEVEIRKKLLKDYNKVEEDFNS 91
+ EVE K + +D N+
Sbjct: 330 IDKKLEVEKALKKQRKKVGTSDDNNT 355
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to EccC
in Actinobacteria) and the WXG100 target proteins are
the only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 29.6 bits (67), Expect = 0.35
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 68 VEKEVEIRKKLLKDYNKVEEDFNSLAEYNDYLEEIEEIVFNLCNNIDIL 116
++KE++ RKKL +Y S++ YN E + + +N D +
Sbjct: 883 IKKEIDRRKKLFSEYG-----VASISMYNKASGEKLPQIVIIIDNYDAV 926
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and
is likely to be a general function of this domain;
Various RING fingers exhibit binding activity towards
E2 ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 27.5 bits (61), Expect = 0.39
Identities = 12/44 (27%), Positives = 15/44 (34%), Gaps = 4/44 (9%)
Query: 6 CPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYEC 49
CP C + P + CGH C C+ G C C
Sbjct: 1 CPICLEEYLKDPVILP----CGHTFCRSCIRKWLESGNNTCPIC 40
>gnl|CDD|205173 pfam12978, DUF3862, Domain of Unknown Function with PDB structure
(DUF3862). PDB:3D4E shared structural similarity to
beta-lactamase inhibitory proteins (BLIP) which already
include 1XXM, 1S0W, 1JTG, 2G2U, 2G2W, 2B5R, and 3due.
All of structures are involved in beta-lactamase
inhibitor complex. (REF
http://www.topsan.org/Proteins/JCSG/3d4e).
Length = 159
Score = 27.4 bits (61), Expect = 1.5
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 60 VQLFDDSSVEKEVEIRKKLLKDYNKVEEDFNSLAE---YNDYLEEIEE 104
VQL+++S+V K + K +D +D+NSL + Y+D ++++ E
Sbjct: 64 VQLYNNSTVVKSI-SNFKFGRDLKLTLKDYNSLKDGMSYDDVVKKLGE 110
>gnl|CDD|178772 PLN03233, PLN03233, putative glutamate-tRNA ligase; Provisional.
Length = 523
Score = 27.3 bits (60), Expect = 2.2
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 54 RRGNFRVQL-FDDSSVEKE-VEIRKKLLKDYNKVEEDFNSLAEYNDYLEEIEE 104
RR R+ L FDD++ KE E + +++D K+E +S++ +DY E I
Sbjct: 40 RRYKGRLILRFDDTNPSKEKAEFEESIIEDLGKIEIKPDSVSFTSDYFEPIRC 92
>gnl|CDD|215224 PLN02400, PLN02400, cellulose synthase.
Length = 1085
Score = 27.2 bits (60), Expect = 2.2
Identities = 19/70 (27%), Positives = 28/70 (40%), Gaps = 15/70 (21%)
Query: 23 VNICGHPLCEGCVDLLFLKGTGNCYECNQPLRR--GNFRVQLFDDSSVEKEVEIRKKLLK 80
N C P+C C + GT C +C RR G+ RV+ +D
Sbjct: 58 CNECAFPVCRPCYEYERKDGTQCCPQCKTRYRRHKGSPRVEGDEDED------------- 104
Query: 81 DYNKVEEDFN 90
D + +E +FN
Sbjct: 105 DVDDLENEFN 114
>gnl|CDD|224477 COG1561, COG1561, Uncharacterized stress-induced protein [Function
unknown].
Length = 290
Score = 26.8 bits (60), Expect = 2.5
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 6/48 (12%)
Query: 53 LRRGNF--RVQLFDDSSVEKEVEIRKKLLKDY----NKVEEDFNSLAE 94
+ RG +++ + S +KE+EI + LLK ++ F+ AE
Sbjct: 57 ISRGKVECTLRIEREESAQKELEINEDLLKQLVTLLKELAAQFDLAAE 104
>gnl|CDD|151528 pfam11083, Streptin-Immun, Lantibiotic streptin immunity protein.
