RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781170|ref|YP_003065583.1| deoxyribodipyrimidine
photolyase [Candidatus Liberibacter asiaticus str. psy62]
(483 letters)
>gnl|CDD|30764 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication,
recombination, and repair].
Length = 461
Score = 486 bits (1253), Expect = e-138
Identities = 213/475 (44%), Positives = 274/475 (57%), Gaps = 17/475 (3%)
Query: 7 MSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLL 66
S LVW R DLR+TDN AL AAC + +IAVFI PEQ S R + F+ SL
Sbjct: 1 TSTVLVWFRRDLRLTDNAALAAACQSGQPVIIAVFILDPEQLGHA--SPRHAAFLLQSLQ 58
Query: 67 QVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKR 126
+Q+SL++ GI + E T +F+NR YE E +RD L +
Sbjct: 59 ALQQSLAELGIPLLVREGDPEQVLPELAKQLA----ATTVFWNRDYEEWERQRDAALAQP 114
Query: 127 L-QHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLT 185
L + + SF D++L PG + + + YKV+TPF KA L P L
Sbjct: 115 LTEVGIAVHSFWDALLHEPGEVRTGSGEPYKVFTPFYKAWRDRLRILRPVPAPDVLDALR 174
Query: 186 GPVTPSNIPRFFDYPFQAID--PMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTS 243
P P + +F GE+ AL L+ F E + Y RD PA+ GTS
Sbjct: 175 DEEPPPEE---ISLPDFSKFDVLLFTGGEKAALARLQDFLAEGLDDYERTRDFPALDGTS 231
Query: 244 QLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCM 303
+LSPYL+ GV+SPR+ + L D + G + +NELIWREFY+HL+ YPS+
Sbjct: 232 RLSPYLAFGVISPREVYAALLAAESD----AREGTAALINELIWREFYQHLLYHYPSLSR 287
Query: 304 GKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVK 363
+PF T I W + QAW++G TG+PI+DAAMRQLN G+MHNR+RMI ASFL K
Sbjct: 288 FEPFAEKTLNIPWEDNPAHFQAWQEGKTGYPIVDAAMRQLNQTGYMHNRMRMIVASFLTK 347
Query: 364 DLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGT 423
DLL+DWR GE+YFM QL+DGD ASNNGGWQWAASTG D+ PYFRIFNP Q ++FDP G
Sbjct: 348 DLLIDWREGEKYFMRQLIDGDPASNNGGWQWAASTGTDAAPYFRIFNPVTQAEKFDPDGE 407
Query: 424 FIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAK 478
FIR W+PEL N+P +YIH P + L ++YP PIVDHK++ L Y AAK
Sbjct: 408 FIRRWVPELRNLPDKYIHEPWEL-SEVVLGVDYPKPIVDHKESREQALAAYEAAK 461
>gnl|CDD|146197 pfam03441, FAD_binding_7, FAD binding domain of DNA photolyase.
Length = 275
Score = 377 bits (970), Expect = e-105
Identities = 137/275 (49%), Positives = 172/275 (62%), Gaps = 8/275 (2%)
Query: 211 GEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDL 270
GE+ AL L F KE++ Y + RD PA GTS+LSPYL G +SPRQ + +++
Sbjct: 2 GEKAALKRLESFLKERLADYAKDRDDPAADGTSRLSPYLHFGEISPRQVYQAVRKAAGAP 61
Query: 271 LIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSH---LLQAWK 327
GA ++L+ELIWREFY L+ P + P + + W KD LL+AW+
Sbjct: 62 GSAASEGAEAFLSELIWREFYIQLLYHNPDLERE-NLNPAYDGLPWAKDRPDEYLLEAWE 120
Query: 328 QGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLAS 387
+G TG+P++DAAMRQL GWMHNRLRMI ASFL K LL+DWR GEEYF L+D D AS
Sbjct: 121 EGRTGYPLVDAAMRQLRQTGWMHNRLRMIVASFLTKKLLIDWREGEEYFAETLIDADPAS 180
Query: 388 NNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSW- 446
NNGGWQW A TG D+ PYFRIFNP Q +FDP G +IR W+PEL +P +YIH P
Sbjct: 181 NNGGWQWQAGTGTDAAPYFRIFNPVKQSDKFDPNGEYIRRWVPELAGLPDRYIHEPWKAP 240
Query: 447 ---LDKNDLSLNYPLPIVDHKKACHHTLNQYYAAK 478
L +YP PIVDHK+A L+ Y AA+
Sbjct: 241 RPVQAGAVLGKDYPKPIVDHKEARKRALDAYKAAR 275
>gnl|CDD|35355 KOG0133, KOG0133, KOG0133, Deoxyribodipyrimidine
photolyase/cryptochrome [Replication, recombination and
repair, Signal transduction mechanisms].
