RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14494
(470 letters)
>gnl|CDD|223492 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication,
recombination, and repair].
Length = 461
Score = 386 bits (994), Expect = e-131
Identities = 157/464 (33%), Positives = 247/464 (53%), Gaps = 35/464 (7%)
Query: 3 VYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIKK 62
+ VFI D L G R F+ +S+ L +L L++R + + +
Sbjct: 31 IIAVFILDPEQL------GHASPRHAAFLLQSLQALQQSLAELGIPLLVREGDPEQVLPE 84
Query: 63 LVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKPY 122
L +L V N DYE RD + + L +G S+ D ++ E E+ +G+PY
Sbjct: 85 LAKQLAATTVFWNRDYEEWERQRDAALAQPLTEVGIAVHSFWDALLHEPGEVRTGSGEPY 144
Query: 123 SIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDLGFCKSNL 182
+F+ + K W ++++ + + + + + ISL D S
Sbjct: 145 KVFTPFYKAWRDRLRILRPVPAPDVLDALRD---------EEPPPEEISLPDF----SKF 191
Query: 183 SSLGIKTGASGAKILLNNFIK-KIKNYNINRNYPSINGTSYLSIHLRFGTISIRKLVKLI 241
L G A L +F+ + +Y R++P+++GTS LS +L FG IS R+ +
Sbjct: 192 DVLLFTGGEKAALARLQDFLAEGLDDYERTRDFPALDGTSRLSPYLAFGVISPRE----V 247
Query: 242 FKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVV-NKSFKKEYDNILWESDNYAK 300
+ + G +++LIWR+FYQ +LY YP++ + F ++ NI WE +
Sbjct: 248 YAALLAAESDAREGTAALINELIWREFYQHLLYHYPSLSRFEPFAEKTLNIPWEDNPAH- 306
Query: 301 KNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKL 360
F W +G TGYP++D+A+ QLN +GYMHNR+RM+ ASFL K++ I+W+ GE YF +L
Sbjct: 307 --FQAWQEGKTGYPIVDAAMRQLNQTGYMHNRMRMIVASFLTKDLLIDWREGEKYFMRQL 364
Query: 361 NDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYI 420
D D ASNNG WQW+AS+G + P+FRIFNP+ Q++KFD G FIR+++P+L L +KYI
Sbjct: 365 IDGDPASNNGGWQWAASTGTDAAPYFRIFNPVTQAEKFDPDGEFIRRWVPELRNLPDKYI 424
Query: 421 HSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYNFIK 464
H PW+ S ++LG +YPKPI++H S++ L Y K
Sbjct: 425 HEPWELSE-------VVLGVDYPKPIVDHKESREQALAAYEAAK 461
>gnl|CDD|217559 pfam03441, FAD_binding_7, FAD binding domain of DNA photolyase.
Length = 276
Score = 336 bits (864), Expect = e-114
Identities = 119/273 (43%), Positives = 174/273 (63%), Gaps = 4/273 (1%)
Query: 190 GASGAKILLNNFIK-KIKNYNINRNYPSINGTSYLSIHLRFGTISIRKLVKLIFKFIKKH 248
G A L +F+K ++ +Y +R+ P+ +GTS LS +L FG IS R++ + + K
Sbjct: 2 GEKAALKRLESFLKERLADYAKDRDDPAADGTSRLSPYLHFGEISPRQVYQAVRKAQGDS 61
Query: 249 YKTDC-IGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESDNYAKKNFLNWC 307
+ G +LS+LIWR+FY +LY P++ ++ YD + W D + W
Sbjct: 62 PEGGAKQGAEAFLSELIWREFYIQLLYHNPDLERENLNDAYDGLPWAKDRPDEYLLEAWE 121
Query: 308 KGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKLNDFDLAS 367
+G TGYPL+D+A+ QL +G+MHNRLRM+ ASFL K + I+W+ GE YFA L D D AS
Sbjct: 122 EGRTGYPLVDAAMRQLRQTGWMHNRLRMIVASFLTKKLLIDWREGEEYFAETLIDADPAS 181
Query: 368 NNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYIHSPWKAS 427
NNG WQW A +G + P+FRIFNP+ QS KFD G +IR+++P+L+ L ++YIH PWKA
Sbjct: 182 NNGGWQWQAGTGTDAAPYFRIFNPVKQSDKFDPNGEYIRRWVPELAGLPDRYIHEPWKAP 241
Query: 428 SYKLEKAGIILGKNYPKPILEHSLSKKNILKRY 460
+ +AG +LGK+YPKPI++H ++K L Y
Sbjct: 242 --RPVQAGCVLGKDYPKPIVDHKEARKRALDAY 272
>gnl|CDD|132595 TIGR03556, photolyase_8HDF, deoxyribodipyrimidine photo-lyase,
8-HDF type. This model describes a narrow clade of
cyanobacterial deoxyribodipyrimidine photo-lyase. This
group, in contrast to several closely related proteins,
uses a chromophore that, in other lineages is modified
further to become coenzyme F420. This chromophore is
called 8-HDF in most articles on the DNA photolyase and
FO in most literature on coenzyme F420 [DNA metabolism,
DNA replication, recombination, and repair].