Streptococcal species produce a lantibiotic, streptin,
in a similar manner to the production of nisin and
subtilin by other lactic acid bacteria, in order to
compete against competing bacteria within the
environment. The immunity protein protects the bacterium
from destruction by its own lantibiotic. In general,
there is little homology between the immunity proteins
of different genera of bacteria.
Length = 99
Score = 25.8 bits (57), Expect = 3.4
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 83 NKVEEDFNSLA-EYNDYLEEIEEIVFNLCNNIDILETNK 120
+VEE+ L + + YL+E E++V L + IL T+K
Sbjct: 55 EQVEEEILKLQNQLSLYLDEYEKLVRRLEKFVKILNTSK 93
>gnl|CDD|184798 PRK14704, PRK14704, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 618
Score = 26.7 bits (59), Expect = 3.4
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 8/67 (11%)
Query: 47 YECNQPLRRGNFRVQLFD-DSS--VEKEVEIRKKLLKDYNKVEEDFNSLAEYNDYLEEIE 103
++ NQ ++ G LFD D + V K VE KK L+ Y +E A +E E
Sbjct: 124 FQANQNMQHGGQSFALFDVDLAPYVRKTVERHKKRLQSYPLTKEQIEEFAW-----KETE 178
Query: 104 EIVFNLC 110
+ C
Sbjct: 179 NDTYQAC 185
>gnl|CDD|215343 PLN02638, PLN02638, cellulose synthase A (UDP-forming), catalytic
subunit.
Length = 1079
Score = 26.8 bits (59), Expect = 4.0
Identities = 8/32 (25%), Positives = 15/32 (46%)
Query: 24 NICGHPLCEGCVDLLFLKGTGNCYECNQPLRR 55
++C P+C C + G +C +C +R
Sbjct: 40 DVCAFPVCRPCYEYERKDGNQSCPQCKTKYKR 71
>gnl|CDD|215639 PLN03226, PLN03226, serine hydroxymethyltransferase; Provisional.
Length = 475
Score = 26.5 bits (59), Expect = 4.3
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 72 VEIRKKLLKDYNKVEEDFNSLAEYNDYLEEIEEI 105
V I K+ K++ K +DF E ND+ ++IE +
Sbjct: 417 VTIALKIQKEHGKKLKDFKKGLESNDFSKDIEAL 450
>gnl|CDD|236172 PRK08173, PRK08173, DNA topoisomerase III; Validated.
Length = 862
Score = 26.2 bits (58), Expect = 5.1
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 68 VEKEVEIRKKLLKDYNKVEEDF 89
VE+E +IR+ + +DY +V +F
Sbjct: 205 VEREEKIRRFVPRDYWEVRAEF 226
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 26.1 bits (58), Expect = 5.5
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 68 VEKEVEIRKKLLKDYNKVEEDFNSLAEYND 97
V++E EIR +DY K+E + A+Y
Sbjct: 206 VDREREIRAFDPEDYWKIEALLDKEAQYFY 235
>gnl|CDD|239003 cd02048, neuroserpin, Neuroserpin is a inhibitory member of the
SERine Proteinase INhibitor (serpin) family that reacts
preferentially with tissue-type plasminogen activator
(tPA). It is located in neurons in regions of the brain
where tPA is also found, suggesting that neuroserpin is
the selective inhibitor of tPA in the central nervous
system (CNS). This subgroup corresponds to clade I of
the serpin superfamily.
Length = 388
Score = 26.0 bits (57), Expect = 5.6
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 73 EIRKKLLKDYNKVEEDFNSLAEYNDYL-EEIEEIVFNLCNNI 113
EIR L D K E+F+ L + + + + +E VFNL N++
Sbjct: 49 EIRHSLGYDGLKNGEEFSFLKDLSSMITAKEKEYVFNLANSL 90
>gnl|CDD|232935 TIGR00354, polC, DNA polymerase, archaeal type II, large subunit.
