RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10800
(81 letters)
>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 = 38.6 bits (90), Expect = 9e-06
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 26 TCPSCK-VKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAF 69
CP C R+ VL C HVFC C+ ++ + CP C
Sbjct: 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.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 = 397
Score = 38.8 bits (90), Expect = 6e-05
Identities = 20/45 (44%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 25 LTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAF 69
L C CK VLT C H FC C+R R + Q KCP C A
Sbjct: 27 LRCHICKDFFDVPVLTSCSHTFCSLCIR-RCLSNQPKCPLCRAED 70
>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 = 35.9 bits (83), Expect = 7e-05
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 27 CPSCK-VKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKC 65
CP C KD V+ C H FC C+R E+ CP C
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger). The
C3HC4 type zinc-finger (RING finger) is a cysteine-rich
domain of 40 to 60 residues that coordinates two zinc
ions, and has the consensus sequence:
C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C
where X is any amino acid. Many proteins containing a
RING finger play a key role in the ubiquitination
pathway.
Length = 40
Score = 35.5 bits (82), Expect = 1e-04
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 27 CPSCKVKRKDAV-LTKCFHVFCWDCLRTRYETRQRKCPKC 65
CP C + KD V + C H+FC C+ + E+ CP C
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 35.9 bits (82), Expect = 7e-04
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 24 TLTCPSCKVKRKDAVLTK-CFHVFCWDCLRTRYETRQRKCPKC 65
+L CP C ++ + T C H FC +C+ T KCP C
Sbjct: 274 SLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNC 316
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 32.9 bits (75), Expect = 0.001
Identities = 20/44 (45%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 25 LTCPSCKVKRKDA-VLTKCFHVFCWDCLRTRYETRQRKCPKCNA 67
L CP C +D VLT C HVFC +C+ RY ++ KCP C
Sbjct: 3 LECPICLDLLRDPVVLTPCGHVFCRECIL-RYLKKKSKCPICRT 45
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase
[Signal transduction mechanisms].
Length = 391
Score = 34.3 bits (78), Expect = 0.002
Identities = 15/45 (33%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 25 LTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAF 69
L C C + T C H FC C+R R+ Q CP C
Sbjct: 26 LRCRICDCRISIPCETTCGHTFCSLCIR-RHLGTQPFCPVCREDP 69
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 33.7 bits (77), Expect = 0.004
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 27 CPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQ-RKCPKCNA 67
C C + + T C H+FC CL + ++ CP C A
Sbjct: 218 CFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRA 259
>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2;
Provisional.
Length = 193
Score = 32.4 bits (73), Expect = 0.011
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 15/56 (26%)
Query: 27 CPSCKVKRKDAVLTKCFHVFCWDCLR----TRYETRQR-----------KCPKCNA 67
C C + +D V+T C H+FCW C+ +RQR KCP C +
Sbjct: 21 CNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKS 76
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 31.9 bits (72), Expect = 0.019
Identities = 16/66 (24%), Positives = 24/66 (36%), Gaps = 3/66 (4%)
Query: 6 QAGTLDEVMLEEIREYKETLTCPSCK---VKRKDAVLTKCFHVFCWDCLRTRYETRQRKC 62
G+L + +E E + + C C +K + C H F C+ KC
Sbjct: 305 TKGSLKPLSIERAVEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKC 364
Query: 63 PKCNAA 68
P C A
Sbjct: 365 PVCRTA 370
>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11
RING-H2 finger. Apc11 is one of the subunits of the
anaphase-promoting complex or cyclosome. The APC
subunits are cullin family proteins with ubiquitin
ligase activity. Polyubiquitination marks proteins for
degradation by the 26S proteasome and is carried out by
a cascade of enzymes that includes ubiquitin-activating
enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and
ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and
is responsible for recruiting E2s to the APC and for
mediating the subsequent transfer of ubiquitin to APC
substrates in vivo. In Saccharomyces cerevisiae this
RING-H2 finger protein defines the minimal ubiquitin
ligase activity of the APC, and the integrity of the
RING-H2 finger is essential for budding yeast cell
viability.
Length = 85
Score = 30.1 bits (68), Expect = 0.035
Identities = 18/48 (37%), Positives = 19/48 (39%), Gaps = 4/48 (8%)
Query: 26 TCPSCKVKRKDA--VLTKCFHVFCWDCLRTRYETRQRK--CPKCNAAF 69
TCP CK D V KC H F C+ T K CP C F
Sbjct: 34 TCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMCRQTF 81
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 29.3 bits (66), Expect = 0.040
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 34 RKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNA 67
++ V+ C HVF +CL ++ CP C A
Sbjct: 13 GEEVVVLPCGHVFHKECLD-KWLRSSNTCPLCRA 45
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 30.9 bits (70), Expect = 0.041
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 38 VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAF 69
+L+ C HVFC +C+ ++ + CP C F
Sbjct: 196 ILSNCNHVFCIECI-DIWKKEKNTCPVCRTPF 226
>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation
motif. This zinc-finger is the dimerisation motif for
LisH proteins, and is also a typical RING-type of plant
ubiquitin ligases.
