RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7859
(455 letters)
>gnl|CDD|133382 cd01107, HTH_BmrR, Helix-Turn-Helix DNA binding domain of the BmrR
transcription regulator. Helix-turn-helix (HTH)
multidrug-efflux transporter transcription regulator,
BmrR and YdfL of Bacillus subtilis, and related
proteins; N-terminal domain. Bmr is a membrane protein
which causes the efflux of a variety of toxic substances
and antibiotics. BmrR is comprised of two distinct
domains that harbor a regulatory (effector-binding) site
and an active (DNA-binding) site. The conserved
N-terminal domain contains a winged HTH motif that
mediates DNA binding, while the C-terminal domain binds
coactivating, toxic compounds. BmrR shares the
N-terminal DNA binding domain with other transcription
regulators of the MerR superfamily that promote
transcription by reconfiguring the spacer between the
-35 and -10 promoter elements.
Length = 108
Score = 30.2 bits (69), Expect = 0.67
Identities = 16/56 (28%), Positives = 32/56 (57%), Gaps = 5/56 (8%)
Query: 399 RRLD---KEIKEVLEDYSQDQEKKMILLTGRRVTLAEELKRVKQIQEKLEEFIKAL 451
R L +EIKE+L+ + D+ +K+ L + L E++ +++I LE+ +K +
Sbjct: 55 RDLGFPLEEIKEILDADNDDELRKL--LREKLAELEAEIEELQRILRLLEDRLKQI 108
>gnl|CDD|224264 COG1345, FliD, Flagellar capping protein [Cell motility and
secretion].
Length = 483
Score = 32.0 bits (73), Expect = 0.73
Identities = 13/74 (17%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 381 MLKVTSNALRQQI--MNREARRLDKEIKEVLEDYSQDQEKKMILLTGRRVTLAEELKRVK 438
+L VT + + +N++ + LDK+IK + E + TL + + ++
Sbjct: 412 LLAVTGGIITGRTDSLNKQIKSLDKDIK----SLDKRLEAAEERYKTQFNTLDDMMTQMN 467
Query: 439 QIQEKLEEFIKALN 452
L + + +++
Sbjct: 468 SQSSYLTQQLVSVS 481
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 31.3 bits (72), Expect = 1.2
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 390 RQQIMNREARRLDKEIKEVLEDYSQDQEKKMILLTGRRVTLAEELKRVKQIQEKLEEFIK 449
R ++ E R L KE E L+ + EK+ L + L ++ + +++ +E+LEE I+
Sbjct: 81 RNELQKLEKRLLQKE--ENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIE 138
Query: 450 ALNTE 454
E
Sbjct: 139 EQLQE 143
>gnl|CDD|226256 COG3733, TynA, Cu2+-containing amine oxidase [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 654
Score = 30.9 bits (70), Expect = 1.7
Identities = 15/83 (18%), Positives = 27/83 (32%), Gaps = 10/83 (12%)
Query: 196 AVSECFWKMVRETVEQQADAFKATRFNLET----------EWKNSFPRIRELDRDELFEK 245
++ K E V +AD K F T ++ I ++E
Sbjct: 34 PLTADEIKQAVEIVRAEADFKKNFAFTEVTLLEPDKQEVLAFRLENKPIERKALAVVYEL 93
Query: 246 ARGEILDEIVNLSQVSVQHWEEV 268
I + +V+L V W+ +
Sbjct: 94 DGKGIYEAVVDLDNNKVLSWQPI 116
>gnl|CDD|99939 cd05507, Bromo_brd8_like, Bromodomain, brd8_like subgroup. In
mammals, brd8 (bromodomain containing 8) interacts with
the thyroid hormone receptor in a ligand-dependent
fashion and enhances thyroid hormone-dependent
activation from thyroid response elements. Brd8 is
thought to be a nuclear receptor coactivator.
