RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8390
(422 letters)
>gnl|CDD|221887 pfam12998, ING, Inhibitor of growth proteins N-terminal
histone-binding. Histones undergo numerous
post-translational modifications, including acetylation
and methylation, at residues which are then probable
docking sites for various chromatin remodelling
complexes. Inhibitor of growth proteins (INGs)
specifically bind to residues that have been thus
modified. INGs carry a well-characterized C-terminal
PHD-type zinc-finger domain, binding with lysine
4-tri-methylated histone H3 (H3K4me3), as well as this
N-terminal domain that binds unmodified H3 tails.
Although these two regions can bind histones
independently, together they increase the apparent
association of the ING for the H3 tail.
Length = 104
Score = 107 bits (270), Expect = 2e-28
Identities = 34/104 (32%), Positives = 62/104 (59%), Gaps = 1/104 (0%)
Query: 2 LYLEDYIELVEILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAAS-MTPEQRQR 60
LYLEDY++ +E LP EL+ FTE+R +D Q Q + +L ++ +F + S ++ + +
Sbjct: 1 LYLEDYLDDLENLPLELQRNFTEIREIDAQVQKIIKELDEQIQKFIKENGSNLSNPKEEE 60
Query: 61 EYENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKF 104
+ + +E K +EK+ LA Q E +K+ R+L++D++K
Sbjct: 61 LLKRIQEELIKAQELQDEKVQLANQAYELVDKHIRRLDKDLEKL 104
>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
finger [Chromatin structure and dynamics].
Length = 271
Score = 85.8 bits (212), Expect = 7e-19
Identities = 32/85 (37%), Positives = 38/85 (44%), Gaps = 15/85 (17%)
Query: 321 GSALGAGEEEMDTGYGPDEPRYCRCNEQAHYNFYTIFCSQVAFGVMVACDSKNCPYEWYH 380
E YC FC QV++G MVACD+ NC EW+H
Sbjct: 202 NGGSTKSRGVSSEDNSEGEELYC-------------FCQQVSYGQMVACDNANCKREWFH 248
Query: 381 CECVGIAPDNPPKGKWYCPLCLEKM 405
ECVG+ PPKGKWYCP C +
Sbjct: 249 LECVGLK--EPPKGKWYCPECKKAA 271
Score = 36.1 bits (83), Expect = 0.028
Identities = 23/140 (16%), Positives = 53/140 (37%), Gaps = 6/140 (4%)
Query: 4 LEDYIELVEILPQELRDRFTEMRLLDLQSQNSLDQLQNK--VNQFYQMAASMTPEQRQRE 61
L D + + +P E RFTE+ +D + + + L+ + + S T E+ +
Sbjct: 7 LNDITDHLANVPSETDIRFTELSEIDAKVCDIIKNLRQMISILKKIIDLDSQTYEEVE-- 64
Query: 62 YENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEK 121
+ LL+E + ++ + + + + K R+ + + + + I
Sbjct: 65 -DGLLKEIRELLLKAIYIQKEKSDLADRAEKLLRRHRKLLDDRIAKRPHEKV-AARIENC 122
Query: 122 RVTDSQQKENQRSNLVAARS 141
S+ + N S+ S
Sbjct: 123 HDAVSRLERNSYSSAARRSS 142
>gnl|CDD|201356 pfam00628, PHD, PHD-finger. PHD folds into an interleaved type of
Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 51
Score = 52.9 bits (127), Expect = 2e-09
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 357 FCSQV-AFGVMVACDSKNCPYEWYHCECVGIA--PDNPPKGKWYCPLCLEK 404
C +V G ++ CD C W+H C+G P+ P+G+WYCP C K
Sbjct: 4 VCGKVDDDGELLLCD--GCD-RWFHLACLGPPLEPEEIPEGEWYCPECKPK 51
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD)
finger is a C4HC3 zinc-finger-like motif found in
nuclear proteins thought to be involved in epigenetics
and chromatin-mediated transcriptional regulation. The
PHD finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet known
if PHD fingers have a common molecular function. Several
reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is a
ubiquitin ligase have been refuted as these domains were
RING fingers misidentified as PHD fingers.
Length = 47
Score = 48.4 bits (115), Expect = 7e-08
Identities = 18/47 (38%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 357 FCSQV-AFGVMVACDSKNCPYEWYHCECVGIAPD-NPPKGKWYCPLC 401
C + G ++ CD C WYH C+G P GKWYCP C
Sbjct: 4 VCGKPDDGGELLQCD--GCD-RWYHQTCLGPPLLEEEPDGKWYCPKC 47
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 45.9 bits (109), Expect = 3e-05
Identities = 32/177 (18%), Positives = 72/177 (40%), Gaps = 22/177 (12%)
Query: 2 LYLEDYIELVEILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQRE 61
LED +L+E L +EL+ +L ++Q + ++L+ ++ E+R E
Sbjct: 196 ELLEDIEDLLEALEEELK---ELKKLEEIQEEQEEEELEQEIEAL---------EERLAE 243
Query: 62 YENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEI--L 119
E + EE +I+ + + E+++++ + LE I + L
Sbjct: 244 LEEEKERL-------EELKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEEL 296
Query: 120 EKRVTDSQQKENQRSNLVAARSK-MNTLRNLRSELPNATDKRSVASSALTQEYKYSN 175
E+ + + +++ L+ + + L++L L +K S L + + N
Sbjct: 297 EREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKN 353
Score = 34.0 bits (78), Expect = 0.16
Identities = 29/142 (20%), Positives = 62/142 (43%), Gaps = 8/142 (5%)
Query: 16 QELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQREYENLLQEYNKPMID 75
+ L +R ++ + ++ L++L + N+ ++ E+R +E E L+E K +
Sbjct: 325 KSLEERLEKLEEKLEKLESELEELAEEKNELAKLL-----EERLKELEERLEELEKELEK 379
Query: 76 SEEKI-NLATQIQEF--FNKYTRKLEQDIQKFKLELEADNSGITEILEKRVTDSQQKENQ 132
+ E++ L IQE ++IQ+ ELE + + LE+ + ++ E Q
Sbjct: 380 ALERLKQLEEAIQELKEELAELSAALEEIQEELEELEKELEELERELEELEEEIKKLEEQ 439
Query: 133 RSNLVAARSKMNTLRNLRSELP 154
+ L + + L + P
Sbjct: 440 INQLESKELMIAELAGAGEKCP 461
Score = 30.1 bits (68), Expect = 2.5
Identities = 26/140 (18%), Positives = 55/140 (39%), Gaps = 16/140 (11%)
Query: 24 EMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQR--QREYENLLQEYNKPMIDSEEKIN 81
E LL+L L++L+ ++++ + A + E ++E L +E + + E
Sbjct: 472 EKELLELYEL-ELEELEEELSREKE-EAELREEIEELEKELRELEEELIELLELEEALKE 529