Length = 55
Score = 28.8 bits (65), Expect = 0.061
Identities = 13/54 (24%), Positives = 17/54 (31%), Gaps = 5/54 (9%)
Query: 15 LEEIREYKETLTCPSCKVKRKDA----VLTKCFHVFCWDCLRT-RYETRQRKCP 63
L + CP K D V+ C HV+ L + KCP
Sbjct: 1 LPYAHHFHSIFVCPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGGKFKCP 54
>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING
and CCCH-type Zn-fingers [General function prediction
only].
Length = 259
Score = 30.0 bits (67), Expect = 0.087
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 5 EQAGTLDEVMLEEIREYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPK 64
E +E + K C CK + V+T+C H FC C +Y +K +
Sbjct: 177 EWNAEYEEAPVISGPGEKIPFLCGICKKDYESPVVTECGHSFCSLCAIRKY----QKGDE 232
Query: 65 C 65
C
Sbjct: 233 C 233
>gnl|CDD|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional.
Length = 242
Score = 28.5 bits (63), Expect = 0.28
Identities = 16/41 (39%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 34 RKDAVLTKCFHVFCWDCL----RTRYET-RQRKCPKCNAAF 69
R +L C H+FC C+ RTR ET CP C F
Sbjct: 189 RYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRF 229
>gnl|CDD|227539 COG5214, POL12, DNA polymerase alpha-primase complex,
polymerase-associated subunit B [DNA replication,
recombination, and repair].
Length = 581
Score = 28.4 bits (63), Expect = 0.33
Identities = 4/25 (16%), Positives = 7/25 (28%)
Query: 6 QAGTLDEVMLEEIREYKETLTCPSC 30
L E+ + I + P
Sbjct: 363 PDSMLKELFIPRITPILDRNAGPKA 387
>gnl|CDD|234734 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
Length = 943
Score = 28.1 bits (64), Expect = 0.44
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 12 EVMLEEIREYKETLTCPSCKVKR-KDAVL 39
E + EE+ +Y CPSCK KR K L
Sbjct: 394 EYVREELEKYMSERPCPSCKGKRLKPEAL 422
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 28.0 bits (62), Expect = 0.49
Identities = 15/62 (24%), Positives = 20/62 (32%), Gaps = 1/62 (1%)
Query: 4 IEQAGTLDEVMLEEIREYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCP 63
EQ D + E P + C H+ CL+ E RQ+ CP
Sbjct: 280 EEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE-RQQTCP 338
Query: 64 KC 65
C
Sbjct: 339 IC 340
>gnl|CDD|233062 TIGR00630, uvra, excinuclease ABC, A subunit. This family is a
member of the ABC transporter superfamily of proteins of
which all members for which functions are known except
the UvrA proteins are involved in the transport of
material through membranes. UvrA orthologs are involved
in the recognition of DNA damage as a step in nucleotide
excision repair. 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 = 925
Score = 27.7 bits (62), Expect = 0.59
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 9 TLDEVMLEEIREYKETLTCPSCKVKR 34
T E M E + ++ CPSC R
Sbjct: 390 TESESMREYLEKFMSERPCPSCGGTR 415
>gnl|CDD|235198 PRK04011, PRK04011, peptide chain release factor 1; Provisional.
Length = 411
Score = 27.5 bits (62), Expect = 0.63
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 13/53 (24%)
Query: 16 EEIREYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAA 68
E++R+ + T CP+C + + V + R E ++ CPKC +
Sbjct: 320 EDLRKDRVTYKCPNCGYEEEKTV-------------KRREELPEKTCPKCGSE 359
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
This family consists of the archaeal A' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 867
Score = 27.4 bits (61), Expect = 0.70
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 2 KKIEQAGTLDEVMLEEIREY-KETLTCPSCKVKRKDAVLTKCFH 44
K E+ G L ++E+I + + + CP C ++K K +
Sbjct: 118 KLKEEGGDLASTLIEKIVKEAAKRMKCPHCGEEQKKIKFEKPTY 161
>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 = 27.3 bits (60), Expect = 0.83
Identities = 15/63 (23%), Positives = 22/63 (34%), Gaps = 8/63 (12%)
Query: 20 EYKETLTCPSCKVKR------KDAVLTKCFHVFCWDCLRTRYETRQRKCPK--CNAAFGA 71
E E CP CK R K + +C+H C C+ + +CP C
Sbjct: 6 EEMEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRK 65
Query: 72 NDY 74
+
Sbjct: 66 IKF 68
>gnl|CDD|223256 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication,
recombination, and repair].
