RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14619
(344 letters)
>gnl|CDD|182159 PRK09946, PRK09946, hypothetical protein; Provisional.
Length = 270
Score = 39.0 bits (91), Expect = 0.002
Identities = 27/114 (23%), Positives = 43/114 (37%), Gaps = 10/114 (8%)
Query: 228 SQIKSNSECFESTSTTDCSQITCTSECSEIINTPECSKIITTSECSQITFTSERSQITTT 287
+QI S S S I + E + + T S+I + + S+I T R ++ T
Sbjct: 113 AQIASMGYSVRIGSVGFNSHIGSSGERARVAVTGNSSRISSAGDSSRIANTGMRVRVCTL 172
Query: 288 -ECSQIKSNSECFESTSTTDCSQITCTSECSEIINTPECSKIITTSECSQITFT 340
E + S D QI + I N+ + II + E S + T
Sbjct: 173 GERCHV---------ASNGDLVQIASFGANARIANSGDNVHIIASGENSTVVST 217
Score = 29.4 bits (66), Expect = 2.5
Identities = 23/158 (14%), Positives = 56/158 (35%), Gaps = 1/158 (0%)
Query: 131 SQITFTSERSQITTTECSQIKSNSECFESTSTTDCSQITCTSECSEIINTPECSKIITTS 190
+ F + + C + + D ++I C + + I ++I +
Sbjct: 60 ADENFAHQEVSSMQKLATDPGERPFCSQFARSDDHARIGCCEDNARIATAGYAAQIASMG 119
Query: 191 ECSQITFTSECSHITFTSECFQTTFTSECSQITFT-ECSQIKSNSECFESTSTTDCSQIT 249
+I SHI + E + T S+I+ + S+I + + + +
Sbjct: 120 YSVRIGSVGFNSHIGSSGERARVAVTGNSSRISSAGDSSRIANTGMRVRVCTLGERCHVA 179
Query: 250 CTSECSEIINTPECSKIITTSECSQITFTSERSQITTT 287
+ +I + ++I + + I + E S + +T
Sbjct: 180 SNGDLVQIASFGANARIANSGDNVHIIASGENSTVVST 217
>gnl|CDD|224715 COG1802, GntR, Transcriptional regulators [Transcription].
Length = 230
Score = 30.8 bits (70), Expect = 0.90
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 69 LLIQMLRNHLLIQMLRNHLLIQMLRNHHLIRMLRNHLLIRMLRNHLQI 116
L + N L++++R LL + L R + + H I
Sbjct: 145 ALAEAAGNPYLLEIIRRLLLARRPLRLALYRSAEERA-RQAIDEHRAI 191
Score = 28.5 bits (64), Expect = 4.0
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 87 LLIQMLRNHHLIRMLRNHLLI-RMLRNHLQIRTNAQKP 123
L + N +L+ ++R LL R LR L +
Sbjct: 145 ALAEAAGNPYLLEIIRRLLLARRPLRLALYRSAEERAR 182
>gnl|CDD|237072 PRK12355, PRK12355, conjugal transfer mating pair stabilization
protein TraN; Reviewed.
Length = 558
Score = 30.9 bits (70), Expect = 1.0
Identities = 28/195 (14%), Positives = 53/195 (27%), Gaps = 31/195 (15%)
Query: 121 QKPPSPQNECSQITFTSERSQITTTECSQIKSNSECFESTSTTDC---SQITCTSECSEI 177
Q + + + Q + + D + C
Sbjct: 212 QGTVTAGAGFTSSGTCGNGDRRVGNSLFQGGVTFTLTLTMTVPDKTYTPTVVWVESC--- 268
Query: 178 INTPECSKI--ITTSEC--SQITFTSECSHITFTSECFQTTFTSECSQITFTECSQIKSN 233
P C +T C T T + I T +C+ T +C C+ + N
Sbjct: 269 ---PFCKADGTLTGETCTEPGGTRTRVINGIPVTRDCWAYQDTYQCQSADTGNCATLADN 325
Query: 234 SECFESTSTTDCSQITCTSECSEIINTPECSKIITTSECSQITFTSERSQITTTECS--Q 291
C + C+ + C T C + +++ T C
Sbjct: 326 PACTLVSRQ--CAFYSNGGGCLHEEATYSCPE--------------KKTSGTVMVCGGDV 369
Query: 292 IKSNSECFESTSTTD 306
+ +CF+++ST
Sbjct: 370 FCLDGDCFDTSSTNS 384
>gnl|CDD|219539 pfam07729, FCD, FCD domain. This domain is the C-terminal ligand
binding domain of many members of the GntR family. This
domain probably binds to a range of effector molecules
that regulate the transcription of genes through the
action of the N-terminal DNA-binding domain pfam00392.