Query: 82 --------LATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEKRVTDSQQKENQR 133
L ++E + Q +++ +LE + E+LE+ +KE
Sbjct: 530 ELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELE 589
Query: 134 SNLVAARSKMNTLRNLRSEL 153
R ++ L+ EL
Sbjct: 590 E----LRERLKELKKKLKEL 605
Score = 29.0 bits (65), Expect = 5.4
Identities = 33/159 (20%), Positives = 63/159 (39%), Gaps = 19/159 (11%)
Query: 3 YLEDYIEL--VEILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQR 60
LE+ L + +ELR+R E++ + + L QL+ + + +
Sbjct: 574 LLEELRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSL-------ELSEAEN 626
Query: 61 EYENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGI----- 115
E E +E EK+NL +++E +LE+ +++ + E+ + I
Sbjct: 627 ELEEAEEELE----SELEKLNLQAELEELLQAALEELEEKVEELEAEIRRELQRIENEEQ 682
Query: 116 -TEILEKRVTDSQQKENQRSNLVAARSKMNTLRNLRSEL 153
E LE+ ++ E R L K+ + L EL
Sbjct: 683 LEEKLEELEQLEEELEQLREELEELLKKLGEIEQLIEEL 721
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 43.5 bits (103), Expect = 2e-04
Identities = 27/145 (18%), Positives = 61/145 (42%), Gaps = 7/145 (4%)
Query: 16 QELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQREYENLLQEYNKPMID 75
+EL + E + L+ L+ + + Q + E+ E E L E + + +
Sbjct: 796 EELEEELEEAERRLDALERELESLEQRRERLEQEIEEL--EEEIEELEEKLDELEEELEE 853
Query: 76 SEEKI-NLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEKRVTDSQQKENQRS 134
E+++ L +++E + +LE ++++ + E E + E+ + ++ E R
Sbjct: 854 LEKELEELKEELEELEAEK-EELEDELKELEEEKEELEEELRELESELAELKEEIEKLRE 912
Query: 135 NLVAARSKMNTLRNLRSELPNATDK 159
L +K+ L ELP ++
Sbjct: 913 RLEELEAKL---ERLEVELPELEEE 934
Score = 33.1 bits (76), Expect = 0.33
Identities = 32/172 (18%), Positives = 69/172 (40%), Gaps = 5/172 (2%)
Query: 4 LEDYIELVEILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQREYE 63
L++ E + L +L E++ L + ++ D L+ Q ++ + E+ +RE
Sbjct: 669 LKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQL--EELKRELA 726
Query: 64 NLLQEYNKPMIDSEEKINLATQIQEFFNKYT---RKLEQDIQKFKLELEADNSGITEILE 120
L +E + EE +++E + +LE++++ + L I E+ E
Sbjct: 727 ALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEE 786
Query: 121 KRVTDSQQKENQRSNLVAARSKMNTLRNLRSELPNATDKRSVASSALTQEYK 172
KR ++ E L A +++ L L ++ L +E +
Sbjct: 787 KRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIE 838
Score = 28.9 bits (65), Expect = 5.8
Identities = 27/150 (18%), Positives = 62/150 (41%), Gaps = 9/150 (6%)
Query: 4 LEDYIELVEILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQREYE 63
LE+ E +E L +EL + E+ L+ + ++L+ N+ ++ E+R E +
Sbjct: 276 LEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEEL------EERLEELK 329
Query: 64 NLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEKRV 123
++ + + + E + Q+ + +LE+ + ELE + E L +
Sbjct: 330 EKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELE 389
Query: 124 TDSQQKENQRSNLVAARSKMNTLRNLRSEL 153
+ + N+ L + ++ +L L
Sbjct: 390 AELAEIRNELEEL---KREIESLEERLERL 416
Score = 28.5 bits (64), Expect = 8.9
Identities = 22/127 (17%), Positives = 54/127 (42%), Gaps = 16/127 (12%)
Query: 4 LEDYIELVEILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQREYE 63
LE+ ++ +E +EL E++ + + ++L++++ + E+ + E E
Sbjct: 840 LEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKEL---------EEEKEELE 890
Query: 64 NLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEKRV 123
L+E E L +I++ + LE +++ ++EL + E E +
Sbjct: 891 EELRELES------ELAELKEEIEKLRERLEE-LEAKLERLEVELPELEEELEEEYEDTL 943
Query: 124 TDSQQKE 130
++E
Sbjct: 944 ETELERE 950
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 42.7 bits (101), Expect = 4e-04
Identities = 39/184 (21%), Positives = 68/184 (36%), Gaps = 12/184 (6%)
Query: 5 EDYIELVEILPQELRDRFTEMRLLDLQSQNS-LDQLQNKVNQFYQMAASMTPEQRQREYE 63
E Y EL ELR+ + +L L+ L++LQ ++ + + +T E + E E
Sbjct: 213 ERYKELKA----ELRELELALLVLRLEELREELEELQEELKEAEEELEELTAELQ--ELE 266
Query: 64 NLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEKRV 123
L+E + + EE+I + +LEQ Q + L + E+ +
Sbjct: 267 EKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLE 326
Query: 124 TDSQQKENQRSNLVAARSKMNTLRN----LRSELPNATDKRSVASSAL-TQEYKYSNFNS 178
+ + L K+ L+ L +EL + S L E + S
Sbjct: 327 ELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRS 386
Query: 179 GVAS 182
VA
Sbjct: 387 KVAQ 390
Score = 38.9 bits (91), Expect = 0.005
Identities = 32/156 (20%), Positives = 68/156 (43%), Gaps = 14/156 (8%)
Query: 4 LEDYIELVEILPQELRDRFTEM--RLLDLQS-QNSLDQLQNKVNQFYQMA-ASMTPEQRQ 59
L ++ +E +ELR +E+ + +LQ +L +++ Q Q+ + +RQ
Sbjct: 258 LTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQ 317
Query: 60 REY--ENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITE 117
E L + +K +EE L +++E L+++++ + ELE + + E
Sbjct: 318 LEELEAQLEELESKLDELAEELAELEEKLEE--------LKEELESLEAELEELEAELEE 369
Query: 118 ILEKRVTDSQQKENQRSNLVAARSKMNTLRNLRSEL 153
+ + +Q E RS + ++ +L N L
Sbjct: 370 LESRLEELEEQLETLRSKVAQLELQIASLNNEIERL 405
Score = 32.0 bits (73), Expect = 0.66
Identities = 28/193 (14%), Positives = 63/193 (32%), Gaps = 16/193 (8%)
Query: 30 LQSQNSLDQLQNKVNQFYQMAASMTPE-----QRQREYENLLQEYNKPMIDSEEKINLAT 84
L+ + +++L+ K+ + + A + + E E L++ K + + +I+
Sbjct: 673 LERRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALR 732
Query: 85 QIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEKRVTDSQQKENQRSNLVAARSKMN 144