Bromodomains are 110 amino acid long domains, that are
found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 104
Score = 28.9 bits (65), Expect = 1.8
Identities = 11/36 (30%), Positives = 21/36 (58%)
Query: 117 QSDTHHKPVLSPDELTTIRKNLQRSNIDCDADYIKD 152
+ +H V P +L+TI+KN++ I A++ +D
Sbjct: 32 IAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRD 67
>gnl|CDD|223860 COG0789, SoxR, Predicted transcriptional regulators
[Transcription].
Length = 124
Score = 29.3 bits (66), Expect = 2.0
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 385 TSNALRQQIMNREARRLD---KEIKEVLEDYSQDQEKKMILLTGRRVTLAEELKRVKQIQ 441
T L + + R L EIKE+L+ S + I L R LAE L+ ++
Sbjct: 40 TPEDLELLQIIKTLRELGFSLAEIKELLDLLSAG---ESIALELRERLLAERLEELEAKI 96
Query: 442 EKLEEFIKALN 452
+L+ + L
Sbjct: 97 AELQRIEEELR 107
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 29.8 bits (68), Expect = 3.7
Identities = 13/59 (22%), Positives = 34/59 (57%), Gaps = 3/59 (5%)
Query: 397 EARRLDKEIKEVLEDYSQDQEK---KMILLTGRRVTLAEELKRVKQIQEKLEEFIKALN 452
R+L+K+++ + + Y + E+ + I + + L E LK++++I+++ E+ + L
Sbjct: 349 SVRQLEKQLESLEKQYDEITERIAEQEIAYSELQEELEEILKQLEEIEKEQEKLSEMLQ 407
>gnl|CDD|143332 cd02439, DMB-PRT_CobT, Nicotinate-nucleotide-dimethylbenzimidazole
phosphoribosyltransferase (DMB-PRT), also called CobT.
Nicotinate-nucleotide-dimethylbenzimidazole
phosphoribosyltransferase (DMB-PRT/CobT, not to be
confused with the CobT subunit of cobaltochelatase,
which does not belong to this group) catalyzes the
synthesis of alpha-ribazole-5'-phosphate, from
nicotinate mononucleotide (NAMN) and
5,6-dimethylbenzimidazole (DMB). This function is
essential to the anaerobic biosynthesis pathway of
cobalamin (vitamin B12), which is the largest and most
complex cofactor in a number of enzyme-catalyzed
reactions in bacteria, archaea and eukaryotes. Only
eubacteria and archaebacteria can synthesize vitamin
B12; multicellular organisms have lost this ability
during evolution. DMB-PRT/CobT works sequentially with
CobC (a phosphatase) to couple the lower ligand of
cobalamin to a ribosyl moiety. DMB is the most common
lower ligand of cobamides; other lower ligands include
adenine, 5-methoxybenzimidazole or phenol. It has been
suggested that earlier metabolic or enzymatic steps may
control which lower ligand is available to DMB-PRT/CobT.
In Salmonella enterica, for example, the lower ligand is
DMB under aerobic conditions and adenine or
2-methyladenine under anaerobic conditions. Salmonella
enterica DMB-PRT/CobT is a homodimer with two active
sites, each active site is comprised of residues from
both monomers. This group includes two distinct
subfamilies, one archaeal-like, the other comprised of
bacterial sequences.
Length = 315
Score = 29.4 bits (67), Expect = 3.8
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 350 LKAAVIEEALRRHSWEHKDCCDVV 373
K AV+EEAL R+ + D DV+
Sbjct: 183 RKIAVVEEALARNGPDPDDPLDVL 206
>gnl|CDD|219951 pfam08644, SPT16, FACT complex subunit (SPT16/CDC68). Proteins in
this family are subunits the FACT complex. The FACT
complex plays a role in transcription initiation and
promotes binding of TATA-binding protein (TBP) to a TATA
box in chromatin.
Length = 152
Score = 28.4 bits (64), Expect = 4.4
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 7/44 (15%)
Query: 387 NALRQQIMNREARRLDKEIKEVLEDYSQDQEKKMILLTGRRVTL 430
L++++ RE R KE +V+E QEK ++ R L
Sbjct: 88 KELQKRVKKRETER--KEKADVVE-----QEKLILNRNKRPPRL 124
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
modification].
