RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10035
(102 letters)
>gnl|CDD|215364 PLN02678, PLN02678, seryl-tRNA synthetase.
Length = 448
Score = 88.6 bits (220), Expect = 4e-22
Identities = 34/71 (47%), Positives = 49/71 (69%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCSK 62
LD++LFR EKGGDPE +R++Q+ RF +VELVD+VI D +WRQ + + D+ K N +K
Sbjct: 2 LDINLFREEKGGDPELIRESQRRRFASVELVDEVIALDKEWRQRQFELDSLRKEFNKLNK 61
Query: 63 VIGEKMKAKEP 73
+ + AKE
Sbjct: 62 EVAKLKIAKED 72
>gnl|CDD|217020 pfam02403, Seryl_tRNA_N, Seryl-tRNA synthetase N-terminal domain.
This domain is found associated with the Pfam tRNA
synthetase class II domain (pfam00587) and represents
the N-terminal domain of seryl-tRNA synthetase.
Length = 108
Score = 66.8 bits (164), Expect = 6e-16
Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 2 VLDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCS 61
+LD+ L R +PE V++ + R +V VD+++E D + R+ + + + +N S
Sbjct: 1 MLDIKLIRE----NPEAVKEKLRKRGVDVLDVDELLELDEERRELQVELEELQAERNELS 56
Query: 62 KVIGEKMKAKE 72
K IG+ K KE
Sbjct: 57 KEIGKAKKKKE 67
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 57.2 bits (139), Expect = 4e-11
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCSK 62
LDL L R +P+ VR+ K R + VDK++E D + R+ + + +N SK
Sbjct: 2 LDLKLIRE----NPDAVREKLKKRGGDALDVDKLLELDEERRKLLRELEELQAERNELSK 57
Query: 63 VIGEKMKAKE 72
IG +K E
Sbjct: 58 EIGRALKRGE 67
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 48.1 bits (116), Expect = 7e-08
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCSK 62
LD+ L R +PE V++ R VD+++E D + R+ + + + +N SK
Sbjct: 2 LDIKLIRE----NPEAVKEALAKRGF-PLDVDELLELDEERRELQTELEELQAERNALSK 56
Query: 63 VIGEKMKAKE 72
IG+ + E
Sbjct: 57 EIGQAKRKGE 66
>gnl|CDD|232965 TIGR00414, serS, seryl-tRNA synthetase. This model represents
the seryl-tRNA synthetase found in most organisms. This
protein is a class II tRNA synthetase, and is
recognized by the pfam model tRNA-synt_2b. The
seryl-tRNA synthetases of two archaeal species,
Methanococcus jannaschii and Methanobacterium
thermoautotrophicum, differ considerably and are
included in a different model [Protein synthesis, tRNA
aminoacylation].
Length = 418
Score = 40.0 bits (94), Expect = 5e-05
Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFKNVEL-VDKVIENDLKWRQFRHKADNFNKFKNLCS 61
LD L R +P+ V+++ K R +V++ ++K+I D + ++ + + +N S
Sbjct: 2 LDRKLLR----NNPDLVKESLKARGLSVDIDLEKLIALDDERKKLLSEIEELQAKRNELS 57
Query: 62 KVIGEKMKAKEPVGDS 77
K IG+ K+ +
Sbjct: 58 KQIGKAKGQKKDKIEE 73
>gnl|CDD|130818 TIGR01757, Malate-DH_plant, malate dehydrogenase, NADP-dependent.
This model represents the NADP-dependent malate
dehydrogenase found in plants, mosses and green algae
and localized to the chloroplast. Malate dehydrogenase
converts oxaloacetate into malate, a critical step in
the C4 cycle which allows circumvention of the effects
of photorespiration. Malate is subsequenctly transported
from the chloroplast to the cytoplasm (and then to the
bundle sheath cells in C4 plants). The plant and moss
enzymes are light regulated via cysteine disulfide
bonds. The enzyme from Sorghum has been crystallized.
