RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7641
(85 letters)
>gnl|CDD|237414 PRK13529, PRK13529, malate dehydrogenase; Provisional.
Length = 563
Score = 65.9 bits (162), Expect = 2e-14
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 11 DEQGFPSSQVNLRLHSILRQSM---GLAFSLRERQQLGIHGLMPPTIKNQDQQIEVCRES 67
DE+ LR ++L + G AF+ ER++ G+ GL+PP ++ ++Q E
Sbjct: 4 DEKKKRPLYTPLRGPALLNNPLLNKGTAFTEEEREEFGLEGLLPPAVETLEEQAERAYRQ 63
Query: 68 VRRFQEDLNKFTYLSELQ 85
+ DL K YL LQ
Sbjct: 64 YQSKPTDLEKHIYLRNLQ 81
>gnl|CDD|215594 PLN03129, PLN03129, NADP-dependent malic enzyme; Provisional.
Length = 581
Score = 63.4 bits (155), Expect = 2e-13
Identities = 21/53 (39%), Positives = 35/53 (66%)
Query: 33 GLAFSLRERQQLGIHGLMPPTIKNQDQQIEVCRESVRRFQEDLNKFTYLSELQ 85
GLAF+ ER +LG+ GL+PP + +Q+ Q++ E++R + L K+ L +LQ
Sbjct: 54 GLAFTETERDRLGLRGLLPPAVLSQELQVKRFMENLRALESPLAKYRALMDLQ 106
>gnl|CDD|240357 PTZ00317, PTZ00317, NADP-dependent malic enzyme; Provisional.
Length = 559
Score = 63.1 bits (154), Expect = 2e-13
Identities = 20/53 (37%), Positives = 32/53 (60%)
Query: 33 GLAFSLRERQQLGIHGLMPPTIKNQDQQIEVCRESVRRFQEDLNKFTYLSELQ 85
G AF+ ER+ LGI GL+PPT++ +QQ+E R + +NK+ +L +
Sbjct: 31 GTAFTAEEREHLGIEGLLPPTVETLEQQVERLWTQFNRIETPINKYQFLRNIH 83
>gnl|CDD|237002 PRK11857, PRK11857, dihydrolipoamide acetyltransferase; Reviewed.
Length = 306
Score = 27.1 bits (60), Expect = 0.96
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 7/33 (21%)
Query: 44 LGI-----HGLMPPTIKNQDQ--QIEVCRESVR 69
LGI GLM P IKN + +E+ +E R
Sbjct: 171 LGIAVDTEAGLMVPVIKNAQKLSIVEIAKEISR 203
>gnl|CDD|117602 pfam09036, Bcr-Abl_Oligo, Bcr-Abl oncoprotein oligomerisation
domain. The Bcr-Abl oncoprotein oligomerisation domain
consists of a short N-terminal helix (alpha-1), a
flexible loop and a long C-terminal helix (alpha-2).
Together these form an N-shaped structure, with the
loop allowing the two helices to assume a parallel
orientation. The monomeric domains associate into a
dimer through the formation of an antiparallel coiled
coil between the alpha-2 helices and domain swapping of
two alpha-1 helices, where one alpha-1 helix swings
back and packs against the alpha-2 helix from the
second monomer. Two dimers then associate into a
tetramer. The oligomerisation domain is essential for
the oncogenicity of the Bcr-Abl protein.
Length = 71
Score = 26.0 bits (57), Expect = 1.3
Identities = 8/25 (32%), Positives = 20/25 (80%)
Query: 53 TIKNQDQQIEVCRESVRRFQEDLNK 77
++ + +Q++E C+ S+RR ++++NK
Sbjct: 26 SVGDIEQELERCKASIRRLEQEVNK 50
>gnl|CDD|232888 TIGR00233, trpS, tryptophanyl-tRNA synthetase. This model
represents tryptophanyl-tRNA synthetase. Some members of
the family have a pfam00458 domain amino-terminal to the
region described by this model [Protein synthesis, tRNA
aminoacylation].
Length = 327
Score = 26.5 bits (59), Expect = 1.4
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 57 QDQQIEVCRESVRRFQEDLNKFTYLSEL 84
QDQ +E+ R+ RF + F E
Sbjct: 148 QDQHLELTRDLAERFNKKFKNFFPKPES 175
>gnl|CDD|214693 smart00488, DEXDc2, DEAD-like helicases superfamily.
