RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780526|ref|YP_003064939.1| putative transcription
regulator protein [Candidatus Liberibacter asiaticus str. psy62]
(223 letters)
>gnl|CDD|129095 smart00862, Trans_reg_C, Transcriptional regulatory protein, C
terminal. This domain is almost always found associated
with the response regulator receiver domain. It may play
a role in DNA binding.
Length = 78
Score = 68.4 bits (168), Expect = 2e-12
Identities = 27/78 (34%), Positives = 49/78 (62%), Gaps = 1/78 (1%)
Query: 144 GEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKLR- 202
GE L +E R+LE L+ N G+ V++ ++ A++G D+ V++N ++ HIS+LRKKL
Sbjct: 1 GEPIKLTPKEFRLLELLLRNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60
Query: 203 NKLGFDPVDSKRFLGYSI 220
+ +++ R +GY +
Sbjct: 61 DGANPRLIETVRGVGYRL 78
>gnl|CDD|131209 TIGR02154, PhoB, phosphate regulon transcriptional regulatory
protein PhoB. PhoB is a DNA-binding response regulator
protein acting with PhoR in a 2-component system
responding to phosphate ion. PhoB acts as a positive
regulator of gene expression for phosphate-related genes
such as phoA, phoS, phoE and ugpAB as well as itself. It
is often found proximal to genes for the high-affinity
phosphate ABC transporter (pstSCAB; GenProp0190) and
presumably regulates these as well.
Length = 226
Score = 63.9 bits (156), Expect = 3e-11
Identities = 41/132 (31%), Positives = 66/132 (50%), Gaps = 3/132 (2%)
Query: 92 DSGVDDVVNKPIHHREILARVAAIYRRLK--VSNNRAETGPIRVFSDGRDPEVQGEVFPL 149
++G DD + KP RE+LAR+ A+ RR++ +S+ E G + + G+ L
Sbjct: 96 ETGADDYITKPFSPRELLARIKAVLRRIRPQLSDEVIEVGDLSLDPVAHRVFRGGQPLSL 155
Query: 150 PRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKLRNKLGFDP 209
E R+L + M + + ++ Q+ ++G D VEE V+ HI +LRK L DP
Sbjct: 156 GPTEFRLLHFFMTHPERVYSREQLLDRVWGR-DVYVEERTVDVHIRRLRKALNPFGLEDP 214
Query: 210 VDSKRFLGYSID 221
V + R GY
Sbjct: 215 VQTVRGAGYRFS 226
>gnl|CDD|182950 PRK11083, PRK11083, DNA-binding response regulator CreB;
Provisional.
Length = 228
Score = 62.3 bits (152), Expect = 1e-10
Identities = 37/131 (28%), Positives = 61/131 (46%), Gaps = 5/131 (3%)
Query: 94 GVDDVVNKPIHHREILARVAAIYRRLKVSNNRA---ETGPIRVFSDGRDPEVQGEVFPLP 150
G DD V KP RE+ ARV I RR+K + G + G L
Sbjct: 97 GADDYVAKPFSPREVAARVRTILRRVKKFAAPSPVIRIGHFELDEPAARISYFGTPLTLT 156
Query: 151 RRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKLRN-KLGFDP 209
R E +L+ L+ + G+ ++ Q+ ++ ++ + V++HI LR KLR P
Sbjct: 157 RYEFLLLKTLLLSPGRVFSRQQLMDIVWEDAQDSYDRT-VDTHIKTLRAKLRAINPDLSP 215
Query: 210 VDSKRFLGYSI 220
+++ R +GYS+
Sbjct: 216 INTHRGMGYSL 226
>gnl|CDD|182755 PRK10816, PRK10816, DNA-binding transcriptional regulator PhoP;
Provisional.