This model represents the large subunit, DP2, of a two
subunit novel Archaeal replicative DNA polymerase first
characterized for Pyrococcus furiosus. Structure of DP2
appears to be organized as a ~950 residue component
separated from a ~300 residue component by a ~150 residue
intein. The other subunit, DP1, has sequence similarity
to the eukaryotic DNA polymerase delta small subunit [DNA
metabolism, DNA replication, recombination, and repair].
Length = 1095
Score = 26.0 bits (57), Expect = 5.9
Identities = 19/69 (27%), Positives = 27/69 (39%), Gaps = 20/69 (28%)
Query: 46 CYECNQPLRR----------GNFRVQLFDDSSVEKEVEIRKKLLKDYNK----------V 85
C +CN RR GN SV K +E+ K L ++YN +
Sbjct: 1015 CTKCNTKYRRIPLVGKCLKCGNNLTLTVSKGSVMKYLELSKFLAENYNVSSYTKQRLMIL 1074
Query: 86 EEDFNSLAE 94
E+ NS+ E
Sbjct: 1075 EQGINSMFE 1083
>gnl|CDD|192566 pfam10392, COG5, Golgi transport complex subunit 5. The COG
complex, the peripheral membrane oligomeric protein
complex involved in intra-Golgi protein trafficking,
consists of eight subunits arranged in two lobes bridged
by Cog1. Cog5 is in the smaller, B lobe, bound in with
Cog6-8, and is itself bound to Cog1 as well as,
strongly, to Cog7.
Length = 132
Score = 25.3 bits (56), Expect = 6.2
Identities = 12/67 (17%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 52 PLRRGNFRVQLFDDSSVEKEVEIRKKLLKDYNKVEEDFNSLAEYNDYLEEIEEIVFNLCN 111
PL+R N+ +Q D IR + ++ ++ +S+ + L ++ + L
Sbjct: 34 PLKRLNYDIQELDR-------RIRTLITSNHLELLSHLSSIKSASSILSTLKSSLEYLSA 86
Query: 112 NIDILET 118
+ + L++
Sbjct: 87 SYERLKS 93
>gnl|CDD|223719 COG0646, MetH, Methionine synthase I (cobalamin-dependent),
methyltransferase domain [Amino acid transport and
metabolism].
Length = 311
Score = 25.7 bits (57), Expect = 7.0
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 78 LLKDYNKVEEDFNSLAEYNDYLEEIE-EIVFNLCNNI-----DILETN 119
+L+ Y E DF L N+ L + +++ + DI+ETN
Sbjct: 26 MLQSYGLDEADFRGLKGNNELLNLTKPDVIEAIHRAYIEAGADIIETN 73
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 25.6 bits (57), Expect = 7.8
Identities = 22/78 (28%), Positives = 30/78 (38%), Gaps = 30/78 (38%)
Query: 6 CPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRVQLFDD 65
C +C KYR+P PL +G C +C L V
Sbjct: 1040 CTKCGA-KYRRP-----------PL------------SGKCPKCGGNL---ILTVH---K 1069
Query: 66 SSVEKEVEIRKKLLKDYN 83
SVEK +E+ KKL ++Y
Sbjct: 1070 GSVEKYLEVSKKLAEEYG 1087
>gnl|CDD|222743 pfam14421, LmjF365940-deam, A distinct subfamily of CDD/CDA-like
deaminases. A distinct branch of the CDD/CDA-like
deaminases prototyped by Leishmania LmjF36.5940. Members
of this family are widely distributed across several
microbial eukaryotes such as kinetoplastids, chlorophyte
algae, stramenopiles and the alveolate Perkinsus. Domain
architectures suggest that these proteins might possess
mRNA editing or DNA mutagenizing activity.