Length = 471
Score = 305 bits (782), Expect = 4e-99
Identities = 153/463 (33%), Positives = 238/463 (51%), Gaps = 32/463 (6%)
Query: 6 VFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIKKLVI 65
+F D NIL + R+ ++ + EL Q S L+I + I +L
Sbjct: 32 LFCLDPNIL----QADDMAPARVAYLIGCLQELQQRYQQAGSQLLILQGDPVQLIPQLAQ 87
Query: 66 KLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKPYSIF 125
+L AV N D EP RD+ + LK G + DQ++ +EIL +G PY+++
Sbjct: 88 QLGAKAVYWNLDVEPYGRKRDRAVAAALKEAGIAVVTLWDQLLHSPDEILTGSGNPYTVY 147
Query: 126 SFYQKKWIEKVKSNKCYLQSYPVKSYLNNLV-----HSSKLHKIINNNIISLNDLGFCKS 180
+ + K W K PV + L + + + DLGF
Sbjct: 148 TPFWKNWSSLPKPT-------PVAT-PTELEGLTEAELEAAAPLGVIALPTAKDLGFDWD 199
Query: 181 NLSSLGIKTGASGAKILLNNFIKK-IKNYNINRNYPSINGTSYLSIHLRFGTISIRKLVK 239
L ++ G + A+ L F + I +Y RN+P+++GTS LS L+FG I IR + +
Sbjct: 200 G--DLILEPGETAAQARLEEFCDRAIADYQEQRNFPALDGTSQLSPALKFGVIGIRTVWQ 257
Query: 240 LIFKFIKKHYKTDCIGYF-TWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESDNY 298
+ + + TW +L WR+FYQ LY +P + + ++ + N WE++
Sbjct: 258 ATQEAHENSRSEEARNSIRTWQQELAWREFYQHALYHFPELADGPYRSLFQNFPWENN-- 315
Query: 299 AKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFAN 358
+ +F WC+G TGYP++D+A+ QLN +G+MHNR RM+ ASFL K++ INW+WGE YF
Sbjct: 316 -EAHFQAWCEGRTGYPIVDAAMRQLNETGWMHNRCRMIVASFLTKDLIINWQWGEKYFMQ 374
Query: 359 KLNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNK 418
KL D DLA+NNG WQWSASSG +P RIFNP Q++KFD + +IR++LP+L + K
Sbjct: 375 KLIDGDLAANNGGWQWSASSGMDPKP-LRIFNPASQAQKFDPEAEYIRRWLPELRSVDTK 433
Query: 419 YIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYN 461
+ + LE+ + YP PI++H+ ++ + Y
Sbjct: 434 DLVT---GKITPLERRAV----GYPLPIVDHNQQQQLFKQLYQ 469
>gnl|CDD|236734 PRK10674, PRK10674, deoxyribodipyrimidine photolyase; Provisional.