Length = 223
Score = 61.3 bits (149), Expect = 2e-10
Identities = 48/168 (28%), Positives = 84/168 (50%), Gaps = 5/168 (2%)
Query: 57 GEKVLELPRIIRAHS-QVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAI 115
E L L R R++ +P++ ++ S Q ++ +G DD V KP H E++AR+ A+
Sbjct: 56 DEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQAL 115
Query: 116 YRR-LKVSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIF 174
RR +++ P +V R+ + EV L E I+E L+ N GK V+K +
Sbjct: 116 MRRNSGLASQVISLPPFQVDLSRRELSINDEVIKLTAFEYTIMETLIRNNGKVVSKDSLM 175
Query: 175 SAIYGLFD-EAVEENVVESHISKLRKKLRNKLGFDPVDSKRFLGYSID 221
+Y D E E + ++ + +LRKK++ + + + + R GY D
Sbjct: 176 LQLYP--DAELRESHTIDVLMGRLRKKIQAQYPQEVITTVRGQGYRFD 221
>gnl|CDD|183172 PRK11517, PRK11517, transcriptional regulatory protein YedW;
Provisional.
Length = 223
Score = 60.3 bits (146), Expect = 3e-10
Identities = 45/157 (28%), Positives = 77/157 (49%), Gaps = 3/157 (1%)
Query: 65 RIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVSNN 124
+ +R Q P+I ++ S+ + DSG +D + KP E+LARV A R+ N+
Sbjct: 64 QTLRTAKQTPVICLTARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQHHALNS 123
Query: 125 RAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGL-FDE 183
E +R+ S + L R+E ++L L + G+ + +T I S I+G+ FD
Sbjct: 124 TLEISGLRMDSVSQSVSRDNISITLTRKEFQLLWLLASRAGEIIPRTVIASEIWGINFDS 183
Query: 184 AVEENVVESHISKLRKKLRNKLGFDPVDSKRFLGYSI 220
+ N V+ I +LR K+ + + + R +GYS
Sbjct: 184 --DTNTVDVAIRRLRAKVDDPFPEKLIATIRGMGYSF 218
>gnl|CDD|130454 TIGR01387, cztR_silR_copR, heavy metal response regulator. Members
of this family contain a response regulator receiver
domain (Pfam:PF00072) and an associated transcriptional
regulatory region (Pfam:PF00486). This group is
separated phylogenetically from related proteins with
similar architecture and contains a number of proteins
associated with heavy metal resistance efflux systems
for copper, silver, cadmium, and/or zinc. Most members
encoded by genes adjacent to genes for encoding a member
of the heavy metal sensor histidine kinase family
(TIGRFAMs:TIGR01386), its partner in the two-component
response regulator system.
Length = 218
Score = 57.5 bits (139), Expect = 3e-09
Identities = 47/173 (27%), Positives = 84/173 (48%), Gaps = 20/173 (11%)
Query: 57 GEKVLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIY 116
G ++L+ R R+ Q P++ ++ S+ + D G DD + KP E+LARV +
Sbjct: 57 GWQILQTLR--RSGKQTPVLFLTARDSVADKVKGLDLGADDYLVKPFSFSELLARVRTLL 114
Query: 117 RR--------LKVSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRV 168
RR L++++ R ++ RV L R+E ++L LM G+ +
Sbjct: 115 RRSHSLNSTVLEIADLRMDSVRHRVSRGNIRIT-------LTRKEFQLLWLLMRRTGEVL 167
Query: 169 AKTQIFSAIYGL-FDEAVEENVVESHISKLRKKLRNKLGFDPVDSKRFLGYSI 220
+T I S ++G+ FD + NVV+ I +LR K+ + + + R +GY +
Sbjct: 168 PRTVIASLVWGMNFDS--DTNVVDVAIRRLRAKVDDPFEEKLIHTIRGMGYVL 218
>gnl|CDD|185376 PRK15479, PRK15479, transcriptional regulatory protein TctD;
Provisional.