+ +LE+ I + EL TE+ + ++ E L A +++
Sbjct: 733 KDLARLEAEVEQLEERIAQLSKEL-------TELEAEIEELEERLEEAEEELAEAEAEIE 785
Query: 145 TLRNLRSELPNATDKRSVASSALTQEYKYSNFNSGVASSAGNNAINYSLSNIGAGGMAIT 204
L +L A L E N + + I A +
Sbjct: 786 ELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLES----LERRIAATERRLE 841
Query: 205 AAASQAIAATQQM 217
Q ++ +
Sbjct: 842 DLEEQIEELSEDI 854
Score = 32.0 bits (73), Expect = 0.71
Identities = 31/173 (17%), Positives = 63/173 (36%), Gaps = 11/173 (6%)
Query: 8 IELVEILPQ--ELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQR--QREYE 63
EL E+ + EL +R E +++ +++L+ ++ Q + ++ + E
Sbjct: 754 KELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELT 813
Query: 64 NLLQEYNKP---MIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILE 120
L +E + E +I + E + +L +DI+ E+E I E+
Sbjct: 814 LLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELES 873
Query: 121 KRVTDSQQKENQRSNLVAARS----KMNTLRNLRSELPNATDKRSVASSALTQ 169
+ ++ + L RS LR L S+ + L Q
Sbjct: 874 ELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRELEELREKLAQ 926
>gnl|CDD|206034 pfam13863, DUF4200, Domain of unknown function (DUF4200). This
family is found in eukaryotes. It is a coiled-coil
domain of unknwon function.
Length = 126
Score = 36.1 bits (84), Expect = 0.007
Identities = 23/104 (22%), Positives = 52/104 (50%), Gaps = 3/104 (2%)
Query: 24 EMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQREYENLLQEYNKPMIDSEEKINLA 83
EM + L ++ + + Q + E+++ E + L +++K + ++E K A
Sbjct: 8 EMEEVQLALDAKREEFERREELLKQREEEL--EKKEEELQESLIKFDKFLKENEAKRRRA 65
Query: 84 TQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEKRVTDSQ 127
+ E K ++ E++I++ K ELE + I + LE+++ + Q
Sbjct: 66 EKKAEEEKKLRKEKEEEIKELKAELEELKAEIEK-LEEKLEEYQ 108
>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein. This family consists
of several eukaryotic mitotic checkpoint (Mitotic arrest
deficient or MAD) proteins. The mitotic spindle
checkpoint monitors proper attachment of the bipolar
spindle to the kinetochores of aligned sister chromatids
and causes a cell cycle arrest in prometaphase when
failures occur. Multiple components of the mitotic
spindle checkpoint have been identified in yeast and
higher eukaryotes. In S.cerevisiae, the existence of a
Mad1-dependent complex containing Mad2, Mad3, Bub3 and
Cdc20 has been demonstrated.
Length = 722
Score = 37.6 bits (87), Expect = 0.013
Identities = 37/193 (19%), Positives = 71/193 (36%), Gaps = 31/193 (16%)
Query: 3 YLEDYIELVEILPQELRD------RFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASM--- 53
L E E+L +EL D RF +MR + ++L+N++ + + +
Sbjct: 275 KLRSMKEDNELLKEELEDLQSRLERFEKMREKLADLELEKEKLENELKSWKSLLQDIGLN 334
Query: 54 --TPEQRQREYENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEAD 111
TP+ R L E + E+ ++++ ++LE +Q+ +LE +
Sbjct: 335 LRTPDDLSRRIVVLQNE---ELQLKEKNGSISSSA--------KQLETTLQQLQLERQKA 383
Query: 112 NSGITEILEKRVTDSQQKEN-QRSNLVAARSK---MNTLRNLRSEL-----PNATDKRSV 162
S I E+ +K QR + + + L + EL KR
Sbjct: 384 VSEILELKKKLEALKALVRRLQRRLTLVTKERDGLRAILNSYDKELTETSVSGQLMKRLE 443
Query: 163 ASSALTQEYKYSN 175
+ L Q+ +
Sbjct: 444 EAEDLVQKVQSHL 456
>gnl|CDD|133949 PHA01399, PHA01399, membrane protein P6.
Length = 242
Score = 34.6 bits (79), Expect = 0.067
Identities = 32/108 (29%), Positives = 48/108 (44%), Gaps = 6/108 (5%)
Query: 206 AASQAIAATQQMKQGRRTAS---LKASYEAIHGGAGSSADII---SKELAGAAQTAIAAI 259
AA QAI++ G A+ + + AI GAG++AD +KEL AA I I
Sbjct: 106 AAWQAISSFASAAWGYIQAAWEWIAGAVAAIWKGAGAAADAAWEAAKELGSAAGGVIGGI 165
Query: 260 QDTHKKNKKKSVGGSSNLSMGTINMNTTSSALHSLMMETSSSNSKLHG 307
D K N + GG++ +G + A+ + + SSS G
Sbjct: 166 WDFIKDNPELIAGGAAAAWLGKDGLILAGLAVAAFFLLKSSSGGGGGG 213
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 34.9 bits (81), Expect = 0.067
Identities = 28/90 (31%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 179 GVASSAGNNAINYSLSNIGAGGMAITAAA------SQAIAATQQMKQ--GRRTASLKASY 230
G A++AG + YS G G A AA + A AA +++ R S+K+S+
Sbjct: 312 GGAAAAGGASSAYSAGAAGGSGAAGVAAGLGGVARAGASAAASPLRRAASRAAESMKSSF 371
Query: 231 EAIHGGAGSSADIISKELAGAAQTAIAAIQ 260
A GA S+ A AA A AA
Sbjct: 372 RA---GARSTGGGAGGAAAAAAAGAAAAGP 398
Score = 28.7 bits (65), Expect = 6.9
Identities = 18/96 (18%), Positives = 34/96 (35%), Gaps = 2/96 (2%)
Query: 196 IGAGGMAITAAASQAIAATQQMKQGRRTA-SLKASYEAIHGGAGSSADIISKELAGAAQT 254
G G A AA+ A G +A S A+ + G + +++ A AA +
Sbjct: 296 AGGGAAAAGGAAAAARGGA-AAAGGASSAYSAGAAGGSGAAGVAAGLGGVARAGASAAAS 354
Query: 255 AIAAIQDTHKKNKKKSVGGSSNLSMGTINMNTTSSA 290
+ ++ K S + + G ++A
Sbjct: 355 PLRRAASRAAESMKSSFRAGARSTGGGAGGAAAAAA 390
Score = 28.3 bits (64), Expect = 8.0
Identities = 20/60 (33%), Positives = 25/60 (41%), Gaps = 15/60 (25%)
Query: 196 IGAGGMAITAAASQAIAATQQMKQGRRTASLKASYEAIHGGAGSSADIISKELAGAAQTA 255
+ AGG A+ AAA +AA G A A+ A GGA AG A +A
Sbjct: 279 LAAGGAAVAAAAGAGLAA----GGGAAAAGGAAA--AARGGAA---------AAGGASSA 323
>gnl|CDD|219925 pfam08598, Sds3, Sds3-like. Repression of gene transcription is
mediated by histone deacetylases containing
repressor-co-repressor complexes, which are recruited to
promoters of target genes via interactions with
sequence-specific transcription factors. The
co-repressor complex contains a core of at least seven
proteins. This family represents the conserved region
found in Sds3, Dep1 and BRMS1-homologue p40 proteins.