Length = 169
Score = 25.5 bits (56), Expect = 7.8
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 46 CYECNQPLRR-----GNFRVQLFDDSSVEKEVE 73
C C + LR+ +FRV +FD + K
Sbjct: 133 CGACEEWLRKIAEYNPDFRVYMFDSTECRKVYI 165
>gnl|CDD|237910 PRK15103, PRK15103, paraquat-inducible membrane protein A;
Provisional.
Length = 419
Score = 25.8 bits (57), Expect = 8.1
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 2 DDQECPRCKTTKY-RKP-----TLKLMV 23
D CPRC T Y R+ TL L+V
Sbjct: 234 DQPVCPRCHTKGYVRRRNSLQWTLALLV 261
>gnl|CDD|151878 pfam11439, CesA, Type III secretion system filament chaperone
CesA. This family represents a chaperone protein for
the type III secretion system - TTSS - translocon
protein EspA, to prevent the latter's
self-polymerisation. The TTSS is a highly specialised
bacterial protein secretory pathway, similar in many
ways to the flagellar system, that is essential for the
pathogenesis of many Gram-negative bacteria. The twenty
or so proteins making up the TTSS apparatus, referred
to as the needle complex, allow the injection of
virulence proteins (known as effectors) directly into
the cytoplasm of the eukaryotic host cells they infect;
however, the injection process itself is mediated by a
subset of extracellular proteins that are secreted by
the needle complex to the bacterial surface and
assembled into the type III translocon - EspA. EspB and
EspD. EspA polymerises into an extracellular filament,
and, as with other fibrous proteins, is apt to undergo
massive polymerisation when overexpressed. CesA is the
secretion chaperone protein that binds to EspA. CesA is
dimeric and helical, and it traps EspA in a monomeric
state and inhibits its polymerisation.
Length = 93
Score = 24.7 bits (53), Expect = 8.1
Identities = 9/30 (30%), Positives = 20/30 (66%)
Query: 65 DSSVEKEVEIRKKLLKDYNKVEEDFNSLAE 94
D + E+E KK++ +++ ++E+ N L+E
Sbjct: 12 DKKIRSEIEAIKKIIAEFDVIKENVNELSE 41
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 25.6 bits (57), Expect = 8.1
Identities = 12/45 (26%), Positives = 21/45 (46%)
Query: 61 QLFDDSSVEKEVEIRKKLLKDYNKVEEDFNSLAEYNDYLEEIEEI 105
L D V + + +KL K+Y ++E EY E++E+
Sbjct: 21 ALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQEDLEDA 65
>gnl|CDD|225129 COG2219, PRI2, Eukaryotic-type DNA primase, large subunit [DNA
replication, recombination, and repair].
Length = 363
Score = 25.5 bits (56), Expect = 8.4
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 50 NQPLRRGNFRVQLFDDSSVEKEVEIRKKLLKDYNKVEEDFNSLAEYNDYLEEIEEIV 106
N+ LR+G + + + +E R+ + + N + E E ++ LEEI E+
Sbjct: 165 NRVLRKGYVYLTKEELIRLLEE-AFRENIEESLNMLREILEVPDEVSELLEEISELA 220
>gnl|CDD|185388 PRK15491, PRK15491, replication factor A; Provisional.
Length = 374
Score = 25.6 bits (56), Expect = 8.8
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 56 GNFRVQLFDDSSVEKEVEIRKKLLKDYNKVEEDFNSLAEYNDYLEEIE 103
G RV L+D + ++ KL + E N A N+Y +E+E
Sbjct: 214 GKIRVTLWDG-----KTDLADKL--ENGDSVEIINGYARTNNYSQEVE 254
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 0.140 0.427
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,064,774
Number of extensions: 535026
Number of successful extensions: 1003
Number of sequences better than 10.0: 1
Number of HSP's gapped: 997
Number of HSP's successfully gapped: 114
Length of query: 120
Length of database: 10,937,602
Length adjustment: 83
Effective length of query: 37
Effective length of database: 7,256,220
Effective search space: 268480140
Effective search space used: 268480140
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 (24.4 bits)