RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14597
(191 letters)
>gnl|CDD|216356 pfam01196, Ribosomal_L17, Ribosomal protein L17.
Length = 97
Score = 42.0 bits (100), Expect = 1e-05
Identities = 28/102 (27%), Positives = 46/102 (45%), Gaps = 20/102 (19%)
Query: 37 LRSIVTALLKYERIEVYHYDGDEAR-------------DTHKETMDMADFWIEEKNIVHK 83
LR++ T+L+++ERIE E R D H ++ ++ +K +V K
Sbjct: 2 LRNLATSLIRHERIETTLAKAKELRPYAEKLITLAKKGDLHARRQALS--FLRDKELVKK 59
Query: 84 LFKVLVPRFQNTTVSYTRAYNAPIPHATPEKSDLSFHSVIEL 125
LF L PR+ + YTR P + D + ++IEL
Sbjct: 60 LFDELAPRYADRNGGYTRIIKLG-----PRRGDNAPMAIIEL 96
>gnl|CDD|129169 TIGR00059, L17, ribosomal protein L17. Eubacterial and
mitochondrial. The mitochondrial form, from yeast,
contains an additional 110 amino acids C-terminal to the
region found by this model [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 112
Score = 42.4 bits (100), Expect = 1e-05
Identities = 30/104 (28%), Positives = 50/104 (48%), Gaps = 16/104 (15%)
Query: 33 RVKKLRSIVTALLKYERIEVYHYDGDEARDTHKETMDMA---DF--------WIEEKNIV 81
R LR++ +AL+++E+I+ E R ++ + +A +F +I K IV
Sbjct: 12 RKALLRNLASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNRREAKAYIRNKEIV 71
Query: 82 HKLFKVLVPRFQNTTVSYTRAYNAPIPHATPEKSDLSFHSVIEL 125
HKLF + PR+ YTR I P + D + ++IEL
Sbjct: 72 HKLFSEIAPRYAQRPGGYTR-----ILKLGPRRGDAAEMAIIEL 110
>gnl|CDD|223281 COG0203, RplQ, Ribosomal protein L17 [Translation, ribosomal
structure and biogenesis].
Length = 116
Score = 42.2 bits (100), Expect = 1e-05
Identities = 29/105 (27%), Positives = 47/105 (44%), Gaps = 18/105 (17%)
Query: 33 RVKKLRSIVTALLKYERIEVYHYDGDEARDTHKETM-------DMAD-----FWIEEKNI 80
R LR++ T+L+++ERIE E R E + D+A+ + +K+
Sbjct: 17 RKAMLRNLATSLIEHERIETTLPKAKELR-RVVEKLITLAKKGDLANRRLAFARLRDKDA 75
Query: 81 VHKLFKVLVPRFQNTTVSYTRAYNAPIPHATPEKSDLSFHSVIEL 125
V KLF + PR+ YTR I + D + ++IEL
Sbjct: 76 VKKLFDEIAPRYAERNGGYTR-----ILKLGFRRGDNAPMAIIEL 115
>gnl|CDD|235522 PRK05591, rplQ, 50S ribosomal protein L17; Validated.
Length = 113
Score = 36.6 bits (86), Expect = 0.001
Identities = 34/120 (28%), Positives = 50/120 (41%), Gaps = 24/120 (20%)
Query: 20 KHRRL-RNPEGPQGRVKKLRSIVTALLKYERIEVYHYDGDEAR-------------DTHK 65
K R+L R R LR++ T+L+++ERIE E R D H
Sbjct: 3 KGRKLGRTSSH---RKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHA 59
Query: 66 ETMDMADFWIEEKNIVHKLFKVLVPRFQNTTVSYTRAYNAPIPHATPEKSDLSFHSVIEL 125
A + +K VHKLF + PR+ + YTR I + D + ++IEL
Sbjct: 60 RRQAFA--RLRDKEAVHKLFDEIAPRYADRNGGYTR-----ILKLGFRRGDNAPMAIIEL 112
>gnl|CDD|236848 PRK11107, PRK11107, hybrid sensory histidine kinase BarA;
Provisional.
Length = 919
Score = 30.6 bits (70), Expect = 0.47
Identities = 19/41 (46%), Positives = 20/41 (48%), Gaps = 16/41 (39%)
Query: 144 IQNVLLDEAKKEYRAQKYAEIAQDLESRANADSSAKSEELA 184
IQNV LD AKK RAQ+ A I KSE LA
Sbjct: 274 IQNVELDLAKK--RAQEAARI--------------KSEFLA 298
>gnl|CDD|219788 pfam08314, Sec39, Secretory pathway protein Sec39. Mnaimneh et al
identified Sec39p as a protein involved in ER-Golgi
transport in a large scale promoter shut down analysis
of essential yeast genes. Kraynack et al. (2005) showed
that Sec39p (Dsl3p) is required for Golgi-ER retrograde
transport and is part of a very stable protein complex
that also includes Dsl1p (in mammals ZW10), Tip20p
(Rint-1) and the ER localized Q-SNARE proteins Ufe1p
(syntaxin-18), Sec20p and Use1p. This was confirmed in a
genome-wide analysis of protein complexes by Gavin et al
(2006).