Length = 531
Score = 237 bits (605), Expect = 6e-63
Identities = 141/506 (27%), Positives = 207/506 (40%), Gaps = 50/506 (9%)
Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQK 70
+ W R LR+ DN AL AA + V VFI PE+ + + F+ SL + +
Sbjct: 8 VHWFRKGLRLHDNPALLAAAAGKE-PVRPVFILDPEEAGSSNVGRNRWRFLLQSLEDLDQ 66
Query: 71 SLSQKGI---VFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRL 127
SL + VF+ H + +E Q V KL + E + RD ++
Sbjct: 67 SLRELNSRLFVFRGHPIAVLSRLLE-------QVGVQKLKFEYDMEPDGKVRDATIKSLA 119
Query: 128 QHRVI-CKSFDDSVLLPPGSILNHALQMYKV-YTPFRKALIQNLVQADLRSLPVPAIRLT 185
+ S L P I+ + Y FR V + + +PA+ L+
Sbjct: 120 TELGLSVVSPVSHTLYLPDKIIEANGGKPPLSYKTFRG------VCQSMSAPKIPALVLS 173
Query: 186 G---PVTP---------SNIPRFFDYPFQ---AIDPMFPIGEQNALHILRKFCKEKVYYY 230
G P + +P F + ++ GE AL L K ++
Sbjct: 174 GLAVEKHPNFLANSKASAVVPTLELLRFIPSNYGEVVWRGGESEALKRLDAHLKVPLWVA 233
Query: 231 VEQ-----RDIPAIQGTSQLSPYLSIGVLSPRQ--CWNRLKEEFVDLLIKPKSGAFSWLN 283
+ + T+ LSPYL G LS R RLK+ +L
Sbjct: 234 NLELRYSNANSRVKISTTVLSPYLKFGCLSVRYFYRCVRLKQVKWKAKKNSLPPESLFLG 293
Query: 284 ELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQL 343
++ WREF+ P P +I W+K+ L AW +G TG+P +DA MRQL
Sbjct: 294 QVAWREFFYTAAFNTPYF-DDMPGNKILLQIPWDKNPPKLAAWLEGLTGYPWLDAGMRQL 352
Query: 344 NTIGWMHNRLRMITASFLVK-DLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDS 402
GW H+R R I ASFL + DLL+ WR G + FM LLD D + N G W W +ST +
Sbjct: 353 LASGWEHHRSRTIVASFLTRGDLLISWREGLDVFMEYLLDADSSKNAGNWMWLSSTSHFF 412
Query: 403 VPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHS------WLDKNDLSLNY 456
+ R+++P GK+ DP G +IR WLPEL + P +I+ P + L ++Y
Sbjct: 413 DQFDRVYSPVALGKKLDPDGLYIRQWLPELRSGPMHFIYEPWAAPEGVQTAAGELLGVDY 472
Query: 457 PLPIVDHKKACHHTLNQYYAAKKQSL 482
P PIV A +
Sbjct: 473 PKPIVKLASA-AKRNMEAMGCMWSIG 497
>gnl|CDD|144461 pfam00875, DNA_photolyase, DNA photolyase. This domain binds a
light harvesting cofactor.
Length = 164
Score = 155 bits (394), Expect = 3e-38
Identities = 64/172 (37%), Positives = 91/172 (52%), Gaps = 10/172 (5%)
Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQK 70
LVW R DLR+ DN AL AA + VI VFI P Q H + A + F+ SL + +
Sbjct: 2 LVWFRRDLRLHDNPALAAAAASGA-PVIPVFILDPAQLGSHKLGAARRWFLLESLADLDE 60
Query: 71 SLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHR 130
SL++ GI + D E L + + +++NR YE E RRD +++ L+
Sbjct: 61 SLAKLGIPLIVRRG----DPAEVLPELAKELGASAVYWNRDYEPYERRRDAAVKEALREA 116
Query: 131 VI-CKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPA 181
I SFDD +L+PPG +L + YKV+TPF KA ++ L+ LP PA
Sbjct: 117 GIEVHSFDDHLLVPPGEVLTKKGEPYKVFTPFWKAWLKELLPP----LPAPA 164
>gnl|CDD|32860 COG3046, COG3046, Uncharacterized protein related to
deoxyribodipyrimidine photolyase [General function
prediction only].