Length = 289
Score = 26.2 bits (58), Expect = 1.8
Identities = 12/66 (18%), Positives = 24/66 (36%), Gaps = 5/66 (7%)
Query: 11 DEQGFPSSQVNLRLHSILRQSMG-----LAFSLRERQQLGIHGLMPPTIKNQDQQIEVCR 65
+ + S + + + +L + L SL R+ L ++ + +N EVCR
Sbjct: 86 QKVEYESDEESEKQAQLLHELGREKPKVLGLSLTSRKNLCLNPEVRTLKQNGLVVDEVCR 145
Query: 66 ESVRRF 71
Sbjct: 146 SLTASK 151
>gnl|CDD|132274 TIGR03230, lipo_lipase, lipoprotein lipase. Members of this
protein family are lipoprotein lipase (EC 3.1.1.34), a
eukaryotic triacylglycerol lipase active in plasma and
similar to pancreatic and hepatic triacylglycerol
lipases (EC 3.1.1.3). It is also called clearing factor.
It cleaves chylomicron and VLDL triacylglycerols; it
also has phospholipase A-1 activity.
Length = 442
Score = 26.4 bits (58), Expect = 2.0
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 9 IEDEQGFPSSQVNLRLHSILRQSMGLAFSLRERQQLGIHGLMP--PTIKNQDQQI 61
+++E +P V+L +S+ G+A SL + + I GL P PT + D
Sbjct: 110 MQEEFNYPWDNVHLLGYSLGAHVAGIAGSLTKHKVNRITGLDPAGPTFEYADAPS 164
>gnl|CDD|235681 PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 975
Score = 25.9 bits (58), Expect = 2.5
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 12/44 (27%)
Query: 42 QQLGIHGLMPPTIKNQ------DQQIEVCRESVRRFQEDLNKFT 79
++LGI G K ++ E CRESV R+ ++ ++T
Sbjct: 100 KELGISG------KKDIEEYGIEKFNEKCRESVLRYTDEWEEYT 137
>gnl|CDD|237062 PRK12328, nusA, transcription elongation factor NusA;
Provisional.
Length = 374
Score = 25.3 bits (56), Expect = 4.2
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 59 QQIEVCRESVRRFQEDLNKFTYLSE 83
Q+IEV + R Q D KF LSE
Sbjct: 59 QKIEVVADDDERLQNDPEKFISLSE 83
>gnl|CDD|143399 cd07080, ALDH_Acyl-CoA-Red_LuxC, Acyl-CoA reductase LuxC. Acyl-CoA
reductase, LuxC, (EC=1.2.1.50) is the fatty acid
reductase enzyme responsible for synthesis of the
aldehyde substrate for the luminescent reaction
catalyzed by luciferase. The fatty acid reductase, a
luminescence-specific, multienzyme complex (LuxCDE),
reduces myristic acid to generate the long chain fatty
aldehyde required for the luciferase-catalyzed reaction
resulting in the emission of blue-green light.
Mutational studies of conserved cysteines of LuxC
revealed that the cysteine which aligns with the
catalytic cysteine conserved throughout the ALDH
superfamily is the LuxC acylation site. This CD is
composed of mainly bacterial sequences but also includes
a few archaeal sequences similar to the Methanospirillum
hungateiacyl acyl-CoA reductase RfbN.
Length = 422
Score = 25.3 bits (56), Expect = 4.4
Identities = 8/27 (29%), Positives = 11/27 (40%)
Query: 24 LHSILRQSMGLAFSLRERQQLGIHGLM 50
L IL + +G L E G G +
Sbjct: 82 LERILERELGSPGILDEWVPPGRGGYI 108
>gnl|CDD|240427 PTZ00470, PTZ00470, glycoside hydrolase family 47 protein;
Provisional.