Length = 935
Score = 27.2 bits (61), Expect = 0.90
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 12 EVMLEEIREYKETLTCPSCKVKR 34
E + EE+ +Y CPSCK R
Sbjct: 386 ESIREELEKYMSEKPCPSCKGTR 408
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 25.4 bits (56), Expect = 1.3
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 23 ETLTCPSCKVKRKDAVLTKCFH-VFCWDCLRTRYETRQRKCPKCNA 67
E C C + ++ V C H C +C + ++KCP C
Sbjct: 1 EDDLCVICLERPRNVVFLPCGHLCLCEECAKRLR--SKKKCPICRQ 44
>gnl|CDD|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
Gram-positive type. This model describes a polypeptide
chain of DNA polymerase III. Full-length homologs of
this protein are restricted to the Gram-positive
lineages, including the Mycoplasmas. This protein is
designated alpha chain and given the gene symbol polC,
but is not a full-length homolog of other polC genes.
The N-terminal region of about 200 amino acids is rich
in low-complexity sequence, poorly alignable, and not
included n this model [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1213
Score = 26.6 bits (59), Expect = 1.3
Identities = 9/43 (20%), Positives = 15/43 (34%), Gaps = 10/43 (23%)
Query: 27 CPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAF 69
CP+CK + + ++ + CPKC A
Sbjct: 686 CPNCKY----------SEFITDGSVGSGFDLPDKDCPKCGAPL 718
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 26.5 bits (59), Expect = 1.3
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 6 QAGTLDEVMLEEIREYKETLTCPSCKVKRK 35
L+E ML + E++E TC C K
Sbjct: 122 SQAGLEEEMLPIMNEFREIETCVECSAKTL 151
>gnl|CDD|213380 cd12195, CIPK_C, C-terminal regulatory domain of Calcineurin B-Like
(CBL)-interacting protein kinases. CIPKs are
serine/threonine protein kinases (STKs), catalyzing the
transfer of the gamma-phosphoryl group from ATP to S/T
residues on protein substrates. They comprise a unique
family in higher plants of proteins that interact with
the calcineurin B-like (CBL) calcium sensors to form a
signaling network that decode specific calcium signals
triggered by a variety of environmental stimuli
including salinity, drought, cold, light, and mechanical
perturbation, among others. The specificity of the
response relies on differences in expression and
localization of both CBLs and CIPKs, as well as on the
interaction specificity of CBL-CIPK combinations. There
are 25, 30, and 43 CIPK genes identified in the
Arabidopsis thaliana, Oryza sativa, and Zea mays
genomes, respectively. The founding member of the CIPK
family is Arabidopsis thaliana CIPK24, also called SOS2
(Salt Overlay Sensitive 2). CIPKs contain an N-terminal
catalytic kinase domain and a C-terminal regulatory
domain that contains the FISL (also called NAF for
Asn-Ala-Phe) and PPI-binding motifs, which are involved
in the interaction with CBLs and PP2C-type protein
phosphatases, respectively. Studies using SOS2, SOS3,
and ABI2 phosphatase show that the binding of CBL and
PP2C-type protein phosphatase to CIPK is mutually
exclusive. The binding of CBL to CIPK is inhibitory to
kinase activity.
Length = 116
Score = 26.4 bits (59), Expect = 1.4
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 34 RKDAVLTKCFHVFCWDCLR 52
+K A T +H F D LR
Sbjct: 94 KKSAGDTLEYHKFWKDLLR 112
>gnl|CDD|218188 pfam04641, Rtf2, Replication termination factor 2. It is vital for
effective cell-replication that replication is not
stalled at any point by, for instance, damaged bases.
Rtf2 stabilizes the replication fork stalled at the
site-specific replication barrier RTS1 by preventing
replication restart until completion of DNA synthesis by
a converging replication fork initiated at a flanking
origin. The RTS1 element terminates replication forks
that are moving in the cen2-distal direction while
allowing forks moving in the cen2-proximal direction to
pass through the region. Rtf2 contains a C2HC2 motif
related to the C3HC4 RING-finger motif, and would appear
to fold up, creating a RING finger-like structure but
forming only one functional Zn2+ ion-binding site.