Length = 472
Score = 264 bits (677), Expect = 3e-83
Identities = 124/396 (31%), Positives = 219/396 (55%), Gaps = 31/396 (7%)
Query: 69 IDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKPYSIFSFY 128
+ + N+ YE RD +++ L+ + C+ + D V+ ++ + Y +F+ +
Sbjct: 97 VTHLFYNYQYEVNERQRDAAVERALRNVVCQ--GFDDSVLLPPGSVMTGNHEMYKVFTPF 154
Query: 129 QKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDLGFCKSNLSSLGIK 188
+ ++++++ V + K+ + + + + +
Sbjct: 155 KNAFLKRLREG------------DPECVPAPKVRSSGAIEPLPPIPFNYPQQSFDTALFP 202
Query: 189 TGASGAKILLNNFIKK-IKNYNINRNYPSINGTSYLSIHLRFGTISIRKLVKLIFKFIKK 247
G A L F ++ Y R++P+++GTS LS +L G +S R+ + + + +
Sbjct: 203 VGEKAAIAQLRQFCQQGAGEYEQQRDFPAVDGTSRLSAYLATGVLSPRQCLH---RLLAE 259
Query: 248 HYK--TDCIGYFTWLSQLIWRDFYQMILYCYPNVV-NKSFKKEYDNILWESDNYAKKNFL 304
+ G WL++LIWR+FY+ ++ YP++ ++ F D + W+S+ +
Sbjct: 260 QPQALDGGAG-SVWLNELIWREFYRHLMVAYPSLCKHRPFIAWTDRVQWQSN---PAHLQ 315
Query: 305 NWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKLNDFD 364
W +G TGYP++D+A+ QLNS+G+MHNRLRM+TASFL+K++ I+W+ GE YF ++L D D
Sbjct: 316 AWQQGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGD 375
Query: 365 LASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYIHSPW 424
LA+NNG WQW+AS+G + P+FRIFNP Q ++FD G FIR++LP+L + K IH PW
Sbjct: 376 LAANNGGWQWAASTGTDAAPYFRIFNPTTQGERFDRDGEFIRRWLPELRDVPGKAIHQPW 435
Query: 425 KASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRY 460
+ + EKAG+ L +YP+PI++H ++ L Y
Sbjct: 436 RWA----EKAGVTL--DYPQPIVDHKQARLATLAAY 465
>gnl|CDD|131813 TIGR02766, crypt_chrom_pln, cryptochrome, plant family. At least
five major families of cryptochomes and photolyases
share FAD cofactor binding, sequence homology, and the
ability to react to short wavelengths of visible light.
Photolysases are responsible for light-dependent DNA
repair by removal of two types of uv-induced DNA
dimerizations. Cryptochromes have other functions, often
regulatory and often largely unknown, which may include
circadian clock entrainment and control of development.
Members of this subfamily are known so far only in
plants; they may show some photolyase activity in vitro
but appear mostly to be regulatory proteins that respond
to blue light.
Length = 475
Score = 202 bits (516), Expect = 1e-59
Identities = 126/431 (29%), Positives = 212/431 (49%), Gaps = 36/431 (8%)
Query: 33 KSIIELSINLQNYDSDLI-IRYAIASKEIKKLVIKLNIDAVMINHDYEPQAIIRDKLIKK 91
+S+ L +L++ + L+ IR + V + NH Y+P +++RD K+
Sbjct: 51 QSLAHLDQSLRSLGTCLVTIRSTDTVAALLDCVRSTGATRLFFNHLYDPVSLVRDHRAKE 110
Query: 92 ELKVIGCKFFSYKDQVIFEKNEILNKTGKPYSIFSFYQKKWIEKVKSNKCYLQSYPVKSY 151
L G S+ +++E E+ ++ G+P+++F+ + W +C Y +S
Sbjct: 111 VLTAQGISVQSFNADLLYEPWEVYDELGRPFTMFAAF---W------ERCLSMPYDPESP 161
Query: 152 LNNLVHSSKLHKIINNNI--ISLNDLGF-CKSNLSSLGIKT-----GASGAKILLNNFIK 203
L KII+ ++ S +DLGF S S + G S A L FI
Sbjct: 162 L------LPPKKIISGDVSKCSADDLGFEDDSEKGSNALLARAWSPGWSNADKALTEFIN 215
Query: 204 K-IKNYNINRNYPSINGTSYLSIHLRFGTISIRKLVKLI-FKFI-----KKHYKTDCIGY 256
+ Y+ NR TS LS +L FG +S+RK+ L+ K I + +
Sbjct: 216 GPLLEYSKNRKKADSATTSLLSPYLHFGEVSVRKVFHLVRMKQIAWANEGNSAGEESVNL 275
Query: 257 FTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESDNYAKKNFLNWCKGYTGYPLI 316
