RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12795
(121 letters)
>gnl|CDD|218318 pfam04898, Glu_syn_central, Glutamate synthase central domain. The
central domain of glutamate synthase connects the amino
terminal amidotransferase domain with the FMN-binding
domain and has an alpha / beta overall topology. This
domain appears to be a rudimentary form of the
FMN-binding TIM barrel according to SCOP.
Length = 288
Score = 153 bits (390), Expect = 1e-47
Identities = 53/108 (49%), Positives = 66/108 (61%), Gaps = 18/108 (16%)
Query: 1 MGNDAPLACLSEFQPLLYDYFKQLFAQLLPVLLSVTTMYCSLSLQVTNPPIDPFREKVVM 60
MG+D PLA LSE LLYDYFKQLFAQ VTNPPIDP RE++VM
Sbjct: 33 MGDDTPLAVLSEKPRLLYDYFKQLFAQ------------------VTNPPIDPIREEIVM 74
Query: 61 SLMCPIGPEANILEPSAKQCHRLFLPNPLLSLYDLEVIRLNTHRGWKV 108
SL +GPE N+LEP+ +Q RL L +P+LS +LE ++ G+K
Sbjct: 75 SLETYLGPEGNLLEPTPEQARRLKLDSPILSNSELEALKNLNEEGFKA 122
>gnl|CDD|236968 PRK11750, gltB, glutamate synthase subunit alpha; Provisional.
Length = 1485
Score = 98.8 bits (247), Expect = 3e-25
Identities = 38/91 (41%), Positives = 47/91 (51%), Gaps = 18/91 (19%)
Query: 1 MGNDAPLACLSEFQPLLYDYFKQLFAQLLPVLLSVTTMYCSLSLQVTNPPIDPFREKVVM 60
MG+D P+A LS +YDYF+Q FAQ VTNPPIDP RE VM
Sbjct: 489 MGDDTPMAVLSSQPRSIYDYFRQQFAQ------------------VTNPPIDPLREAHVM 530
Query: 61 SLMCPIGPEANILEPSAKQCHRLFLPNPLLS 91
SL IG E N+ + HR+ +P+LS
Sbjct: 531 SLATCIGREMNVFCETEGHAHRVIFKSPVLS 561
>gnl|CDD|205672 pfam13494, DUF4119, Domain of unknown function, B. Theta Gene
description (DUF4119). Based on Bacteroides
thetaiotaomicron gene BT_0594, a putative
uncharacterized protein. As seen in gene expression
experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22
31), it appears to be upregulated in the presence of
host or vs when in culture.
Length = 95
Score = 29.9 bits (67), Expect = 0.11
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 92 LYDLEVIRLNTHRGWKVMKVS 112
+ D ++ +N H G+K+M+ S
Sbjct: 75 IADWRILYINKHGGYKLMEFS 95
>gnl|CDD|234942 PRK01318, PRK01318, membrane protein insertase; Provisional.
Length = 521
Score = 27.5 bits (62), Expect = 1.6
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 18 YDYFKQLFAQLLPVLLSVTTMYCSLSLQVTNPPIDPFREKVVMSLMCPI 66
D + L LLP+L+ + TM+ L ++ P DP + K +M M P+
Sbjct: 430 PDPYFILHIGLLPILMGI-TMF--LQQKLNPTPTDPMQAK-IMKFM-PL 473
>gnl|CDD|220881 pfam10816, DUF2760, Domain of unknown function (DUF2760). This is
a bacterial family of uncharacterized proteins.
Length = 126
Score = 26.4 bits (59), Expect = 2.4
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 103 HRGWKVMKVSL 113
HRGWK +V L
Sbjct: 98 HRGWKATEVRL 108
>gnl|CDD|236777 PRK10857, PRK10857, DNA-binding transcriptional regulator IscR;
Provisional.