Length = 254
Score = 26.5 bits (59), Expect = 1.5
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 33 KRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGAND 73
K K L C VF L+ E + + CP C + D
Sbjct: 121 KYKFVALWPCGCVFSEKALK---EVKSKVCPVCGKPYSEED 158
>gnl|CDD|161792 TIGR00262, trpA, tryptophan synthase, alpha subunit. Tryptophan
synthase catalyzes the last step in the biosynthesis of
tryptophan. The alpha chain is responsible for the aldol
cleavage of indoleglycerol phosphate to indole and
glyceraldehyde 3-phosphate. In bacteria and plants each
domain is found on a separate subunit (alpha and beta
chains), while in fungi the two domains are fused
together on a single multifunctional protein. The
signature pattern for trpA contains three conserved
acidic residues
[LIVM]-E-[LIVM]-G-x(2)-[FYC]-[ST]-[DE]-[PA]-[LIVMY]-
[AGLI]-[DE]-G and this is located between residues 43-58
of the model. The Sulfolobus solfataricus trpA is known
to be quite divergent from other known trpA sequences
[Amino acid biosynthesis, Aromatic amino acid family].
Length = 256
Score = 26.2 bits (58), Expect = 1.6
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 2 KKIEQAGTLDEVMLEEIREYKETL 25
K IE+ E ML+ + E+ + L
Sbjct: 232 KIIEENLNTPEKMLQALEEFVQNL 255
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1066
Score = 26.2 bits (59), Expect = 2.1
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 13/38 (34%)
Query: 1 MKKIEQAG-------------TLDEVMLEEIREYKETL 25
M+ IE+AG TL E ++EEIREY + L
Sbjct: 774 MEHIEEAGVHSGDSACSLPPQTLSEEIIEEIREYTKKL 811
>gnl|CDD|215621 PLN03188, PLN03188, kinesin-12 family protein; Provisional.
Length = 1320
Score = 26.1 bits (57), Expect = 2.2
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 12 EVMLEEIREYKETLTC---PSCKVKRKDAVLTK 41
EV+LEEI++ + L S RK L K
Sbjct: 989 EVLLEEIQDLRSQLQYYIDSSLPSARKRNSLLK 1021
>gnl|CDD|232977 TIGR00440, glnS, glutaminyl-tRNA synthetase. This protein is a
relatively rare aminoacyl-tRNA synthetase, found in the
cytosolic compartment of eukaryotes, in E. coli and a
number of other Gram-negative Bacteria, and in
Deinococcus radiodurans. In contrast, the pathway to
Gln-tRNA in mitochondria, Archaea, Gram-positive
Bacteria, and a number of other lineages is by
misacylation with Glu followed by transamidation to
correct the aminoacylation to Gln. This enzyme is a
class I tRNA synthetase (hit by the pfam model
tRNA-synt_1c) and is quite closely related to
glutamyl-tRNA synthetases [Protein synthesis, tRNA
aminoacylation].
Length = 522
Score = 25.3 bits (55), Expect = 3.8
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 10 LDEVMLEEIREYKETLTCPSCKVKRKD 36
+DE+ EEIREY+ TLT P +D
Sbjct: 95 VDELTPEEIREYRGTLTDPGKNSPYRD 121
>gnl|CDD|233030 TIGR00575, dnlj, DNA ligase, NAD-dependent. All proteins in this
family with known functions are NAD-dependent DNA
ligases. Functions of these proteins include DNA repair,
DNA replication, and DNA recombination. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). The member of this
family from Treponema pallidum differs in having three
rather than just one copy of the BRCT (BRCA1 C Terminus)
domain (pfam00533) at the C-terminus. It is included in
the seed [DNA metabolism, DNA replication,
recombination, and repair].
Length = 652
Score = 25.3 bits (56), Expect = 4.1
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 12 EVMLE----EIREYKETLTCPSCK---VKRKDAVLTKCFHVFC 47
V+LE R + CPSC VK ++ + +C ++ C
Sbjct: 376 RVLLEKRTGSERPIRFPTHCPSCGSPLVKIEEEAVIRCPNLNC 418
>gnl|CDD|150144 pfam09371, Tex_N, Tex-like protein N-terminal domain. This
presumed domain is found at the N-terminus of
Bordetella pertussis tex. This protein defines a novel
family of prokaryotic transcriptional accessory
factors.
Length = 193
Score = 24.7 bits (55), Expect = 5.2
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 5 EQAGTLDEVMLEEIREYKETLTCPSCKV-KRKDAVL 39
E G LDEV L EI E L ++ KRK+ +L
Sbjct: 34 EATGGLDEVQLREIEERLTYLR----ELEKRKETIL 65
>gnl|CDD|235424 PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional.
Length = 554
Score = 25.1 bits (56), Expect = 5.3
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 16 EEIREYKETLTCP 28
EEIREY+ TLT P
Sbjct: 130 EEIREYRGTLTEP 142
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
0.325 0.137 0.449
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,926,725
Number of extensions: 282623
Number of successful extensions: 581
Number of sequences better than 10.0: 1
Number of HSP's gapped: 575
Number of HSP's successfully gapped: 61
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.2 bits)