F L + R++ + I + +P K W D + F W +G TGYPL+
Sbjct: 276 F--LRSIGLREYSRYISFNHPFSHEKPLLGHLKFFPWAVD---ENYFKAWRQGRTGYPLV 330
Query: 317 DSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKLNDFDLASNNGNWQWSA 376
D+ + +L ++G++H+R+R+V +SF +K + + W+WG YF + L D DL S+ WQ+ +
Sbjct: 331 DAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWRWGMKYFWDTLLDADLESDALGWQYIS 390
Query: 377 SSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYIHSPWKASSYKLEKAGI 436
S + RI NP ++ KFD G ++R++LP+L++L ++IH PW A L+ AG+
Sbjct: 391 GSLPDGRELDRIDNPQLEGYKFDPNGEYVRRWLPELARLPTEWIHHPWDAPESVLQAAGV 450
Query: 437 ILGKNYPKPIL 447
LG NYP PI+
Sbjct: 451 ELGSNYPLPIV 461
>gnl|CDD|234002 TIGR02765, crypto_DASH, cryptochrome, DASH family. Photolyases and
cryptochromes are related flavoproteins. Photolyases
harness the energy of blue light to repair DNA damage by
removing pyrimidine dimers. Cryptochromes do not repair
DNA and are presumed to act instead in some other
(possibly unknown) process such as entraining circadian
rhythms. This model describes the cryptochrome DASH
subfamily, one of at least five major subfamilies, which
is found in plants, animals, marine bacteria, etc.
Members of this family bind both folate and FAD. They
may show weak photolyase activity in vitro but have not
been shown to affect DNA repair in vivo. Rather, DASH
family cryptochromes have been shown to bind RNA (Vibrio
cholerae VC1814), or DNA, and seem likely to act in
light-responsive regulatory processes [Cellular
processes, Adaptations to atypical conditions,
Regulatory functions, DNA interactions].
Length = 429
Score = 140 bits (355), Expect = 5e-37
Identities = 99/403 (24%), Positives = 185/403 (45%), Gaps = 45/403 (11%)
Query: 27 RIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIKKLVIKLNIDAVMINHD---YEPQAI 83
R +F+ +S+ +L +L+ SDL++R + +L+ +L + V ++ + E
Sbjct: 55 RGKFLLESLKDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFLHQEVGSEEKSVE 114
Query: 84 IRDKLIKKELKVIGCKFFS----YKDQVIFEKNEILNKTGKPYSIFSFYQKKWIEKVKSN 139
+ L + + + ++D + F+ ++ P +F+ ++K+ K
Sbjct: 115 RLLQQALARLGIHVEQHWGSTLYHEDDLPFDLEDL------P-DVFTQFRKQVEAKCSIR 167
Query: 140 KCYLQSYPVKSYLNNLVHSSKLHKIINNNII-SLNDLGFCKSNLS-SLGIKTGASGAKIL 197
P L L + + I +L DLG S + L G +
Sbjct: 168 -------PPLPAPEKLPP---LPSVDDPGWIPTLEDLGEESSEVDRGLPFVGGETAGLAR 217
Query: 198 LNNFI--KKIKNYNINRNYPSINGTSY---LSIHLRFGTISIRKLVKLIFKFIKKHYKTD 252
L + K +K+Y RN + G Y S L G +S R++ + + ++ + D
Sbjct: 218 LKEYFWSKDLKSYKETRN--GMLGPDYSTKFSPWLALGCVSPRQIYEELQRYETERGAND 275
Query: 253 CIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDN---ILWESDNYAKKNFLNWCKG 309
+ + +L+WRD+++ Y N + F+ W D K F W G
Sbjct: 276 --STYWVIFELLWRDYFRFYALKYGN---RLFRFGGLRGKHPKWSFD---AKRFEQWKTG 327
Query: 310 YTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKLNDFDLASNN 369
TGYPL+D+ + +LN++G+M NR R ASFL+K++G++W++G +F +L D+D+ SN
Sbjct: 328 TTGYPLVDANMRELNATGFMSNRGRQNVASFLVKDLGLDWRYGAEWFETQLVDYDVCSNW 387
Query: 370 GNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQL 412
GNWQ+ A G + R FN Q++ +D G ++ ++P+L
Sbjct: 388 GNWQYLAGVGNDPRG-SRQFNIEKQAQDYDPDGEYVATWVPEL 429
>gnl|CDD|216167 pfam00875, DNA_photolyase, DNA photolyase. This domain binds a
light harvesting cofactor.