Length = 184
Score = 34.2 bits (79), Expect = 0.071
Identities = 34/145 (23%), Positives = 55/145 (37%), Gaps = 20/145 (13%)
Query: 17 ELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQRE--YENLLQEYNKPMI 74
ELRD+ RL LQ++ L+ L + Y E+R L +EY I
Sbjct: 16 ELRDQLYRERLAQLQTE--LELLLQGTHPEYLEPLKDLEERRDDRLKVAELRREYKLECI 73
Query: 75 DSE--------------EKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILE 120
+ E EK L ++ E + +LE++ + L++ + G+
Sbjct: 74 EREYEAERQAAKQEFEKEKRLLRERLLEELEEKIYRLEEE--RRSLDITDSDYGLLGSHP 131
Query: 121 KRVTDSQQKENQRSNLVAARSKMNT 145
R T ++ LVA R K N
Sbjct: 132 NRRTRKLRRRVNSPELVAKRKKKNN 156
>gnl|CDD|197732 smart00451, ZnF_U1, U1-like zinc finger. Family of C2H2-type zinc
fingers, present in matrin, U1 small nuclear
ribonucleoprotein C and other RNA-binding proteins.
Length = 35
Score = 29.1 bits (66), Expect = 0.30
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 4/32 (12%)
Query: 393 KGKWYCPLCLEKMA--ASKANHYGGSSRKHRK 422
G +YC LC S H G +KH+K
Sbjct: 1 TGGFYCKLCNVTFTDEISVEAHLKG--KKHKK 30
>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. This
model represents a group of paralogous families in
plasmodium species alternately annotated as reticulocyte
binding protein, 235-kDa family protein and rhoptry
protein. Rhoptry protein is localized on the cell
surface and is extremely large (although apparently
lacking in repeat structure) and is important for the
process of invasion of the RBCs by the parasite. These
proteins are found in P. falciparum, P. vivax and P.
yoelii.
Length = 2757
Score = 32.7 bits (74), Expect = 0.51
Identities = 22/124 (17%), Positives = 57/124 (45%), Gaps = 15/124 (12%)
Query: 1 MLYLEDYIELVEILPQELRDRFTEMRLLDLQSQNSLDQL-----QNKVNQFYQMAASMTP 55
++ ++D+ ++++ + D ++ ++ + + + Y++A +
Sbjct: 499 LMRMKDFKDIIDFMELYKPDEVPSKNIIGFDIDQNIKAKLYKEIEAGLKESYELAKNW-- 556
Query: 56 EQRQREYENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQD--IQKFKLELEADNS 113
++ E + L+E N E+ I+L +I++ F+KY ++ I K KLEL+
Sbjct: 557 KKLIHEIKKELEEEN------EDSIHLEKEIKDLFDKYLEIDDEIIYINKLKLELKEKIK 610
Query: 114 GITE 117
I++
Sbjct: 611 NISD 614
>gnl|CDD|219640 pfam07916, TraG_N, TraG-like protein, N-terminal region. The
bacterial sequences found in this family are similar to
the N-terminal region of the TraG protein. This is a
membrane-spanning protein, with three predicted
transmembrane segments and two periplasmic regions. TraG
protein is known to be essential for DNA transfer in the
process of conjugation, with the N-terminal portion
being required for F pilus assembly. The protein is
thought to interact with the periplasmic domain of TraN
to stabilise mating-cell interactions.
Length = 462
Score = 31.9 bits (73), Expect = 0.59
Identities = 20/103 (19%), Positives = 33/103 (32%), Gaps = 4/103 (3%)
Query: 131 NQRSNLVAARSKMNTLRNLRSELPNATD--KRSVASSALTQE-YKYSNFNSGVASSAG-N 186
R + L L +V + L+ Y+Y +S AS G
Sbjct: 222 KARLLAQVNPALSALAAQLFGGLLATAAAVDEAVLRALLSPLSYQYFQGSSASASDYGRQ 281
Query: 187 NAINYSLSNIGAGGMAITAAASQAIAATQQMKQGRRTASLKAS 229
N + +L N A + A+A+TQ + Q +
Sbjct: 282 NMMINALRNGVTRFAAALGDTAAALASTQALAQQSLAWAPAGD 324
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 31.1 bits (71), Expect = 0.59
Identities = 19/93 (20%), Positives = 41/93 (44%), Gaps = 10/93 (10%)
Query: 33 QNSLDQLQNKVNQFYQMAASMTPEQR---QREYENLLQEYNKPMIDSEEKINLATQIQEF 89
Q +LQ + + + AA+++ E R Q+E + QE + +++++ QE
Sbjct: 52 QKKEKELQKEEQKLQKQAATLSEEARKAKQQELQQKQQELQQKQQAAQQELQQKQ--QEL 109
Query: 90 FNKYTRKLEQDIQKFKLELEADNSGITEILEKR 122
K+++ I++ A G +L+K
Sbjct: 110 LQPIYDKIDKAIKEV-----AKEKGYDLVLDKS 137
Score = 27.6 bits (62), Expect = 7.2
Identities = 12/64 (18%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 73 MIDSEEKINLATQIQEFFNKYTRKLE---QDIQKFKLELEADNSGITE-ILEKRVTDSQQ 128
+ +S Q+++ F K +L+ +++QK + +L+ + ++E + + + QQ
Sbjct: 27 LSESPAGKAAQKQLEKEFKKLQAELQKKEKELQKEEQKLQKQAATLSEEARKAKQQELQQ 86
Query: 129 KENQ 132
K+ +
Sbjct: 87 KQQE 90
>gnl|CDD|217303 pfam02958, EcKinase, Ecdysteroid kinase. This family includes
ecdysteroid 22-kinase, an enzyme responsible for the
phosphorylation of ecdysteroids (insect growth and
moulting hormones) at C-22, to form physiologically
inactive ecdysteroid 22-phosphates.