Length = 522
Score = 24.7 bits (54), Expect = 6.7
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 11 DEQGFPSSQVNLRLHSILRQS-MGLAFSLRE 40
++ GFP+S++NL G L E
Sbjct: 193 EDTGFPASEINLATGRKSYPGWAGGCSILSE 223
>gnl|CDD|198425 cd10027, UDG_F1, Family 1 of Uracil-DNA glycosylase (UDG)
enzymes. Uracil-DNA glycosylases (UDGs) are DNA repair
enzymes that catalyze the removal of mismatched uracil
from DNA to initiate DNA base excision repair pathway.
Family 1 enzymes are active against uracil in both
ssDNA and dsDNA, and recognize uracil explicitly in an
extrahelical conformation via a combination of protein
and bound-water interactions. Family 1 enzymes are
present in Eubacteria, Eukarya and in some eukaryotic
viruses. Members of Family 1 are the most efficient
Uracil-DNA glycosylases. Uracil in DNA can arise as a
result of mis-incorporation of dUMP residues by DNA
polymerase or deamination of cytosine. Uracil mispaired
with guanine in DNA is one of the major pro-mutagenic
events, causing G:C->A:T mutations. Thus, UDG is an
essential enzyme for maintaining the integrity of
genetic information. More than five UDG families have
been characterized so far; these families share similar
overall folds, and common active site motifs. However,
they may differ in substrate preferences.
Length = 201
Score = 24.8 bits (55), Expect = 7.0
Identities = 10/27 (37%), Positives = 17/27 (62%), Gaps = 6/27 (22%)
Query: 30 QSMGLAFSLRERQQLGIHGLMPPTIKN 56
Q+ GLAFS+ + +L PP+++N
Sbjct: 53 QAHGLAFSVPKGVKL------PPSLRN 73
>gnl|CDD|213904 TIGR04291, arsen_driv_ArsA, arsenical pump-driving ATPase. The
broader family (TIGR00345) to which the current family
belongs consists of transport-energizing ATPases,
including to TRC40/GET3 family involved in
post-translational insertion of protein C-terminal
transmembrane anchors into membranes from the cyotosolic
face. This family, however, is restricted to ATPases
that energize pumps that export arsenite (or
antimonite).
Length = 566
Score = 24.7 bits (54), Expect = 7.2
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 10/47 (21%)
Query: 42 QQLGIHGLMPPTIKNQD---QQIEVCRESVRRFQEDLNKFT-YLSEL 84
Q L I+G++PPT + D Q I +R Q+ L L+ L
Sbjct: 225 QYLVINGVLPPTEASDDPLAQAIY------KREQKALQHMPAILANL 265
>gnl|CDD|203679 pfam07544, Med9, RNA polymerase II transcription mediator complex
subunit 9. This family of Med9 proteins is conserved
in yeasts. It forms part of the middle region of
Mediator. Med9 has two functional domains. The
species-specific amino-terminal half (aa 1-63) plays a
regulatory role in transcriptional regulation, whereas
this well-conserved carboxy-terminal half (aa 64-149)
has a more fundamental function involved in direct
binding to the amino-terminal portions of Med4 and Med7
and the assembly of Med9 into the Middle module. Also,
some unidentified factor(s) in med9 extracts may impact
the binding of TFIID to the promoter.
Length = 83
Score = 23.7 bits (52), Expect = 9.2
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 53 TIKNQDQQIEVCRESVRRFQEDLNKF 78
+++ Q+ +IE E + R +E L KF
Sbjct: 53 SVEEQEAEIEELEEQIARKREVLQKF 78
>gnl|CDD|173472 PTZ00192, PTZ00192, 60S ribosomal protein L13; Provisional.
Length = 218
Score = 24.1 bits (52), Expect = 9.7
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 28 LRQSMGLAFSLRERQQLGIHGLMPPTI--------KNQDQQIEVCRESVRRFQEDLNKFT 79
++Q +G FSL E + G++ TI KN+ + E +V+R + ++K
Sbjct: 72 MKQRLGRGFSLAELKAAGLNPRFARTIGIRVDRRRKNKSE--EGMNVNVQRLKTYMSKLV 129
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
0.321 0.138 0.386
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,329,089
Number of extensions: 345018
Number of successful extensions: 311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 27
Length of query: 85
Length of database: 10,937,602
Length adjustment: 53
Effective length of query: 32
Effective length of database: 8,586,840
Effective search space: 274778880
Effective search space used: 274778880
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: 53 (24.3 bits)