Length = 221
Score = 57.0 bits (138), Expect = 3e-09
Identities = 42/131 (32%), Positives = 67/131 (51%), Gaps = 5/131 (3%)
Query: 92 DSGVDDVVNKPIHHREILARVAAIYRRLKVSNNRAETGPIRVFSDGRDPEVQGEVFPLPR 151
+ G DD + KP E+ AR+ A+ RR + +F D +QG+ L
Sbjct: 92 NVGADDYLPKPFELEELDARLRALLRRSAGQVQEVQQLGELIFHDEGYFLLQGQPLALTP 151
Query: 152 RERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKLRNKLGFD-PV 210
RE+ +L LM R + V++ Q+F ++ L DE E+ +E +I +LRKKL G D +
Sbjct: 152 REQALLTVLMYRRTRPVSRQQLFEQVFSLNDEVSPES-IELYIHRLRKKL---QGSDVRI 207
Query: 211 DSKRFLGYSID 221
+ R LGY ++
Sbjct: 208 TTLRGLGYVLE 218
>gnl|CDD|182387 PRK10336, PRK10336, DNA-binding transcriptional regulator QseB;
Provisional.
Length = 219
Score = 57.2 bits (138), Expect = 4e-09
Identities = 56/201 (27%), Positives = 91/201 (45%), Gaps = 5/201 (2%)
Query: 3 VLIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIG-KGEKVL 61
+LI+D L+ DG G S++ F + SA D ++ L G G +L
Sbjct: 4 LLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEALYSAPYDAVILDLTLPGMDGRDIL 63
Query: 62 ELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLK- 120
R + P++ ++ +L ++ G DD + KP E+ AR+ A+ RR
Sbjct: 64 REWR--EKGQREPVLILTARDALAERVEGLRLGADDYLCKPFALIEVAARLEALMRRTNG 121
Query: 121 VSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGL 180
++N G + + R + GE L +E +LE LM N G+ + + I +Y
Sbjct: 122 QASNELRHGNVMLDPGKRIATLAGEPLTLKPKEFALLELLMRNAGRVLPRKLIEEKLYT- 180
Query: 181 FDEAVEENVVESHISKLRKKL 201
+DE V N VE H+ LR+KL
Sbjct: 181 WDEEVTSNAVEVHVHHLRRKL 201
>gnl|CDD|182522 PRK10529, PRK10529, DNA-binding transcriptional activator KdpE;
Provisional.
Length = 225
Score = 55.6 bits (134), Expect = 1e-08
Identities = 49/165 (29%), Positives = 71/165 (43%), Gaps = 20/165 (12%)
Query: 61 LELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLK 120
+E R +R S +P+I +S + D+G DD ++KP E+ AR+ RR
Sbjct: 61 IEFIRDLRQWSAIPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRH- 119
Query: 121 VSNNRAETGPIRVFSD------GRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIF 174
S A P+ FSD R E L E R+L L+ N GK + + Q+
Sbjct: 120 -SATPAPD-PLVKFSDVTVDLAARVIHRGEEEVHLTPIEFRLLAVLLNNAGKVLTQRQLL 177
Query: 175 SAIYGLFDEAVEENVVESHISKLR---KKLRNKLGFDPVDSKRFL 216
+ ++G N VE H LR LR KL DP + F+
Sbjct: 178 NQVWG-------PNAVE-HSHYLRIYMGHLRQKLEQDPARPRHFI 214
>gnl|CDD|182612 PRK10643, PRK10643, DNA-binding transcriptional regulator BasR;
Provisional.