Length = 293
Score = 31.9 bits (73), Expect = 0.63
Identities = 19/103 (18%), Positives = 40/103 (38%), Gaps = 30/103 (29%)
Query: 3 YLEDYIELVEILPQELR-------------------DRFTEMRLLDLQSQN----SLDQL 39
Y + + LV+ P E ++ L+D Q +LD
Sbjct: 198 YFDRLLRLVDPNPDEFNVLNHGDLWVNNIMFKYDEEGEPEDVILVDFQLSRYGSPALD-- 255
Query: 40 QNKVNQFYQMAASMTPEQRQREYENLLQEYNKPMIDSEEKINL 82
+ F + S +PE R ++ LL+ Y++ ++++ +K+
Sbjct: 256 ---LLYF--LYTSTSPELRLEHFDELLRYYHESLVETLKKLGY 293
>gnl|CDD|227688 COG5401, COG5401, Spore germination protein [General function
prediction only].
Length = 250
Score = 31.7 bits (72), Expect = 0.66
Identities = 18/99 (18%), Positives = 32/99 (32%), Gaps = 8/99 (8%)
Query: 105 KLELEADNSGITEILEKRVTDS--QQKENQRSNLVAARSKMNTLRNLRSELPNATDKRSV 162
KLE + I + D+ + + S+ + + +K TL+ L NA V
Sbjct: 30 KLEYLVKGGPVIHIFPNKNFDNYKFESSQKSSSQLESVAK-ATLKVAGVALKNA----PV 84
Query: 163 ASSALTQEYKYSNFNSG-VASSAGNNAINYSLSNIGAGG 200
+ + N G + AI + G
Sbjct: 85 NGTPIPSRKLGVNLEPGQPNDAQPGKAITLYFLAVDPDG 123
>gnl|CDD|220265 pfam09491, RE_AlwI, AlwI restriction endonuclease. This family
includes the AlwI (recognises GGATC), Bsp6I (recognises
GC^NGC), BstNBI (recognises GASTC), PleI(recognises
GAGTC) and MlyI (recognises GAGTC) restriction
endonucleases.
Length = 429
Score = 31.6 bits (72), Expect = 0.70
Identities = 13/106 (12%), Positives = 45/106 (42%), Gaps = 8/106 (7%)
Query: 26 RLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQREYENLLQEYNKPMIDSEEKINLATQ 85
+L+ + + + ++++ + A R +Y + + P++ +++ N T+
Sbjct: 171 KLIIINPEK-----KEEIDEILKNTARYPIYTRLEDYFEYMSNIDGPLLPTDDLAN--TK 223
Query: 86 IQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEKRVTDSQQKEN 131
I++ EQ +L ++ + + L+ + + ++K+
Sbjct: 224 IEQLKIIANNIKEQ-FNIAELLSILNSKYVVDELKDELNELKEKKF 268
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 31.2 bits (71), Expect = 0.72
Identities = 25/123 (20%), Positives = 50/123 (40%), Gaps = 13/123 (10%)
Query: 56 EQRQREYENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGI 115
E + + E+ +QE + + +EEK++ +E R L +IQ K + + +
Sbjct: 58 ENQVSQLESEIQEIRERIKRAEEKLSAVKDEREL-----RALNIEIQIAKERINSLEDEL 112
Query: 116 TEILEKR-------VTDSQQKENQRSNLVAARSKM-NTLRNLRSELPNATDKRSVASSAL 167
E++E+ ++ E NL A +++ + +R E + KR L
Sbjct: 113 AELMEEIEKLEKEIEDLKERLERLEKNLAEAEARLEEEVAEIREEGQELSSKREELKEKL 172
Query: 168 TQE 170
E
Sbjct: 173 DPE 175
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 31.5 bits (72), Expect = 0.87
Identities = 14/85 (16%), Positives = 36/85 (42%)
Query: 11 VEILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQREYENLLQEYN 70
V + EL++ E+ + + L++++ + + + A P +++ + E LL+
Sbjct: 325 VGVDFPELKEELKELEEELKELEEELEKIKKLLKKLPKKARGQLPPEKREQLEKLLETKE 384
Query: 71 KPMIDSEEKINLATQIQEFFNKYTR 95
K + EE +++E
Sbjct: 385 KLSEELEELEEELKELKEELESLYS 409
>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein. This family
consists of several Borrelia P83/P100 antigen proteins.
Length = 489
Score = 31.5 bits (71), Expect = 0.88
Identities = 30/132 (22%), Positives = 51/132 (38%), Gaps = 10/132 (7%)
Query: 6 DYIELVEILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASM---TPEQRQREY 62
D +L E QE R +++ + Q D+ Q K F Q A Q+Q+E
Sbjct: 199 DMTDLKERESQEDAKRAQQLKEELDKKQIDADKAQQKA-DFAQDNADKQRDEVRQKQQEA 257
Query: 63 ENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEKR 122
+NL KP S K + Q+ E + K + +I+K E L++
Sbjct: 258 KNL----PKPADTSSPKED--KQVAENQKREIEKAQIEIKKNDEEALKAKDHKAFDLKQE 311
Query: 123 VTDSQQKENQRS 134
S+++ +
Sbjct: 312 SKASEKEAEDKE 323
>gnl|CDD|240058 cd04703, Asparaginase_2_like, A subfamily of the L-Asparaginase
type 2-like enzymes. The wider family, a member of the
Ntn-hydrolase superfamily, includes
Glycosylasparaginase, Taspase 1 and L-Asparaginase type
2 enzymes. The proenzymes undergo autoproteolytic
cleavage before a threonine to generate alpha and beta
subunits. The threonine becomes the N-terminal residue
of the beta subunit and is the catalytic residue.