Length = 2365
Score = 29.6 bits (66), Expect = 4.8
Identities = 25/105 (23%), Positives = 40/105 (38%), Gaps = 24/105 (22%)
Query: 49 LKAAVIEEALRRHSWEHKGSEMLRILQLNTLEDQCVSPSLSERWMYWKYSTE-------- 100
L+ V+ + L + +++ ILQ LSE W WK +
Sbjct: 713 LRRQVMADILSMLPEGIRQTKVRTILQ-----------HLSEAWRCWKANIPWHVPGEPA 761
Query: 101 --EQVKRSYVKSELDKVLQSDTHHKPVLSPD---ELTTIRKNLQR 140
+V R Y+KS+ D S ++ +S T +KNL R
Sbjct: 762 PILEVIRRYIKSKADLWTSSAHFNRERISRGAGVGKTKEKKNLGR 806
>gnl|CDD|218475 pfam05164, ZapA, Cell division protein ZapA. ZapA is a cell
division protein which interacts with FtsZ. FtsZ is part
of a mid-cell cytokinetic structure termed the Z-ring
that recruits a hierarchy of fission related proteins
early in the bacterial cell cycle. The interaction of
FtsZ with ZapA drives its polymerisation and promotes
FtsZ filament bundling thereby contributing to the
spatio-temporal tuning of the Z-ring.
Length = 89
Score = 27.1 bits (61), Expect = 4.9
Identities = 14/49 (28%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 398 ARRLDKEIKEVLEDYSQDQEKKMILLTGRRVTLAEELKRVKQIQEKLEE 446
A LD+++ E+ E +++++L + LA+EL ++K+ +LEE
Sbjct: 27 AEYLDEKLAEIREKGGVLSTERLLVLAA--LNLADELLKLKKELAELEE 73
>gnl|CDD|234129 TIGR03160, cobT_DBIPRT,
nicotinate-nucleotide--dimethylbenzimidazole
phosphoribosyltransferase. Members of this family are
nicotinate-nucleotide--dimethylbenzimidazole
phosphoribosyltransferase, an enzyme of cobalamin
biosynthesis [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 333
Score = 29.0 bits (66), Expect = 5.4
Identities = 11/22 (50%), Positives = 11/22 (50%)
Query: 351 KAAVIEEALRRHSWEHKDCCDV 372
K AVI AL RH D DV
Sbjct: 200 KVAVIRRALERHRPNAGDPLDV 221
>gnl|CDD|99962 cd03786, GT1_UDP-GlcNAc_2-Epimerase, Bacterial members of the
UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are
known to catalyze the reversible interconversion of
UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The
enzyme serves to produce an activated form of ManNAc
residues (UDP-ManNAc) for use in the biosynthesis of a
variety of cell surface polysaccharides; The mammalian
enzyme is bifunctional, catalyzing both the inversion of
stereochemistry at C-2 and the hydrolysis of the
UDP-sugar linkage to generate free ManNAc. It also
catalyzes the phosphorylation of ManNAc to generate
ManNAc 6-phosphate, a precursor to salic acids. In
mammals, sialic acids are found at the termini of
oligosaccharides in a large variety of cell surface
glycoconjugates and are key mediators of cell-cell
recognition events. Mutations in human members of this
family have been associated with Sialuria, a rare
disease caused by the disorders of sialic acid
metabolism. This family belongs to the GT-B structural
superfamily of glycoslytransferases, which have
characteristic N- and C-terminal domains each containing
a typical Rossmann fold. The two domains have high
structural homology despite minimal sequence homology.
The large cleft that separates the two domains includes
the catalytic center and permits a high degree of
flexibility.