Length = 222
Score = 55.0 bits (133), Expect = 1e-08
Identities = 41/157 (26%), Positives = 72/157 (45%), Gaps = 6/157 (3%)
Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLK-V 121
L R + +P++ ++ +L+ + D G DD + KP E+ AR+ A+ RR +
Sbjct: 63 LRRWRQKKYTLPVLILTARDTLEDRVAGLDVGADDYLVKPFALEELHARIRALIRRHQGQ 122
Query: 122 SNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLF 181
N + G + + + + G+ L +E +L LM G V + ++ IY +
Sbjct: 123 GENELQVGNLTLNLGRQQVWLDGQELILTPKEFALLSRLMLKAGSPVHREILYQDIYN-W 181
Query: 182 DEAVEENVVESHISKLRKKLRNKLGFDPVDSKRFLGY 218
D+ N +E HI LR K+G D + + R GY
Sbjct: 182 DDEPSSNTLEVHIHNLRD----KVGKDRIRTVRGFGY 214
>gnl|CDD|163499 TIGR03787, marine_sort_RR, proteobacterial dedicated sortase system
response regulator. This model describes a family of
DNA-binding response regulator proteins, associated with
an adjacent histidine kinase (TIGR03785) to form a
two-component system. This system co-occurs with, and
often is adjacent to, a proteobacterial variant form of
the protein sorting transpeptidase called sortase
(TIGR03784), and a single target protein for the
sortase. We give this protein the gene symbol pdsR, for
Proteobacterial Dedicated Sortase system Response
regulator.
Length = 227
Score = 49.8 bits (119), Expect = 5e-07
Identities = 52/230 (22%), Positives = 99/230 (43%), Gaps = 24/230 (10%)
Query: 3 VLIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKV-- 60
+++D A +++ Y G + + D++ I+ IG GE++
Sbjct: 4 AIVEDEAAIRENYADALKRQGYQVTTYADRPSAMQAFRQRLPDLAIID---IGLGEEIDG 60
Query: 61 -LELPRIIRAHS-QVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118
L + +R+ S +P+I ++ S T+ G DD + K I +LAR+ A++RR
Sbjct: 61 GFMLCQDLRSLSATLPIIFLTARDSDFDTVSGLRLGADDYLTKDISLPHLLARITALFRR 120
Query: 119 LKV------SNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQ 172
+ ++ GP+ + SD Q + L E ++ L + G ++ Q
Sbjct: 121 AEALQKPQKQDDLITRGPLTLDSDRMTVFWQDQPIDLTVTEFWMVHALAKHPGHVKSRQQ 180
Query: 173 IFSAIYGLFDEA---VEENVVESHISKLRKKLRN-KLGFDPVDSKRFLGY 218
L D A V+++ + SHI ++RKK + FD + + +GY
Sbjct: 181 -------LMDAAKIVVDDSTITSHIKRIRKKFQAVDDNFDCIQTVYGMGY 223
>gnl|CDD|182665 PRK10710, PRK10710, DNA-binding transcriptional regulator BaeR;
Provisional.
Length = 240
Score = 47.4 bits (113), Expect = 3e-06
Identities = 41/144 (28%), Positives = 68/144 (47%), Gaps = 4/144 (2%)
Query: 61 LELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLK 120
L L R IR S +P++ ++ L + G DD + KP RE++ARV I RR K
Sbjct: 70 LTLCREIRRFSDIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTILRRCK 129
Query: 121 VSNNRAET---GPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAI 177
+ P+ + +G++ L E R+L+ L GK ++ Q+ + +
Sbjct: 130 PQRELQQQDAESPLIIDESRFQASWRGKMLDLTPAEFRLLKTLSHEPGKVFSREQLLNHL 189
Query: 178 YGLFDEAVEENVVESHISKLRKKL 201
Y + V + ++SHI LR+KL
Sbjct: 190 YDDY-RVVTDRTIDSHIKNLRRKL 212
>gnl|CDD|182864 PRK10955, PRK10955, DNA-binding transcriptional regulator CpxR;
Provisional.