Length = 246
Score = 30.9 bits (70), Expect = 0.98
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 233 IHGGAGSSADIISKELAGAAQTAIAAIQDT 262
+HGGAGS D L GAA+ A AA+ +
Sbjct: 5 VHGGAGSPPDSRLGGLQGAAEAATAALSND 34
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 30.9 bits (70), Expect = 1.2
Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 13/115 (11%)
Query: 12 EILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQREYENLLQEYNK 71
E + + L+ + +D L K+N FY + + E ++ L +
Sbjct: 328 EFFVSSKVLNSSNLSAKQLKIKALVDLLTQKINAFYS--------KERVELDDYLISSWQ 379
Query: 72 PMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEKRVTDS 126
MI E+ I Q+Q+F +K R+L D+ F L EA N + ++ + VT+
Sbjct: 380 AMILLEKAI---AQLQQFLSKLDRQLFLDMLVFHL-REAINC-LGQVTGEVVTED 429
>gnl|CDD|234657 PRK00135, scpB, segregation and condensation protein B; Reviewed.
Length = 188
Score = 30.2 bits (69), Expect = 1.4
Identities = 9/40 (22%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 77 EEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGIT 116
EE ++L Q+ E +++Q +++ + + E D+ G+
Sbjct: 18 EEGLSLE-QLAEILELEPTEVQQLLEELQEKYEGDDRGLK 56
>gnl|CDD|220404 pfam09789, DUF2353, Uncharacterized coiled-coil protein (DUF2353).
Members of this family of uncharacterized proteins have
no known function.
Length = 319
Score = 30.6 bits (69), Expect = 1.4
Identities = 30/151 (19%), Positives = 63/151 (41%), Gaps = 22/151 (14%)
Query: 4 LEDYIELVEILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQREYE 63
LE E ++IL Q+L + QN DQ + ++ +R+ E
Sbjct: 4 LESKTEALKILGQDLE-----------KCQNERDQFKLMAETLQMRYRNLKKSERELELV 52
Query: 64 NLLQEYNKPMIDSEEKINLATQIQEFF--NKYTRKLEQDIQKFKLELEADNSGI-TEILE 120
Q + + ++ +L+ ++++ N+ Q++++ K EL+ D + I +
Sbjct: 53 AACQG-DMKIKPGTKRQDLSQLLEKYREENQQLSTDVQELRQRKAELQGDIKLLRQTIAQ 111
Query: 121 KRVTDSQQKENQ----RSNLVAARSKMNTLR 147
+RV + R++LV S++ LR
Sbjct: 112 QRVEFMGGGVRESFEERNDLV---SQLEKLR 139
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
modification].
Length = 2365
Score = 31.1 bits (70), Expect = 1.5
Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 7/80 (8%)
Query: 242 DIISKELAGAAQTAIAAIQDTHKKNKKKSVGGSSNLSMGTIN-----MNTTSSALHSLMM 296
DII A A +T K+N +K++ +N+S TIN ++
Sbjct: 2038 DIILGFRISAPSGARQETAETEKQNSEKALSRPTNVSTKTINGWGREYVVLDGMIYE--G 2095
Query: 297 ETSSSNSKLHGSTSAAAPME 316
E SS + P+E
Sbjct: 2096 EKFSSKEEWRSEAIRTGPLE 2115
>gnl|CDD|227614 COG5295, Hia, Autotransporter adhesin [Intracellular trafficking
and secretion / Extracellular structures].
Length = 715
Score = 31.0 bits (70), Expect = 1.5
Identities = 21/125 (16%), Positives = 39/125 (31%), Gaps = 8/125 (6%)
Query: 174 SNFNSGVASSAGNNAINYSLSNIGAGGMAITAAASQAIAATQQMKQGRRTASLKASYEAI 233
+ G G+ + SL G A++A+ + I + +I
Sbjct: 69 TLSVVGDGGKDGSTNGDNSLGLTQDTGAAVSASKGEVITNVAAGLKN---VDTMNVIVSI 125
Query: 234 HGGAGSSADIISKELAG-----AAQTAIAAIQDTHKKNKKKSVGGSSNLSMGTINMNTTS 288
+G+ A S LA A T A+ T + ++ S L ++ +
Sbjct: 126 ILNSGTGAASASSTLAAGTTIRAVATGKTAVLSTASASGVQAKATDSALGFENTAVDQQA 185
Query: 289 SALHS 293
A
Sbjct: 186 GAAGL 190
>gnl|CDD|165432 PHA03161, PHA03161, hypothetical protein; Provisional.
Length = 150
Score = 29.7 bits (66), Expect = 1.7
Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 4/81 (4%)
Query: 57 QRQREYENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGIT 116
++Q+ E +LQ + + + +++++L + F+++ +D+Q LEL+ D
Sbjct: 54 KKQKSIEGMLQAVDLSIQEKKKELSLL----KAFDRHKLSAAEDLQDKILELKEDIHFEI 109
Query: 117 EILEKRVTDSQQKENQRSNLV 137
E L SQ++EN N +
Sbjct: 110 EALNHGQPSSQEEENSSENSI 130
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 30.8 bits (70), Expect = 1.8
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 57 QRQREYENLLQEYNKPMIDSEEKI----NLATQIQEFFNKYTRKLEQ---DIQKFKLELE 109
R EN L E ++ + D+ KI Q+++ K +LE+ D+ + E+E
Sbjct: 695 SELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIE 754
Query: 110 ADNSGITEILEKRVTDSQQKENQ 132
S + E LE R+ + ++ ++
Sbjct: 755 NVKSELKE-LEARIEELEEDLHK 776
Score = 30.0 bits (68), Expect = 3.1
Identities = 26/168 (15%), Positives = 64/168 (38%), Gaps = 16/168 (9%)
Query: 2 LYLEDYIELVEILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQRE 61
L + + EL E+ ++ + + ++Q N++ + ++E
Sbjct: 784 LEARLSHSRIPEIQAELSKLEEEVSRIEARLR-EIEQKLNRLTLEKEYL--------EKE 834
Query: 62 YENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEK 121
+ L ++ ID +E+I + E N +LE+++++ + L S + ++ ++
Sbjct: 835 IQELQEQ----RIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKE 890
Query: 122 RVTDSQQKENQRSNLVAARSKMNTLRNLRSELPNATDKRSVASSALTQ 169
R Q + +++ R SEL K L++
Sbjct: 891 RDELEAQLRELERKIEELEAQIEKKRKRLSEL---KAKLEALEEELSE 935
>gnl|CDD|222469 pfam13949, ALIX_LYPXL_bnd, ALIX V-shaped domain binding to HIV.
The binding of the LYPxL motif of late HIV p6Gag and
EIAV p9Gag to this domain is necessary for viral
budding.This domain is generally central between an
N-terminal Bro1 domain, pfam03097 and a C-terminal
proline-rich domain. The retroviruses thus used this
domain to hijack the ESCRT system of the cell.