Length = 164
Score = 119 bits (300), Expect = 8e-32
Identities = 39/134 (29%), Positives = 67/134 (50%), Gaps = 4/134 (2%)
Query: 2 EVYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIK 61
V VFI D L + + R F+ +S+ +L +L L++R ++ +
Sbjct: 26 PVIPVFILDPAQLGSHK----LGAARRWFLLESLADLDESLAKLGIRLVVRRGDPAEVLP 81
Query: 62 KLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKP 121
+L +L AV N DYEP RD +K+ L+ G + S+ D ++ E+L K GKP
Sbjct: 82 ELAKELGASAVYWNRDYEPYERQRDAAVKEALREAGIEVHSFDDHLLVPPGEVLTKKGKP 141
Query: 122 YSIFSFYQKKWIEK 135
Y +F+ + K W+++
Sbjct: 142 YKVFTPFWKAWLKE 155
>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 = 32.1 bits (73), Expect = 0.41
Identities = 11/42 (26%), Positives = 22/42 (52%)
Query: 338 ASFLIKNMGINWKWGENYFANKLNDFDLASNNGNWQWSASSG 379
++F G + + EN++A + +NG+W+W+A G
Sbjct: 134 STFANIGAGAKYYFTENFYARAGVEAQYGLDNGDWEWAALVG 175
>gnl|CDD|223115 COG0037, MesJ, tRNA(Ile)-lysidine synthase MesJ [Cell cycle
control, cell division, chromosome partitioning].
Length = 298
Score = 32.1 bits (73), Expect = 0.47
Identities = 9/58 (15%), Positives = 26/58 (44%)
Query: 61 KKLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKT 118
K+L ++ ++AV ++H + +L++K + +G + + + K+
Sbjct: 42 KELGRRIEVEAVHVDHGLRGYSDQEAELVEKLCEKLGIPLIVERVTDDLGRETLDGKS 99
>gnl|CDD|129679 TIGR00591, phr2, photolyase PhrII. All proteins in this family for
which functions are known are DNA-photolyases used for
the direct repair of UV irradiation induced DNA damage.
Some repair 6-4 photoproducts while others repair
cyclobutane pyrimidine dimers. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 454
Score = 30.9 bits (70), Expect = 1.4
Identities = 38/161 (23%), Positives = 64/161 (39%), Gaps = 24/161 (14%)
Query: 188 KTGASGAKILLNNFI-KKIKNYNINRNYPSINGTSYLSIHLRFGTISIRKLVKLIFKFIK 246
K G + I+L +FI K++ + RN P+ + S LS L FG +S ++ + + +
Sbjct: 223 KPGTTAGLIMLESFIEKRLCFFRTRRNDPNNDALSMLSPWLHFGQLSAQRAARAVERARG 282
Query: 247 KHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILW------------E 294
+ + +F +L+ R +C+ N S Y W
Sbjct: 283 NA--GESVEFF--EEELVVRREL-ADNFCFYNPYYDSLCGAYW---WARTTLDDHAKDKR 334
Query: 295 SDNYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRM 335
Y+ + K T L ++A QL + G MH LRM
Sbjct: 335 EHLYSLEQL---EKSTTHDYLWNAAQEQLVTEGKMHGFLRM 372
>gnl|CDD|225008 COG2097, RPL31A, Ribosomal protein L31E [Translation, ribosomal
structure and biogenesis].