Length = 232
Score = 47.5 bits (113), Expect = 3e-06
Identities = 39/151 (25%), Positives = 68/151 (45%), Gaps = 18/151 (11%)
Query: 67 IRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVSNNRA 126
+R Q P+I ++ S + + G DD + KP + RE++AR+ AI RR S +
Sbjct: 66 LRQTHQTPVIMLTARGSELDRVLGLELGADDYLPKPFNDRELVARIRAILRRSHWSEQQQ 125
Query: 127 --ETGPIRVFSDG-------RDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAI 177
+ G + D ++ G+ L E +L L + G+ V++ + +
Sbjct: 126 NNDNGSPTLEVDALSLNPGRQEASFDGQTLELTGTEFTLLYLLAQHLGQVVSREHLSQEV 185
Query: 178 YGL----FDEAVEENVVESHISKLRKKLRNK 204
G FD A ++ HIS LR+KL ++
Sbjct: 186 LGKRLTPFDRA-----IDMHISNLRRKLPDR 211
>gnl|CDD|182277 PRK10161, PRK10161, transcriptional regulator PhoB; Provisional.
Length = 229
Score = 43.6 bits (102), Expect = 4e-05
Identities = 35/155 (22%), Positives = 72/155 (46%), Gaps = 17/155 (10%)
Query: 73 VPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR---------LKVSN 123
+P++ ++ + + ++G DD + KP +E++AR+ A+ RR +++
Sbjct: 77 IPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRISPMAVEEVIEMQG 136
Query: 124 NRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDE 183
+ RV + G +P G E ++L + M + + ++ Q+ + ++G +
Sbjct: 137 LSLDPTSHRVMA-GEEPLEMGPT------EFKLLHFFMTHPERVYSREQLLNHVWGT-NV 188
Query: 184 AVEENVVESHISKLRKKLRNKLGFDPVDSKRFLGY 218
VE+ V+ HI +LRK L V + R GY
Sbjct: 189 YVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGY 223
>gnl|CDD|182102 PRK09836, PRK09836, DNA-binding transcriptional activator CusR;
Provisional.
Length = 227
Score = 40.7 bits (95), Expect = 3e-04
Identities = 35/164 (21%), Positives = 84/164 (51%), Gaps = 6/164 (3%)
Query: 62 ELPRIIRAHSQ-VPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR-- 118
++ R++R+ ++ +P++ ++ +++ + + G DD + KP E+LARV + RR
Sbjct: 61 DIVRMLRSANKGMPILLLTALGTIEHRVKGLELGADDYLVKPFAFAELLARVRTLLRRGA 120
Query: 119 LKVSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIY 178
+ ++ + + V R G L +E +LE+ + ++G+ + ++ I S ++
Sbjct: 121 AVIIESQFQVADLMVDLVSRKVTRSGTRITLTSKEFTLLEFFLRHQGEVLPRSLIASQVW 180
Query: 179 GL-FDEAVEENVVESHISKLRKKLRNKLGFDPVDSKRFLGYSID 221
+ FD + N ++ + +LR K+ N + + R +GY ++
Sbjct: 181 DMNFDS--DTNAIDVAVKRLRGKIDNDFEPKLIQTVRGVGYMLE 222
>gnl|CDD|181883 PRK09468, ompR, osmolarity response regulator; Provisional.
Length = 239
Score = 32.3 bits (74), Expect = 0.10
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 94 GVDDVVNKPIHHREILARVAAIYRR 118
G DD + KP + RE+LAR+ A+ RR
Sbjct: 99 GADDYLPKPFNPRELLARIRAVLRR 123
>gnl|CDD|117315 pfam08745, UPF0278, UPF0278 family. Members of this family are
uncharacterized proteins about 200 amino acids in
length.
Length = 206
Score = 32.0 bits (73), Expect = 0.14
Identities = 15/51 (29%), Positives = 25/51 (49%)
Query: 163 NRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKLRNKLGFDPVDSK 213
++G R+A+ + A + E + VV I +LR+K R L +DS
Sbjct: 105 DKGLRIAEEAVREAALETYKEEIIREVVGKIIRRLREKYREALRQGILDSA 155
>gnl|CDD|179837 PRK04358, PRK04358, hypothetical protein; Provisional.