Length = 292
Score = 30.4 bits (69), Expect = 1.9
Identities = 22/141 (15%), Positives = 52/141 (36%), Gaps = 16/141 (11%)
Query: 4 LEDYIELVEIL---PQELRDRFTEMRLLDLQSQNS----LDQLQNKVNQFYQMAASMTPE 56
LE++ E +E+L +EL + L +L NK+N + E
Sbjct: 107 LEEHEENLELLSGPEEELEALLPSSSPSKTPEVSEQISRLRELLNKLN-------ELKAE 159
Query: 57 QRQR--EYENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSG 114
+ + E + Q+ + + ++ ++ F + +K + ++ + L
Sbjct: 160 REKLLEELKEKAQDDDISKLLIALNKLGSSNEEQLFEEELKKFDPLQERVEQNLSKQEEL 219
Query: 115 ITEILEKRVTDSQQKENQRSN 135
+ EI E Q++++
Sbjct: 220 LKEIQEANEEFLQERKSDSEQ 240
>gnl|CDD|237179 PRK12709, flgJ, flagellar rod assembly protein/muramidase FlgJ;
Provisional.
Length = 320
Score = 30.3 bits (68), Expect = 2.1
Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 6/88 (6%)
Query: 177 NSGVASSAGNNAINYSLSNIG--AGGMAITAAASQAIAATQ---QMKQGRRTASLKASYE 231
N+GVA+ A +A + +G GG+A A ++A A + R ++ A
Sbjct: 103 NAGVAAGAQGDAGAGGMGGLGGNEGGLAAMNALAKAYANAANNGALAGTRGYSAGSALTP 162
Query: 232 AIHGGAGS-SADIISKELAGAAQTAIAA 258
+ G GS AD +LA AQ A AA
Sbjct: 163 PLKGNGGSPDADAFVDKLAAPAQAASAA 190
>gnl|CDD|218615 pfam05504, Spore_GerAC, Spore germination B3/ GerAC like,
C-terminal. The GerAC protein of the Bacillus subtilis
spore is required for the germination response to
L-alanine. Members of this family are thought to be
located in the inner spore membrane. Although the
function of this family is unclear, they are likely to
encode the components of the germination apparatus that
respond directly to this germinant, mediating the
spore's response.
Length = 171
Score = 29.5 bits (67), Expect = 2.3
Identities = 12/59 (20%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 66 LQEYNKPM-IDSEEKINLATQIQEFFNKY-TRKLEQDIQKFKLELEADNSGITEILEKR 122
+ EY P+ + + +++ ++++ K +++E+ I+K + E + D G E L ++
Sbjct: 80 ISEYQSPLDLFNPKELK---KLEKALEKEIKKEIEKLIKKLQKEYKVDIFGFGEYLRRK 135
>gnl|CDD|163567 TIGR03855, NAD_NadX, aspartate dehydrogenase. Members of this
protein family are L-aspartate dehydrogenase, as shown
for the NADP-dependent enzyme TM_1643 of Thermotoga
maritima. Members lack homology to NadB, the aspartate
oxidase (EC 1.4.3.16) of most mesophilic bacteria
(described by TIGR00551), which this enzyme replaces in
the generation of oxaloacetate from aspartate for the
NAD biosynthetic pathway. All members of the seed
alignment are found adjacent to other genes of NAD
biosynthesis, although other uses of L-aspartate
dehydrogenase may occur.
Length = 229
Score = 29.7 bits (67), Expect = 2.7
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 119 LEKRVTDSQQKENQRSNLVAARSKMNTLRNLRSEL 153
+E RV + EN R++ +AA S + LRNL S L
Sbjct: 193 MEIRVENVPSPENPRTSYLAALSALRLLRNLASPL 227
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 29.9 bits (67), Expect = 2.9
Identities = 35/167 (20%), Positives = 60/167 (35%), Gaps = 35/167 (20%)
Query: 16 QELRDRFTEMRLLDLQSQNSL-------DQLQNKVNQ-----------FYQMAASMTPEQ 57
ELR++ + + L+ ++ L D LQ K+N M + E
Sbjct: 430 SELRNQISLLTSLERSLKSDLGQLKKENDMLQTKLNSMVSAKQKDKQSMQSMEKRLKSEA 489
Query: 58 RQRE-YENLLQEYNKPMIDSEEK--------INLATQIQEFFNKYTRKLEQDIQKFKLEL 108
R E L E K + EE + E + + LE +I+K + +L
Sbjct: 490 DSRVNAEKQLAEEKKRKKEEEETAARAAAQAAASREECAESLKQAKQDLEMEIKKLEHDL 549
Query: 109 EADNSGITEILEKRVTDSQ-QKENQR------SNLVAARSKMNTLRN 148
+ LEK + + +E+++ S L A + K L N
Sbjct: 550 KLKEEECRM-LEKEAQELRKYQESEKETEVLMSALQAMQDKNLMLEN 595
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 30.0 bits (68), Expect = 3.0
Identities = 23/90 (25%), Positives = 36/90 (40%), Gaps = 5/90 (5%)
Query: 56 EQRQREYENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGI 115
EQ Q + + L + + E +++ T RK E+ QK K +LE D
Sbjct: 345 EQLQADLDQL-PSIRSELEEVEARLDALTGKH---QDVQRKYERLKQKIKEQLERDLEKN 400
Query: 116 TEILEK-RVTDSQQKENQRSNLVAARSKMN 144
E L R +QK +L A S++
Sbjct: 401 NERLAAIREEKDRQKAAIEEDLQALESQLR 430
>gnl|CDD|241526 cd13375, PH_SynGAP, Synaptic Ras-GTPase activating protein
Pleckstrin homology (PH) domain. SynGAP is a member of
the RasSynGAP family along with DOC-2/DAB2-interacting
protein (DAB2IP) and neuronal growth-associated protein
(nGAP/RASAL2). SynGAP, a neuronal Ras-GAP, has been
shown display both Ras-GAP activity and Ras-related
protein (Rap)-GAP activity. Saccharomyces cerevisiae
Bud2 and GAP1 members CAPRI (Ca2+-promoted Ras
inactivator) and RASAL (Ras-GTPase-activating-like
protein) also possess this dual activity. Human
DOC-2/DAB2-interacting protein (DAB2IP) is encoded by a
tumor suppressor gene and a newly recognized member of
the Ras-GTPase-activating family. Members here include
mammals, amphibians, and bony fish. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 189
Score = 29.3 bits (65), Expect = 3.0
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 387 APDNPPKGKWYCPLCLEKM 405
A D PPK ++YC LCL+ M
Sbjct: 150 ARDLPPKKRYYCELCLDDM 168
>gnl|CDD|227009 COG4663, FcbT1, TRAP-type mannitol/chloroaromatic compound
transport system, periplasmic component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 363
Score = 29.7 bits (67), Expect = 3.1
Identities = 16/51 (31%), Positives = 25/51 (49%)
Query: 196 IGAGGMAITAAASQAIAATQQMKQGRRTASLKASYEAIHGGAGSSADIISK 246
GA +A A+ AIA + R T+S S + I+GGA A +++
Sbjct: 15 AGAAALATAGLATPAIAQENPKVRWRLTSSWPKSLDTIYGGAEDMAKAVAE 65
>gnl|CDD|175980 cd04013, C2_SynGAP_like, C2 domain present in Ras GTPase activating
protein (GAP) family. SynGAP, GAP1, RasGAP, and
neurofibromin are all members of the Ras-specific GAP
(GTPase-activating protein) family. SynGAP regulates
the MAP kinase signaling pathway and is critical for
cognition and synapse function. Mutations in this gene
causes mental retardation in humans. SynGAP contains a
PH-like domain, a C2 domain, and a Ras-GAP domain. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions.