Length = 363
Score = 28.6 bits (65), Expect = 6.3
Identities = 14/47 (29%), Positives = 26/47 (55%)
Query: 401 LDKEIKEVLEDYSQDQEKKMILLTGRRVTLAEELKRVKQIQEKLEEF 447
L+ KE++ + KK IL+T RV ++ +++++I E L E
Sbjct: 181 LELAKKELILELLGLLPKKYILVTLHRVENVDDGEQLEEILEALAEL 227
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 28.7 bits (65), Expect = 6.4
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 390 RQQIMNREARRLDKEIKEVLEDYSQDQEKKMILLTGRRVTLAEELKRVKQIQEKLEEFIK 449
R ++ E R L +E E L+ + +KK L + L+ + K + + +E+LEE I
Sbjct: 75 RNELQRLERRLLQRE--ETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIA 132
Query: 450 ALNTE 454
E
Sbjct: 133 EQREE 137
>gnl|CDD|213789 TIGR03280, methan_mark_11, methanogenesis imperfect marker protein
11. The first twenty-nine completed genomes with a
member of this protein family include twenty-eight
archaeal methanogens and one other related archaeon,
Ferroglobus placidus DSM 10642. The exact function is
unknown, but the protein likely belongs to a system
usually tightly linked to methanogenesis.
Length = 292
Score = 28.6 bits (64), Expect = 6.8
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 397 EARRLDKEIKEVLEDYSQDQEKKMILLTGRRVTLAEELK----RVKQIQEKLEE 446
+L +E K++L++Y+ E M + G + +ELK + K+ +EE
Sbjct: 201 YKEKLAREFKKLLKEYTLSDETAMAVYDG--LFPPKELKEYGNKAKREMVSIEE 252
>gnl|CDD|223458 COG0381, WecB, UDP-N-acetylglucosamine 2-epimerase [Cell envelope
biogenesis, outer membrane].
Length = 383
Score = 28.4 bits (64), Expect = 9.1
Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 393 IMNREARRLDKEIKEVLEDYSQDQEKKMILLTG-RRVTLAEELKR----VKQIQEKLEEF 447
+ R+ ++ K + + D++KK IL+T RR + E L+ +++I E+ +
Sbjct: 180 ALLNTRDRVLEDSKILAKGL-DDKDKKYILVTAHRRENVGEPLEEICEALREIAEEYPDV 238
Query: 448 I 448
I
Sbjct: 239 I 239
>gnl|CDD|214937 smart00957, SecA_DEAD, SecA DEAD-like domain. SecA protein binds
to the plasma membrane where it interacts with proOmpA
to support translocation of proOmpA through the
membrane. SecA protein achieves this translocation, in
association with SecY protein, in an ATP dependent
manner. This domain represents the N-terminal
ATP-dependent helicase domain, which is related to the.
Length = 380
Score = 28.2 bits (64), Expect = 9.1
Identities = 11/43 (25%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 392 QIMNREARRLDKEIKEVLEDYSQDQEKKMILLTGRRVTLAEEL 434
++ RL ++ EDY+ D++ + + LT + AE+L
Sbjct: 233 HRADKFVPRLKED-----EDYTVDEKSRTVELTEEGIEKAEKL 270
>gnl|CDD|223233 COG0155, CysI, Sulfite reductase, beta subunit (hemoprotein)
[Inorganic ion transport and metabolism].
Length = 510
Score = 28.5 bits (64), Expect = 9.7
Identities = 12/51 (23%), Positives = 17/51 (33%), Gaps = 7/51 (13%)
Query: 364 WEHKDCCDVVLFWRIQQMLKVTSNALRQQIMNREARRLDKEIKEVLEDYSQ 414
D D + LK SN LR I ++ + RL + E
Sbjct: 1 MAPYDPLDN-------ERLKAESNFLRGTIEDQLSDRLSGGLCEDDFRPLL 44
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
0.318 0.132 0.391
Gapped
Lambda K H
0.267 0.0863 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,282,891
Number of extensions: 2262891
Number of successful extensions: 3078
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3047
Number of HSP's successfully gapped: 99
Length of query: 455
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 355
Effective length of database: 6,502,202
Effective search space: 2308281710
Effective search space used: 2308281710
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 (21.7 bits)
S2: 61 (27.0 bits)