Length = 217
Score = 30.7 bits (70), Expect = 0.29
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 163 NRGKRVAKTQI---FSAIYGLFDEAVEENVVESHISKLRKKLRNKLGFDPVDSK 213
N+G RVA+ + Y L E +E VV ISKLR+K R L +DS
Sbjct: 109 NKGLRVAEEAVREAALECYDLSKEEIEREVVGKIISKLREKYREALRKGILDSA 162
>gnl|CDD|150329 pfam09626, DHC, Dihaem cytochrome c. Dihaem cytochrome c (DHC)
is a soluble c-type cytochrome that folds into two
distinct domains, each binding a single haem group and
connected by a small linker region. Despite little
sequence similarity, the N-terminal domain (residues
12-75) is a class I type cytochrome c, that binds one
of the haems, but the domain surrounding the other haem
is structurally unique. DHC binds electrostatically to
an oxygen-binding protein, sphaeroides haem protein
(SHP), as a component of a conserved electron transfer
pathway. DHC acts as the physiological electron donor
for SHP during phototrophic growth. In certain species
DHC is found upstream of pfam01292.
Length = 118
Score = 30.4 bits (69), Expect = 0.39
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 5/61 (8%)
Query: 19 FGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGE----KVLELPRIIRAHSQVP 74
FG D SL+ +L+++A + + L E ++ E P H +VP
Sbjct: 33 FGTD-ASLDPPTRALIWAYLRANAADLGGSRRKILRSLPEPVPLRITESPYFRALHPEVP 91
Query: 75 L 75
Sbjct: 92 A 92
>gnl|CDD|173103 PRK14640, PRK14640, hypothetical protein; Provisional.
Length = 152
Score = 29.2 bits (65), Expect = 0.85
Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 8/81 (9%)
Query: 69 AHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVSNNRAET 128
+H ++ + D + + L+ G+D + K + + + AA+ R+ +N R
Sbjct: 56 SHQVGAIMDVEDPITEEYYLEVSSPGLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFK 115
Query: 129 GPIRVFSDGRDPEVQGEVFPL 149
G I+ VQG++ L
Sbjct: 116 GVIK--------AVQGDMITL 128
>gnl|CDD|182711 PRK10766, PRK10766, DNA-binding transcriptional regulator TorR;
Provisional.
Length = 221
Score = 28.9 bits (65), Expect = 1.2
Identities = 20/56 (35%), Positives = 29/56 (51%)
Query: 57 GEKVLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARV 112
GE L L R +R+ S V +I ++ + + G DD V KP+ RE+L RV
Sbjct: 58 GEDGLMLTRELRSRSTVGIILVTGRTDSIDRIVGLEMGADDYVTKPLELRELLVRV 113
>gnl|CDD|162580 TIGR01884, cas_HTH, CRISPR locus-related DNA-binding protein. Most
but not all examples of this family are associated with
CRISPR loci, a combination of DNA repeats and
characteristic proteins encoded near the repeat cluster.
The C-terminal region of this protein is homologous to
DNA-binding helix-turn-helix domains with predicted
transcriptional regulatory activity.
Length = 203
Score = 28.5 bits (64), Expect = 1.4
Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 13/75 (17%)
Query: 147 FPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKLRNKLG 206
L R E ++LE L A K V + A + S IS+ ++L K G
Sbjct: 139 AGLSREELKVLEVLKAEGEKSVK------------NIAKKLGKSLSTISRHLRELEKK-G 185
Query: 207 FDPVDSKRFLGYSID 221
++ YS+
Sbjct: 186 LVEQKGRKGKRYSLT 200
>gnl|CDD|177346 PHA02102, PHA02102, hypothetical protein.
Length = 72
Score = 28.4 bits (63), Expect = 1.7
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 21 DDGVSLEGFNSLEFEEWLQSS 41
D GV + N + FE+WL SS
Sbjct: 29 DYGVEINDDNEVRFEDWLSSS 49
>gnl|CDD|183013 PRK11173, PRK11173, two-component response regulator; Provisional.