This domain is found in E. coli nanR and dgoR that are
regulators of sugar biosynthesis operons. It is also in
the known structure of FadR where it binds to acyl-coA,
the domain is alpha helical. This family has been named
as FCD for (FadR C-terminal Domain).
Length = 125
Score = 28.9 bits (65), Expect = 1.9
Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 11/67 (16%)
Query: 60 LLIQMLRNHLLIQMLRN-HLLIQMLRNHLLI------QMLRNHH-LIRMLRNH---LLIR 108
+ + N LL ++L ++ LR LL + L H ++ +R
Sbjct: 58 AIAEAAGNPLLAELLERLRDRLRRLRRLLLSSPDRLERSLAEHRAILDAIRAGDAEAARA 117
Query: 109 MLRNHLQ 115
+R HL+
Sbjct: 118 AMREHLE 124
Score = 27.7 bits (62), Expect = 4.0
Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 8/69 (11%)
Query: 6 LLIQMLRNHLLIQMLRN-HLLIQMLRNHLLIQMLRNHLLIQMLRNHL-LIQMLRNH---L 60
+ + N LL ++L ++ LR LL L + L H ++ +R
Sbjct: 58 AIAEAAGNPLLAELLERLRDRLRRLRRLLL---SSPDRLERSLAEHRAILDAIRAGDAEA 114
Query: 61 LIQMLRNHL 69
+R HL
Sbjct: 115 ARAAMREHL 123
Score = 27.0 bits (60), Expect = 9.4
Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 7/46 (15%)
Query: 78 LLIQMLRNHLLIQMLRN-HHLIRMLRNHLLI------RMLRNHLQI 116
+ + N LL ++L +R LR LL R L H I
Sbjct: 58 AIAEAAGNPLLAELLERLRDRLRRLRRLLLSSPDRLERSLAEHRAI 103
>gnl|CDD|214892 smart00895, FCD, This entry represents the C-terminal ligand
binding domain of many members of the GntR family. This
domain probably binds to a range of effector molecules
that regulate the transcription of genes through the
action of the N-terminal DNA-binding domain. This domain
is found in and that are regulators of sugar
biosynthesis operons. Many bacterial transcription
regulation proteins bind DNA through a helix-turn-helix
(HTH) motif, which can be classified into subfamilies on
the basis of sequence similarities. The HTH GntR family
has many members distributed among diverse bacterial
groups that regulate various biological processes. It
was named GntR after the Bacillus subtilis repressor of
the gluconate operon. In general, these proteins contain
a DNA-binding HTH domain at the N terminus, and an
effector binding or oligomerisation domain at the C
terminus. The winged-helix DNA-binding domain is well
conserved in structure for the whole of the GntR family,
and is similar in structure to other transcriptional
regulator families. The C-terminal effector-binding and
oligomerisation domains are more variable and are
consequently used to define the subfamilies. Based on
the sequence and structure of the C-terminal domains,
the GtnR family can be divided into four major groups,
as represented by FadR, HutC, MocR and YtrA, as well as
some minor groups such as those represented by AraR and
PlmA.
Length = 123
Score = 28.9 bits (65), Expect = 2.0
Identities = 12/72 (16%), Positives = 27/72 (37%), Gaps = 12/72 (16%)
Query: 50 HLLI-QMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHH--LIRMLRNH-- 104
H + + N +L+++L + LR L + + + H ++ +R
Sbjct: 57 HRALAEAAGNPVLLELLES------LRARLRRLRRLSLEAARRALDEHRAILDAIRARDA 110
Query: 105 -LLIRMLRNHLQ 115
+R HL+
Sbjct: 111 EAARAAMREHLE 122
Score = 27.3 bits (61), Expect = 5.6
Identities = 10/45 (22%), Positives = 18/45 (40%), Gaps = 5/45 (11%)
Query: 77 HLLI-QMLRNHLLIQMLRNHH----LIRMLRNHLLIRMLRNHLQI 116
H + + N +L+++L + +R L R L H I
Sbjct: 57 HRALAEAAGNPVLLELLESLRARLRRLRRLSLEAARRALDEHRAI 101
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
0.322 0.127 0.374
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,158,013
Number of extensions: 1347654
Number of successful extensions: 1618
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1568
Number of HSP's successfully gapped: 43
Length of query: 344
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 246
Effective length of database: 6,590,910
Effective search space: 1621363860
Effective search space used: 1621363860
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: 40 (21.5 bits)
S2: 59 (26.6 bits)