Length = 89
Score = 27.7 bits (62), Expect = 3.6
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 224 SIHLRFGTISIRKL-----VKLIFKFIKKHYKTDCIGYFTWLSQLIW 265
+I LR R VK+I KF+ +H K + + L++ IW
Sbjct: 12 TIPLRRAKKVPRTKRAPRAVKIIRKFVARHMKAEEVRIDPSLNEKIW 58
>gnl|CDD|119382 cd06522, GH25_AtlA-like, AtlA is an autolysin found in
Gram-positive lactic acid bacteria that degrades
bacterial cell walls by catalyzing the hydrolysis of
1,4-beta-linkages between N-acetylmuramic acid and
N-acetyl-D-glucosamine residues. This family includes
the AtlA and Aml autolysins from Streptococcus mutans
which have a C-terminal glycosyl hydrolase family 25
(GH25) catalytic domain as well as six tandem N-terminal
repeats of the GBS (group B Streptococcus) Bsp-like
peptidoglycan-binding domain. Other members of this
family have one or more C-terminal peptidoglycan-binding
domain(s) (SH3 or LysM) in addition to the GH25 domain.
Length = 192
Score = 28.9 bits (65), Expect = 4.9
Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 322 QLNSSGYMHNRLRMVTASFL-----IKNMGINWKWGENYFANKLNDFDLASNNGNWQWSA 376
+ ++GY + + +AS+L +G W Y N ++ +N G WQW++
Sbjct: 117 TMKAAGYKNTDV-YTSASWLNSRADTSTLGAKRVWVAQYPYNPSSNNLWNTNYGAWQWTS 175
Query: 377 SSG 379
+
Sbjct: 176 QAH 178
>gnl|CDD|234152 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC transporter,
ATP-binding protein. This ABC transporter ATP-binding
protein is found in a number of genomes in operon-like
contexts strongly suggesting a substrate specificity for
2-aminoethylphosphonate (2-AEP). The characterized
PhnSTUV system is absent in the genomes in which this
system is found. These genomes encode systems for the
catabolism of 2-AEP, making the need for a
2-AEP-specific transporter likely [Transport and binding
proteins, Amino acids, peptides and amines].
Length = 353
Score = 29.2 bits (66), Expect = 5.4
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 59 EIKKLVIKLNIDAVMINHDYE 79
EI++L +L + +M+ HD E
Sbjct: 176 EIRQLQRRLGVTTIMVTHDQE 196
>gnl|CDD|176498 cd08555, PI-PLCc_GDPD_SF, Catalytic domain of
phosphoinositide-specific phospholipase C-like
phosphodiesterases superfamily. The PI-PLC-like
phosphodiesterases superfamily represents the catalytic
domains of bacterial phosphatidylinositol-specific
phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic
phosphoinositide-specific phospholipase C (PI-PLC, EC
3.1.4.11), glycerophosphodiester phosphodiesterases
(GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D)
(sphingomyelin phosphodiesterase D, EC 3.1.4.41) from
spider venom, SMases D-like proteins, and phospholipase
D (PLD) from several pathogenic bacteria, as well as
their uncharacterized homologs found in organisms
ranging from bacteria and archaea to metazoans, plants,
and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing
the membrane lipid phosphoinositides to yield two
important second messengers, inositol phosphates and
diacylglycerol (DAG). GP-GDEs play essential roles in
glycerol metabolism and catalyze the hydrolysis of
glycerophosphodiesters to sn-glycerol-3-phosphate (G3P)
and the corresponding alcohols that are major sources of
carbon and phosphate. Both, PI-PLCs and GP-GDEs, can
hydrolyze the 3'-5' phosphodiester bonds in different
substrates, and utilize a similar mechanism of general
base and acid catalysis with conserved histidine
residues, which consists of two steps, a phosphotransfer
and a phosphodiesterase reaction. This superfamily also
includes Neurospora crassa ankyrin repeat protein NUC-2
and its Saccharomyces cerevisiae counterpart, Phosphate
system positive regulatory protein PHO81,
glycerophosphodiester phosphodiesterase (GP-GDE)-like
protein SHV3 and SHV3-like proteins (SVLs). The residues
essential for enzyme activities and metal binding are
not conserved in these sequence homologs, which might
suggest that the function of catalytic domains in these
proteins might be distinct from those in typical
PLC-like phosphodiesterases.