Length = 237
Score = 28.1 bits (63), Expect = 2.2
Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 16/86 (18%)
Query: 94 GVDDVVNKPIHHRE--ILARVAAIYRRLKVSNNRAETGPIRVFS--------DGR---DP 140
G DD + KP + RE I AR + R + + E + + + R P
Sbjct: 96 GADDYITKPFNPRELTIRAR-NLLSRTMNLGTVSEERRSVESYKFNGWELDINSRSLISP 154
Query: 141 EVQGEVFPLPRRERRILEYLMANRGK 166
+ GE + LPR E R + + N GK
Sbjct: 155 D--GEQYKLPRSEFRAMLHFCENPGK 178
>gnl|CDD|128698 smart00421, HTH_LUXR, helix_turn_helix, Lux Regulon. lux regulon
(activates the bioluminescence operon.
Length = 58
Score = 27.9 bits (63), Expect = 2.4
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 10/54 (18%)
Query: 148 PLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKL 201
L RER +L L G +I + G + E V++H+S + +KL
Sbjct: 3 SLTPREREVLRLLA--EGLTNK--EI-AERLG-----ISEKTVKTHLSNIMRKL 46
>gnl|CDD|180904 PRK07239, PRK07239, bifunctional uroporphyrinogen-III
synthetase/response regulator domain protein; Validated.
Length = 381
Score = 26.9 bits (60), Expect = 4.0
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 10/85 (11%)
Query: 117 RRLKVSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSA 176
R L+ + + E IR G V GEV PL +L L A G+ V++ + +A
Sbjct: 282 RTLRAAGHVLE---IR----GHAVVVDGEVKPLSPAPMALLRALAARPGRVVSREDLLAA 334
Query: 177 IYGLFDEAVEENVVESHISKLRKKL 201
+ G +E+ VE+ +++LR L
Sbjct: 335 LPG---GGTDEHAVETAVARLRTAL 356
>gnl|CDD|172377 PRK13856, PRK13856, two-component response regulator VirG;
Provisional.
Length = 241
Score = 27.1 bits (60), Expect = 4.2
Identities = 26/79 (32%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 58 EKVLELPRIIRAHSQVPLIGIS-DYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIY 116
E LE+ R + S VP+I IS D + + G D + KP RE LAR+
Sbjct: 58 EDGLEIVRSLATKSDVPIIIISGDRLEEADKVVALELGATDFIAKPFGTREFLARIRV-- 115
Query: 117 RRLKVSNNRAETGPIRVFS 135
L+V N T R F
Sbjct: 116 -ALRVRPNVVRTKDRRSFC 133
>gnl|CDD|132580 TIGR03541, reg_near_HchA, LuxR family transcriptional regulatory,
chaperone HchA-associated. Members of this protein
family belong to the LuxR transcriptional regulator
family, and contain both autoinducer binding (pfam03472)
and transcriptional regulator (pfam00196) domains.
Members, however, occur only in a few members of the
Gammaproteobacteria that have the
chaperone/aminopeptidase HchA, and are always encoded by
the adjacent gene.
Length = 232
Score = 26.7 bits (59), Expect = 5.1
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 138 RDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKL 197
+ + E L RER +L + G+R A +AI G+ E VE+H+
Sbjct: 161 LEAPLLREAGVLSEREREVLAWTAL--GRRQAD---IAAILGI-----SERTVENHLRSA 210
Query: 198 RKKL 201
R+KL
Sbjct: 211 RRKL 214
>gnl|CDD|162545 TIGR01818, ntrC, nitrogen regulation protein NR(I). This model
represents NtrC, a DNA-binding response regulator that
is phosphorylated by NtrB and interacts with sigma-54.
NtrC usually controls the expression of glutamine
synthase, GlnA, and may be called GlnL, GlnG, etc.
Length = 463
Score = 26.6 bits (59), Expect = 5.8
Identities = 14/51 (27%), Positives = 26/51 (50%)
Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVA 113
LP+I + H Q+P+I ++ + L T + + G + + KP E + V
Sbjct: 61 LPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDLDEAVTLVE 111
>gnl|CDD|178305 PLN02702, PLN02702, L-idonate 5-dehydrogenase.