Length = 387
Score = 29.6 bits (66), Expect = 0.22
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 31 ELVDKVIENDLKWRQFRHKADNFNKFKNLCSKVIGEKMKAKEPVGDSSTLPGE 83
EL V +D + R D K K + +IGE A V + + LPGE
Sbjct: 335 ELATDVSMDDFLRERIRKSEDELLKEKECVAHLIGE-GNAYCAVPEDTMLPGE 386
>gnl|CDD|184228 PRK13671, PRK13671, hypothetical protein; Provisional.
Length = 298
Score = 29.3 bits (66), Expect = 0.31
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 17 EKVRKNQKDRFKNVELVDKVIENDLKWRQFRH-KADNFNKFKNLC 60
+ VR K++ + LV + IEN K ++ A N++ F N C
Sbjct: 235 KIVRNTSKEKLAKIWLVSEGIENLFK----KNINAPNYDSFVNKC 275
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 29.0 bits (65), Expect = 0.34
Identities = 11/53 (20%), Positives = 20/53 (37%)
Query: 31 ELVDKVIENDLKWRQFRHKADNFNKFKNLCSKVIGEKMKAKEPVGDSSTLPGE 83
E+V V +D + + K + + GE + + + LPGE
Sbjct: 391 EIVKDVEIDDYLRERIKKSEAELLAEKRCVAHLTGEGGAFCDLRPEDTMLPGE 443
>gnl|CDD|239453 cd03337, TCP1_gamma, TCP-1 (CTT or eukaryotic type II) chaperonin
family, gamma subunit. Chaperonins are involved in
productive folding of proteins. They share a common
general morphology, a double toroid of 2 stacked rings.
In contrast to bacterial group I chaperonins (GroEL),
each ring of the eukaryotic cytosolic chaperonin (CTT)
consists of eight different, but homologous subunits.
Their common function is to sequester nonnative proteins
inside their central cavity and promote folding by using
energy derived from ATP hydrolysis. The best studied in
vivo substrates of CTT are actin and tubulin.
Length = 480
Score = 27.6 bits (62), Expect = 1.1
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 72 EPVGDSST----LPGETLNVCWSVLKHALHPSL 100
E VGD +T L GE L V L+ +HP++
Sbjct: 84 EEVGDGTTSVIILAGEILAVAEPFLERGIHPTV 116
>gnl|CDD|182913 PRK11029, PRK11029, FtsH protease regulator HflC; Provisional.
Length = 334
Score = 27.4 bits (61), Expect = 1.4
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 22 NQKDRFKNVELVDKVIENDLKWR 44
NQ DRF E D ++++ +KWR
Sbjct: 74 NQADRFVTKEKKDLIVDSYIKWR 96
>gnl|CDD|235634 PRK05877, PRK05877, aminodeoxychorismate synthase component I;
Provisional.
Length = 405
Score = 27.0 bits (60), Expect = 1.6
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 14 GDPEKVRKNQKDRFKNVELVDKVIENDL 41
DP +R + KD +N+ +VD V NDL
Sbjct: 232 ADPSALRASAKDVAENIMIVDLV-RNDL 258
>gnl|CDD|185214 PRK15314, PRK15314, outer membrane protein RatB; Provisional.
Length = 2435
Score = 26.7 bits (58), Expect = 2.2
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 50 ADNFNKFKNLCSKVIGEKMKAKEPVGDSST---LPGETLNV 87
ADNF+ N +GE++ K V DS+T LP NV
Sbjct: 474 ADNFDSTVNAAKVKVGEEINMKITVTDSATNKPLPYRYFNV 514
>gnl|CDD|235689 PRK06069, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 577
Score = 26.2 bits (58), Expect = 3.9
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 5/40 (12%)
Query: 8 FRTEKGGDPEKVRKNQK--DRFKNVELVDK--VIENDLKW 43
FR E G E ++K +K +R+KNV + DK + DLK
Sbjct: 466 FRDESGLA-EALKKIKKLRERYKNVRIEDKSRIYNTDLKD 504
>gnl|CDD|215581 PLN03109, PLN03109, ETHYLENE-INSENSITIVE3-like3 protein;
Provisional.