Length = 675
Score = 30.5 bits (69), Expect = 0.55
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 116 DLSFHSVIELRGNPFPPLVQRAVDSRLHIQNVLLDEAKKEYR-AQKYAEIAQDLESRANA 174
LS +S++ G PF P+ R D L + + +L++ K Y K +I ++L
Sbjct: 494 ALSRYSLVLKPGEPFKPVQIRVHDDPLSLISKVLEQNPKAYTDLDKLLDILKNLVEAGQP 553
Query: 175 DSSAKSEELAQN 186
DS + E A+
Sbjct: 554 DSEEEQVETAER 565
>gnl|CDD|117463 pfam08896, DUF1842, Domain of unknown function (DUF1842). This
domain is found at the N-terminus of proteins that are
functionally uncharacterized.
Length = 114
Score = 26.9 bits (60), Expect = 3.3
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 3/34 (8%)
Query: 118 SFHSVIELRGNPFPPLVQRAVDSRLHIQNVLLDE 151
++ L GNP P V LH+ LLD
Sbjct: 67 ETQILVTLDGNPGGPTSNSLVTFHLHL---LLDG 97
>gnl|CDD|235660 PRK05976, PRK05976, dihydrolipoamide dehydrogenase; Validated.
Length = 472
Score = 27.9 bits (63), Expect = 3.5
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 31 QGRVKKLRSIVTALLKYERIEVYHYDG 57
G V +L V ALLK +I+V+H G
Sbjct: 88 DGIVDRLTKGVAALLKKGKIDVFHGIG 114
>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed.
Length = 1228
Score = 27.9 bits (63), Expect = 3.6
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 66 ETMDMADFWIEEKNIVHKLF--KVLVPRFQNTTVSYT 100
ETMD A FW ++IV + K+ FQ TT+S T
Sbjct: 235 ETMDFAQFWAAYEDIVRRARDGKLTADDFQGTTISLT 271
>gnl|CDD|176913 cd08904, START_STARD6-like, Lipid-binding START domain of mammalian
STARD6 and related proteins. This subgroup includes the
steroidogenic acute regulatory protein (StAR)-related
lipid transfer (START) domains of mammalian STARD6 and
related domains. It belongs to the START domain family,
and in turn to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. STARD6 is expressed in male germ cells of normal
rats, and in the steroidogenic Leydig cells of
perinatal hypothyroid testes. It may play a pivotal role
in the steroidogenesis as well as in the spermatogenesis
of normal rats. STARD6 has also been detected in the rat
nervous system, and may participate in neurosteroid
synthesis.
Length = 204
Score = 27.2 bits (60), Expect = 5.0
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 8/54 (14%)
Query: 96 TVSYTRAYN-------APIPHATPEKSDLSFHSVIELRGNPFPPLVQRAVDSRL 142
+ +Y R YN +P+P P S L ELRGN ++++ + + L
Sbjct: 140 SSNYIRGYNHPCGYVCSPLPE-NPAYSKLVMFVQPELRGNLSRSVIEKTMPTNL 192
>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 = 26.9 bits (59), Expect = 7.4
Identities = 10/40 (25%), Positives = 17/40 (42%)
Query: 148 LLDEAKKEYRAQKYAEIAQDLESRANADSSAKSEELAQNN 187
L+D + E + +KY E+ QD + + Q N
Sbjct: 123 LIDVSLTEEKVKKYEEMNQDSILNNLERPTPEVMPGKQKN 162
>gnl|CDD|239272 cd02974, AhpF_NTD_N, Alkyl hydroperoxide reductase F subunit (AhpF)
N-terminal domain (NTD) family, N-terminal TRX-fold
subdomain; AhpF is a homodimeric flavoenzyme which
catalyzes the NADH-dependent reduction of the
peroxiredoxin AhpC, which in turn catalyzes the
reduction of hydrogen peroxide and organic
hydroperoxides. AhpF contains an NTD forming two
contiguous TRX-fold subdomain similar to Pyrococcus
furiosus protein disulfide oxidoreductase (PfPDO). It
also contains a catalytic core similar to TRX reductase
containing FAD and NADH binding domains with an active
site disulfide. The proposed mechanism of action of AhpF
is similar to a TRX/TRX reductase system. The flow of
reducing equivalents goes from NADH -> catalytic core of
AhpF -> NTD of AhpF -> AhpC -> peroxide substrates. The
N-terminal TRX-fold subdomain of AhpF NTD is redox
inactive, but is proposed to contain an important
residue that aids in the catalytic function of the
redox-active CXXC motif contained in the C-terminal
TRX-fold subdomain.
Length = 94
Score = 25.6 bits (57), Expect = 7.9
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 148 LLDEAKKEYRAQKYAEIAQDLESRANADSSAKSEEL 183
+LD K+ + +E A+ D S KS EL
Sbjct: 1 MLDANLKQQLKAYLERLENPVELVASLDDSEKSAEL 36
>gnl|CDD|191530 pfam06454, DUF1084, Protein of unknown function (DUF1084). This
family consists of several hypothetical plant specific
proteins of unknown function.
Length = 280
Score = 26.6 bits (59), Expect = 8.1
Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 2/22 (9%)
Query: 25 RNPEGPQGRVKKLRSI--VTAL 44
R P +GR KKL + VTA+
Sbjct: 192 RFPIESKGRRKKLHEVGSVTAI 213
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
0.315 0.130 0.366
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,620,965
Number of extensions: 894772
Number of successful extensions: 874
Number of sequences better than 10.0: 1
Number of HSP's gapped: 871
Number of HSP's successfully gapped: 37
Length of query: 191
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 100
Effective length of database: 6,901,388
Effective search space: 690138800
Effective search space used: 690138800
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: 56 (25.3 bits)