Length = 505
Score = 33.8 bits (77), Expect = 0.12
Identities = 39/179 (21%), Positives = 74/179 (41%), Gaps = 24/179 (13%)
Query: 193 IPRFFDYPFQAIDPM-FPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGT----SQLSP 247
+ R F F ++ +P+ AL L+ F +++ + +D + S LS
Sbjct: 207 VERLFPDNFGQVEGFGWPVTRTQALRALKHFIADRLPNFGSYQDAMSADDPHLWHSLLSF 266
Query: 248 YLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELI-WREF----YRHLMAFYPSVC 302
L+IG+L+P + + + + I P + ++ ++I WREF Y M Y
Sbjct: 267 ALNIGLLTPLEVIRAALKAYREGDI-PLNSVEGFVRQIIGWREFMRGIYWLKMPDY---- 321
Query: 303 MGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLR-MITASF 360
+ +N D L + G T + A+ ++ G+ H+ R M+T +F
Sbjct: 322 --------ATRNFFNADRKLPPFYWTGQTKMACLAIAVGRVLDHGYAHHIQRLMVTGNF 372
>gnl|CDD|32197 COG2014, COG2014, Uncharacterized conserved protein [Function
unknown].
Length = 250
Score = 33.0 bits (75), Expect = 0.21
Identities = 40/231 (17%), Positives = 76/231 (32%), Gaps = 63/231 (27%)
Query: 36 KVIAVFIATPEQWRQHGIS------------ARQSHFIYASL-LQVQKSLSQKGIVFQYH 82
K + V + E+ +++G S A I +L + ++SQ I +
Sbjct: 42 KSLGVAMTLFEEVQRYGNSIELKSLEEFIELADSLDPIERTLGVAAINAVSQYYIDLE-- 99
Query: 83 QCSNFDDSIEWLDSYCLQQRVTKLFY-----------NRQYEINEVRRDKLLEKR----- 126
+ + FD LD ++ + ++E+ R+ L KR
Sbjct: 100 EANWFD----ILDLIQRDDKIKMIAEFGNMPPVVRTLKEKFEVYVFERNPKLPKRGTLSD 155
Query: 127 -LQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLT 185
L+++++ + D ++ +++N L M L +A L V LT
Sbjct: 156 TLEYQILPEV--DVIIASASTLVNGTLDMI-------------LDRAKKAKLVV----LT 196
Query: 186 GPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILR--------KFCKEKVY 228
GP F I I AL L+ + + +Y
Sbjct: 197 GPTAQLLPEFFKGTGVTHIAGTKIIDPDKALLKLKFASFKGFHEKSGKYIY 247
>gnl|CDD|144230 pfam00563, EAL, EAL domain. This domain is found in diverse
bacterial signaling proteins. It is called EAL after its
conserved residues. The EAL domain is a good candidate
for a diguanylate phosphodiesterase function. The domain
contains many conserved acidic residues that could
participate in metal binding and might form the
phosphodiesterase active site.
Length = 233
Score = 31.6 bits (72), Expect = 0.51
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 24 KALYAACHNSDAKVIAVFIATPEQW---RQHGISARQSHFI 61
+AL A KV+A + T EQ ++ GI Q +
Sbjct: 190 RALIALARELGIKVVAEGVETEEQLELLKELGIDYVQGYLF 230
>gnl|CDD|32382 COG2200, Rtn, FOG: EAL domain [Signal transduction mechanisms].
Length = 256
Score = 31.4 bits (71), Expect = 0.57
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 3/41 (7%)
Query: 24 KALYAACHNSDAKVIAVFIATPEQW---RQHGISARQSHFI 61
+A+ A H V+A + T EQ R+ G Q +
Sbjct: 196 RAIVALAHKLGLTVVAEGVETEEQLDLLRELGCDYLQGYLF 236
>gnl|CDD|36313 KOG1097, KOG1097, KOG1097, Adenine deaminase/adenosine deaminase
[Nucleotide transport and metabolism].