Length = 179
Score = 28.6 bits (64), Expect = 5.7
Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 5/90 (5%)
Query: 187 IKTGASGAKILLNNFIKKIKNYNINRNYPSINGTSYLSIHLRFGTISIRKLVKLIFKFIK 246
+T A L ++ I +Y N +Y I LS+ ++ + + + + K ++
Sbjct: 51 DRTTAGILPPTLEEVLELIADYLKNPDYTII-----LSLEIKQDSPEYDEFLAKVLKELR 105
Query: 247 KHYKTDCIGYFTWLSQLIWRDFYQMILYCY 276
++ D G S Y
Sbjct: 106 VYFDYDLRGKVVLSSFNALGVDYYNFSSKL 135
>gnl|CDD|227535 COG5210, COG5210, GTPase-activating protein [General function
prediction only].
Length = 496
Score = 29.0 bits (65), Expect = 6.1
Identities = 17/71 (23%), Positives = 27/71 (38%)
Query: 99 KFFSYKDQVIFEKNEILNKTGKPYSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHS 158
F S+K N LNK S+ QK ++ ++K ++ V
Sbjct: 143 DFSSFKGSSSLNSNPELNKEINELSLKEEPQKLRYYELAADKLWISYLDPNPLSFLPVQL 202
Query: 159 SKLHKIINNNI 169
SKL ++I I
Sbjct: 203 SKLRELIRKGI 213
>gnl|CDD|179793 PRK04220, PRK04220, 2-phosphoglycerate kinase; Provisional.
Length = 301
Score = 28.4 bits (64), Expect = 7.2
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 20 QGIIEDRRIEFIF-KSIIELSINLQNYDSDLIIRYAIASKEIKKLVIKLNIDAVMINHDY 78
+ I++ ++ E F K I+ S+ I Y IAS EI++ + K I +
Sbjct: 5 RIIVKGKKYEMPFSKGILARSLTAAGMKPS--IAYEIAS-EIEEELKKEGIKEITK---E 58
Query: 79 EPQAIIRDKLIKKELKVIGCKF 100
E + + KLI+K+ + + K+
Sbjct: 59 ELRRRVYYKLIEKDYEEVAEKY 80
>gnl|CDD|178782 PLN03244, PLN03244, alpha-amylase; Provisional.
Length = 872
Score = 28.8 bits (64), Expect = 7.5
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 15/48 (31%)
Query: 114 ILNKTGKPYSIFS----------FYQKK-----WIEKVKSNKCYLQSY 146
I GK Y IF+ F K+ W+E K K +L+ Y
Sbjct: 288 IDKGQGKEYDIFNVVDDPEWREKFRAKEPPIAYWLESRKGRKAWLKKY 335
>gnl|CDD|237101 PRK12430, PRK12430, putative bifunctional flagellar biosynthesis
protein FliO/FliP; Provisional.
Length = 379
Score = 28.3 bits (63), Expect = 8.5
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 28 IEFIFKSIIELSINLQNYDSDLIIRYAIASKE------IKKLVIKLNIDAVMINHDYEPQ 81
+ +I K I IN +I R ++ S E IK+L + L + I+H Y
Sbjct: 40 LSWILKKISLFKINKIISRMKIIERLSLGSNESIIIVEIKQLRLVLGVTKKNISHLYTLP 99
Query: 82 AIIRDKLIKKELKVI 96
+ +D++IKK +
Sbjct: 100 SNSKDEVIKKTNDTL 114
>gnl|CDD|237785 PRK14671, uvrC, excinuclease ABC subunit C; Provisional.
Length = 621
Score = 28.5 bits (64), Expect = 9.5
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 5/29 (17%)
Query: 194 AKILLNNFIKKIK-NYNIN----RNYPSI 217
A IL NN IK++K YN+N + YP +
Sbjct: 83 ALILENNLIKELKPRYNVNLKDDKTYPYL 111
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 0.139 0.423
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,268,657
Number of extensions: 2421713
Number of successful extensions: 2341
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2304
Number of HSP's successfully gapped: 81
Length of query: 470
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 370
Effective length of database: 6,502,202
Effective search space: 2405814740
Effective search space used: 2405814740
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 (21.9 bits)
S2: 61 (27.5 bits)