Length = 364
Score = 26.3 bits (58), Expect = 5.9
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 53 LIGKGEKVLELPRIIRAHSQVPLIGISDYP-SLQTTLDFFDSGVDDVVNKP-IHHR 106
L+G G + +P A +V ++G+ Y + L+F SG DV KP I HR
Sbjct: 283 LVGMGHNEMTVPLTPAAAREVDVVGVFRYRNTWPLCLEFLRSGKIDV--KPLITHR 336
>gnl|CDD|161781 TIGR00234, tyrS, tyrosyl-tRNA synthetase. This tyrosyl-tRNA
synthetase model starts picking up tryptophanyl-tRNA
synthetases at scores of 0 and below. The proteins found
by this model have a deep split between two groups. One
group contains bacterial and organellar eukaryotic
examples. The other contains archaeal and cytosolic
eukaryotic examples.
Length = 377
Score = 25.8 bits (57), Expect = 8.8
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 5/53 (9%)
Query: 170 KTQIFSAIY--GLFDEAVEENVVESHISKLRKKLRNKLGFDPVDSKRFLGYSI 220
I + GL + EE + L +K++ +GFDP LG+ +
Sbjct: 1 MNNILLLLKKRGLEVQVPEEEELLKL---LERKIKLYVGFDPTAPSLHLGHLV 50
>gnl|CDD|132030 TIGR02985, Sig70_bacteroi1, RNA polymerase sigma-70 factor,
Bacteroides expansion family 1. This group of sigma
factors are members of the sigma-70 family (TIGR02937)
and are found primarily in the genus Bacteroides. This
family appears to have resulted from a lineage-specific
expansion as B. thetaiotaomicron VPI-5482, Bacteroides
forsythus ATCC 43037, Bacteroides fragilis YCH46 and
Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23
members, respectively. There are currentlyonly two known
members of this family outside of the Bacteroides, in
Rhodopseudomonas and Bradyrhizobium.
Length = 161
Score = 26.0 bits (58), Expect = 8.9
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 187 ENVVESHISKLRKKLRNKL 205
VE HISK K+LR +L
Sbjct: 143 VKTVEYHISKALKELRKEL 161
>gnl|CDD|179442 PRK02546, PRK02546, NAD(P)H-quinone oxidoreductase subunit 4;
Provisional.
Length = 525
Score = 25.8 bits (57), Expect = 9.2
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 73 VPLIGISDYPSLQTTLDFFDSGVDDVV 99
VP+IGI YP L T +D+ + +V
Sbjct: 473 VPIIGIGLYPKLVT--QSYDATTNQLV 497
>gnl|CDD|180311 PRK05912, PRK05912, tyrosyl-tRNA synthetase; Validated.
Length = 408
Score = 25.8 bits (58), Expect = 9.3
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 7/37 (18%)
Query: 180 LFDEAVEENVVE--SHISKLRKKLRN-----KLGFDP 209
L +E E ++E + +L +KL LGFDP
Sbjct: 6 LLEELKERGLIEQITDEEELEEKLAKEPLRIYLGFDP 42
>gnl|CDD|165207 PHA02876, PHA02876, ankyrin repeat protein; Provisional.
Length = 682
Score = 25.8 bits (56), Expect = 9.6
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 5/27 (18%)
Query: 84 LQTTLDFFDSG-----VDDVVNKPIHH 105
L+T+L +D+G +DD N P+HH
Sbjct: 253 LETSLLLYDAGFSVNSIDDCKNTPLHH 279
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.321 0.140 0.404
Gapped
Lambda K H
0.267 0.0731 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,855,859
Number of extensions: 253286
Number of successful extensions: 564
Number of sequences better than 10.0: 1
Number of HSP's gapped: 544
Number of HSP's successfully gapped: 48
Length of query: 223
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 133
Effective length of database: 4,049,753
Effective search space: 538617149
Effective search space used: 538617149
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 (21.8 bits)
S2: 55 (25.0 bits)