Length = 164
Score = 26.4 bits (58), Expect = 3.5
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 6 PLACLSEFQPLLYDYFKQLFAQL 28
PLA +SE Q + Y +QLF++L
Sbjct: 27 PLADISERQGISLSYLEQLFSRL 49
>gnl|CDD|132675 TIGR03636, L23_arch, archaeal ribosomal protein L23. This model
describes the archaeal ribosomal protein L23P and
rigorously excludes the bacterial counterpart L23. In
order to capture every known instance of archaeal L23P,
the trusted cutoff is set lower than a few of the
highest scoring eukaryotic cytosolic ribosomal
counterparts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 77
Score = 25.6 bits (57), Expect = 3.6
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 91 SLYDLEVIRLNTH---RGWKVMKVSLMAD 116
L+D++V ++NT RG K V L +
Sbjct: 36 KLFDVKVEKVNTLITPRGEKKAYVKLAEE 64
>gnl|CDD|177877 PLN02233, PLN02233, ubiquinone biosynthesis methyltransferase.
Length = 261
Score = 26.4 bits (58), Expect = 3.9
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 75 PSAKQC--HRLFLPNPLLSLYDL--EVIRLNTHRGWKVMKVS 112
+C R L N + +YD +++ L HR WK M VS
Sbjct: 26 RDVVKCANERQALFNRIAPVYDNLNDLLSLGQHRIWKRMAVS 67
>gnl|CDD|236965 PRK11742, PRK11742, bifunctional NADH:ubiquinone oxidoreductase
subunit C/D; Provisional.
Length = 575
Score = 26.4 bits (59), Expect = 4.3
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 85 LPNPLLSLYDLEVI--RLNTHR 104
LP P + L+DL I RL THR
Sbjct: 43 LPKPYVMLFDLHGIDERLRTHR 64
>gnl|CDD|107254 cd01541, PBP1_AraR, Ligand-binding domain of DNA transcription
repressor specific for arabinose (AraR) which is a
member of the LacI-GalR family of bacterial
transcription regulators. Ligand-binding domain of DNA
transcription repressor specific for arabinose (AraR)
which is a member of the LacI-GalR family of bacterial
transcription regulators. The ligand-binding domain of
AraR is structurally homologous to the periplasmic
sugar-binding domain of ABC-type transporters and both
domains contain the type I periplasmic binding
protein-like fold. The LacI-GalR family repressors are
composed of two functional domains: an N-terminal HTH
(helix-turn-helix) domain, which is responsible for the
DNA-binding specificity, and a C-terminal ligand-binding
domain, which is homologous to the type I periplasmic
binding proteins. As also observed in the periplasmic
binding proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 273
Score = 26.0 bits (58), Expect = 4.8
Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 12/65 (18%)
Query: 40 CSLSLQVTNPPIDPFREKVVMSLMCPIGPEANILEP--SAKQCHRLFLPNPLLSLYDLEV 97
SL L TN DP RE+ + M G + I+EP SA LPNP + LY L++
Sbjct: 30 YSLLLASTNN--DPERERKCLENMLSQGIDGLIIEPTKSA-------LPNPNIDLY-LKL 79
Query: 98 IRLNT 102
+L
Sbjct: 80 EKLGI 84
>gnl|CDD|236959 PRK11713, PRK11713, 16S ribosomal RNA methyltransferase RsmE;
Provisional.
Length = 234
Score = 26.0 bits (58), Expect = 5.3
Identities = 5/18 (27%), Positives = 10/18 (55%), Gaps = 1/18 (5%)
Query: 69 EANILEPSAKQCHRLFLP 86
+ +E +A+Q R +P
Sbjct: 128 QKIAIE-AAEQSGRTRIP 144
>gnl|CDD|218092 pfam04452, Methyltrans_RNA, RNA methyltransferase. RNA
methyltransferases modify nucleotides during ribosomal
RNA maturation in a site-specific manner. The
Escherichia coli member is specific for U1498
methylation.