Length = 399
Score = 29.5 bits (66), Expect = 1.9
Identities = 19/113 (16%), Positives = 38/113 (33%)
Query: 120 DKLLEKRLQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPV 179
+K+LE+ + D+ L G ++ Y + +V ++R+ P
Sbjct: 86 EKVLERYKPLYPLADFLDNIFYLLHGLLIYAPAFRDYAYEALEEFAEDGVVYLEVRTYPP 145
Query: 180 PAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVE 232
G +TP ++ + FPI + + +R E V
Sbjct: 146 QLYTADGDITPEDVVAIVIAALEKAKRDFPIKSKLIMCCIRHMPPEVAEETVS 198
>gnl|CDD|30163 cd01948, EAL, EAL domain. This domain is found in diverse bacterial
signaling proteins. It is called EAL after its conserved
residues and is also known as domain of unknown function
2 (DUF2). The EAL domain has been shown to stimulate
degradation of a second messenger, cyclic di-GMP, and is
a good candidate for a diguanylate phosphodiesterase
function. Together with the GGDEF domain, EAL might be
involved in regulating cell surface adhesiveness in
bacteria..
Length = 240
Score = 28.6 bits (64), Expect = 3.9
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 24 KALYAACHNSDAKVIAVFIATPEQW---RQHGISARQSHFI 61
+A+ A H+ KV+A + T EQ R+ G Q +
Sbjct: 192 RAIIALAHSLGLKVVAEGVETEEQLELLRELGCDYVQGYLF 232
>gnl|CDD|114461 pfam05736, OprF, OprF membrane domain. This domain represents the
presumed membrane spanning region of the OprF proteins.
This region is involved in channel formation and is
thought to form an 8-stranded beta-barrel.
Length = 184
Score = 28.6 bits (64), Expect = 4.0
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 367 VDWRIGEEYFMSQLLDGDLASNNGGWQWAASTG 399
+ E ++ ++ +NG W+WAA G
Sbjct: 143 AKYYFTENFYARAGVEAQYGLDNGDWEWAALVG 175
>gnl|CDD|37525 KOG2314, KOG2314, KOG2314, Translation initiation factor 3, subunit
b (eIF-3b) [Translation, ribosomal structure and
biogenesis].
Length = 698
Score = 27.6 bits (61), Expect = 7.5
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 411 PTIQGKRFDPQGTFIRHWLPELNNVP 436
I+ + P + +W PE NN+P
Sbjct: 347 SGIRDFSWSPTSNLLAYWTPETNNIP 372
>gnl|CDD|146390 pfam03726, PNPase, Polyribonucleotide nucleotidyltransferase, RNA
binding domain. This family contains the RNA binding
domain of Polyribonucleotide nucleotidyltransferase
(PNPase) PNPase is involved in mRNA degradation in a
3'-5' direction.
Length = 80
Score = 27.6 bits (62), Expect = 7.6
Identities = 11/48 (22%), Positives = 19/48 (39%), Gaps = 5/48 (10%)
Query: 18 LRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASL 65
IT + YAA A V+A F ++ ++ I+ +L
Sbjct: 18 YTITGKQERYAALDEIKADVVAAFAEEEDE-----EDEKEIKDIFKAL 60
>gnl|CDD|36684 KOG1471, KOG1471, KOG1471, Phosphatidylinositol transfer protein
SEC14 and related proteins [Lipid transport and
metabolism].
Length = 317
Score = 27.4 bits (60), Expect = 8.9
Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 3/78 (3%)
Query: 192 NIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQG---TSQLSPY 248
N P F ++ + P + +H+L KE + Y+ +P G P
Sbjct: 205 NAPTIFSALWKVVKPFLDEKTRKKIHVLHSKDKESLLKYIPPEVLPEEYGGTCGDLDDPN 264
Query: 249 LSIGVLSPRQCWNRLKEE 266
LS W + +
Sbjct: 265 GGGCDLSDEGPWKEPEIK 282
>gnl|CDD|107382 cd06387, PBP1_iGluR_AMPA_GluR3, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR3 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR3 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 372
Score = 27.3 bits (60), Expect = 9.5
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 302 CMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLN 344
C+ P +PW++ I+ + ++Q QG TG D R+ N
Sbjct: 306 CLANPAVPWSQGIDIERALKMVQV--QGMTGNIQFDTYGRRTN 346
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.324 0.138 0.444
Gapped
Lambda K H
0.267 0.0629 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 6,449,593
Number of extensions: 357705
Number of successful extensions: 974
Number of sequences better than 10.0: 1
Number of HSP's gapped: 957
Number of HSP's successfully gapped: 19
Length of query: 483
Length of database: 6,263,737
Length adjustment: 98
Effective length of query: 385
Effective length of database: 4,146,055
Effective search space: 1596231175
Effective search space used: 1596231175
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: 59 (26.7 bits)