Length = 599
Score = 25.6 bits (56), Expect = 6.4
Identities = 10/28 (35%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 47 RHKADNFNKFKNLC--SKVIGEKMKAKE 72
+H + +F+K + SK + +KM AKE
Sbjct: 247 KHMSPDFDKIRRHVRQSKCLQDKMTAKE 274
>gnl|CDD|197277 cd09180, PLDc_N_DEXD_b, N-terminal putative catalytic domain of
uncharacterized prokaryotic and archeal HKD family
nucleases fused to a DEAD/DEAH box helicase domain.
N-terminal putative catalytic domain of uncharacterized
prokaryotic and archeal HKD family nucleases fused to a
DEAD/DEAH box helicase domain. All members of this
subfamily are uncharacterized. Other characterized
members of the superfamily that have a related domain
architecture ( containing a DEAD/DEAH box helicase
domain), include the DNA/RNA helicase superfamily II
(SF2) and Res-subunit of type III restriction
endonucleases. In addition to the helicase-like region,
members of this subfamily also contain one copy of the
conserved HKD motif (H-x-K-x(4)-D, where x represents
any amino acid residue) in the N-terminal putative
catalytic domain. The HKD motif characterizes the
phospholipase D (PLD, EC 3.1.4.4) superfamily. A few
family members contain additional domains, like a
C-terminal peptidase S24-like domain.
Length = 142
Score = 25.0 bits (55), Expect = 7.2
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 26 RFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCSKVIG 65
+ NVE+ I N++K F KA F + S +IG
Sbjct: 67 DYDNVEVK---IYNNIKSESFHAKAYLFERETGYSSAIIG 103
>gnl|CDD|232931 TIGR00344, alaS, alanine--tRNA ligase. The model describes
alanine--tRNA ligase. This enzyme catalyzes the reaction
(tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
pyrophosphate + AMP) [Protein synthesis, tRNA
aminoacylation].
Length = 851
Score = 25.4 bits (56), Expect = 7.2
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 4/68 (5%)
Query: 6 DLFRTEKGGDPEKVRKNQ---KDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCSK 62
D+ + P+K+ + K K +E + I D K + + KA+ N K L
Sbjct: 715 DILKVTPNELPKKIERFFEEWKALQKELESLKLKI-ADQKIDELKDKAETINGVKVLVEV 773
Query: 63 VIGEKMKA 70
V + MK+
Sbjct: 774 VDAKDMKS 781
>gnl|CDD|222966 PHA03058, PHA03058, Hypothetical protein; Provisional.
Length = 124
Score = 24.8 bits (54), Expect = 7.9
Identities = 11/49 (22%), Positives = 17/49 (34%)
Query: 15 DPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCSKV 63
+ E V K+ + D K + +H+ N KNL S
Sbjct: 71 NTEYVDSLLSRAIKDFNVTDVTFGKVQKTIKRKHRFRNPKVLKNLSSSE 119
>gnl|CDD|233825 TIGR02344, chap_CCT_gamma, T-complex protein 1, gamma subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
gamma chain (part of a paralogous family) from animals,
plants, fungi, and other eukaryotes.
Length = 525
Score = 25.1 bits (55), Expect = 8.7
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 72 EPVGDSST----LPGETLNVCWSVLKHALHPSL 100
E VGD +T L GE L+V L+ +HP++
Sbjct: 84 EEVGDGTTSVIILAGEMLSVAEPFLEQNIHPTI 116
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
0.317 0.135 0.405
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,024,910
Number of extensions: 402304
Number of successful extensions: 402
Number of sequences better than 10.0: 1
Number of HSP's gapped: 401
Number of HSP's successfully gapped: 26
Length of query: 102
Length of database: 10,937,602
Length adjustment: 68
Effective length of query: 34
Effective length of database: 7,921,530
Effective search space: 269332020
Effective search space used: 269332020
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 (21.6 bits)
S2: 53 (24.1 bits)