Length = 224
Score = 25.6 bits (57), Expect = 6.5
Identities = 6/18 (33%), Positives = 10/18 (55%), Gaps = 1/18 (5%)
Query: 69 EANILEPSAKQCHRLFLP 86
+ +E +A+Q R LP
Sbjct: 114 QKIAIE-AAEQSGRTRLP 130
>gnl|CDD|236857 PRK11138, PRK11138, outer membrane biogenesis protein BamB;
Provisional.
Length = 394
Score = 25.7 bits (57), Expect = 8.2
Identities = 12/23 (52%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 22 KQLFAQLLPVLLSVTTMY-CSLS 43
QL LLP LLSVT + CS
Sbjct: 1 MQLRKTLLPGLLSVTLLSGCSSF 23
>gnl|CDD|178689 PLN03144, PLN03144, Carbon catabolite repressor protein 4 homolog;
Provisional.
Length = 606
Score = 25.5 bits (56), Expect = 8.4
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 9/40 (22%)
Query: 59 VMSLMCPIGPEA-----NILEPSAKQCHRLFLPNPLLSLY 93
+ P+ P+ IL P++K H+L PL+S Y
Sbjct: 477 ATGKVDPLHPDLAVDPLGILRPASKLTHQL----PLVSAY 512
>gnl|CDD|131065 TIGR02010, IscR, iron-sulfur cluster assembly transcription
factor IscR. This model describes IscR, an iron-sulfur
binding transcription factor of the ISC iron-sulfur
cluster assembly system [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other, Regulatory
functions, DNA interactions].
Length = 135
Score = 25.0 bits (55), Expect = 8.6
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 6 PLACLSEFQPLLYDYFKQLFAQL 28
LA +SE Q + Y +QLFA+L
Sbjct: 27 TLADISERQGISLSYLEQLFAKL 49
>gnl|CDD|107346 cd06351, PBP1_iGluR_N_LIVBP_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NMDA, AMPA, and kainate receptor subtypes
of ionotropic glutamate receptors (iGluRs). N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NMDA, AMPA, and kainate receptor subtypes
of ionotropic glutamate receptors (iGluRs). While this
N-terminal domain belongs to the periplasmic-binding
fold type I superfamily, the glutamate-binding domain of
the iGluR is structurally homologous to the
periplasmic-binding fold type II. The LIVBP-like domain
of iGluRs is thought to play a role in the initial
assembly of iGluR subunits, but it is not well
understood how this domain is arranged and functions in
intact iGluR. Glutamate mediates the majority of
excitatory synaptic transmission in the central nervous
system via two broad classes of ionotropic receptors
characterized by their response to glutamate agonists:
N-methyl-aspartate (NMDA) and non-NMDA receptors. NMDA
receptors have intrinsically slow kinetics, are highly
permeable to Ca2+, and are blocked by extracellular Mg2+
in a voltage-dependent manner. On the other hand,
non-NMDA receptors have faster kinetics, are weakly
permeable to Ca2+, and are not blocked by extracellular
Mg2+. While non-NMDA receptors typically mediate
excitatory synaptic responses at resting membrane
potentials, NMDA receptors contribute to several forms
of synaptic plasticity and are suggested to play an
important role in the development of synaptic pathways.
Length = 328
Score = 25.5 bits (56), Expect = 9.3
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 84 FLPNPLLSLYDLEVIRLNTHRGWKVM 109
F + + S + L++I LN RGW+ +
Sbjct: 292 FDEDGVRSNFTLDIIELNRSRGWRKV 317
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
0.324 0.138 0.424
Gapped
Lambda K H
0.267 0.0602 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,906,274
Number of extensions: 485878
Number of successful extensions: 539
Number of sequences better than 10.0: 1
Number of HSP's gapped: 537
Number of HSP's successfully gapped: 25
Length of query: 121
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 37
Effective length of database: 7,211,866
Effective search space: 266839042
Effective search space used: 266839042
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 (21.5 bits)
S2: 53 (24.5 bits)