Length = 146
Score = 28.8 bits (65), Expect = 3.1
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 387 APDNPPKGKWYCPLCLEKM 405
A PPK ++YC LCL+K
Sbjct: 20 AKGLPPKKRYYCELCLDKT 38
>gnl|CDD|215364 PLN02678, PLN02678, seryl-tRNA synthetase.
Length = 448
Score = 29.7 bits (67), Expect = 3.2
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 57 QRQREYENLLQEYNK-------PMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELE 109
QRQ E ++L +E+NK I E+ L + +E + T K E ++Q+ K L+
Sbjct: 44 QRQFELDSLRKEFNKLNKEVAKLKIAKEDATELIAETKELKKEITEK-EAEVQEAKAALD 102
Query: 110 ADNSGITEILEKRVTDSQQKEN 131
A I ++ V S + N
Sbjct: 103 AKLKTIGNLVHDSVPVSNDEAN 124
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a zinc-finger
domain with the CxxCx(12)Hx(6)H motif, found in multiple
copies in a wide range of proteins from plants to
metazoans. Some member proteins, particularly those from
plants, are annotated as being RNA-binding.
Length = 25
Score = 25.9 bits (58), Expect = 3.2
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 6/28 (21%)
Query: 396 WYCPLCLEKMAASKA---NHYGGSSRKH 420
+YC LC S++ +H +KH
Sbjct: 1 FYCELC-NVTFTSESQLKSHL--RGKKH 25
>gnl|CDD|222389 pfam13801, Metal_resist, Heavy-metal resistance. This is a
metal-binding protein which is involved in resistance to
heavy-metal ions. The protein forms a four-helix hooked
hairpin, consisting of two long alpha helices each
flanked by a shorter alpha helix. It binds a metal ion
in a type-2 like centre. It contains two copies of an
LTXXQ motif.
Length = 125
Score = 28.4 bits (64), Expect = 3.3
Identities = 15/63 (23%), Positives = 22/63 (34%), Gaps = 14/63 (22%)
Query: 5 EDYIELVEIL------PQELRDRFTEMRLLDLQSQNSLDQLQNKV-NQFYQMAASMTPEQ 57
EL+ +L P LR R LQ +V AA+++PE+
Sbjct: 70 AARRELLALLRAEPFDPAALRAALARQREAR-------AALQARVQEALLDAAAALSPEE 122
Query: 58 RQR 60
R
Sbjct: 123 RAA 125
>gnl|CDD|214604 smart00295, B41, Band 4.1 homologues. Also known as
ezrin/radixin/moesin (ERM) protein domains. Present in
myosins, ezrin, radixin, moesin, protein tyrosine
phosphatases. Plasma membrane-binding domain. These
proteins play structural and regulatory roles in the
assembly and stabilization of specialized plasmamembrane
domains. Some PDZ domain containing proteins bind one or
more of this family. Now includes JAKs.
Length = 201
Score = 29.2 bits (66), Expect = 3.3
Identities = 8/49 (16%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 29 DLQSQNSLDQLQNKVNQFYQMAASMTPEQRQREYENLLQEYNKPMIDSE 77
L L + + ++ + ++ ++PE+ + +Y L ++ P E
Sbjct: 153 QLLDSRKLKEWRERIVELHKELIGLSPEEAKLKYLELARKL--PTYGVE 199
>gnl|CDD|238071 cd00124, MYSc, Myosin motor domain. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Myosins are actin-dependent molecular
motors that play important roles in muscle contraction,
cell motility, and organelle transport. The head domain
is a molecular motor, which utilizes ATP hydrolysis to
generate directed movement toward the plus end along
actin filaments. A cyclical interaction between myosin
and actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 679
Score = 29.5 bits (67), Expect = 3.7
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 11/51 (21%)
Query: 46 FYQMAASMTPEQRQ-------REYENLLQEYNKPMIDSEEKINLATQIQEF 89
FYQ+ A +PE+R+ Y L N+ + + I+ A + +E
Sbjct: 191 FYQLLAGASPEERKKLGLKRPESYRYL----NQGGCNDVDGIDDAEEFEEL 237
>gnl|CDD|220652 pfam10250, O-FucT, GDP-fucose protein O-fucosyltransferase. This
is a family of conserved proteins representing the
enzyme responsible for adding O-fucose to EGF (epidermal
growth factor-like) repeats. Six highly conserved
cysteines are present in O-FucT-1 as well as a DXD-like
motif (ERD), conserved in mammals, Drosophila, and C.
elegans. Both features are characteristic of several
glycosyltransferase families. The enzyme is a
membrane-bound protein released by proteolysis and, as
for most glycosyltransferases, is strongly activated by
manganese.
Length = 315
Score = 29.2 bits (66), Expect = 3.8
Identities = 10/39 (25%), Positives = 15/39 (38%)
Query: 136 LVAARSKMNTLRNLRSELPNATDKRSVASSALTQEYKYS 174
+ L L++E PN K S+AS +K
Sbjct: 236 IATDEIYGRELEPLKAEFPNLVTKESLASKEELAPFKGG 274
>gnl|CDD|236201 PRK08248, PRK08248, O-acetylhomoserine
aminocarboxypropyltransferase; Validated.
Length = 431
Score = 29.4 bits (66), Expect = 3.8
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 180 VASSAGNNAINYSLSNIGAGGMAITAAAS 208
+A S+G AI YS+ NI + G I +++S
Sbjct: 83 LAVSSGQAAITYSILNIASAGDEIVSSSS 111
>gnl|CDD|188502 TIGR03987, TIGR03987, TIGR03987 family protein. Conserved
hypothetical protein.
Length = 120
Score = 28.0 bits (63), Expect = 3.8
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 286 TTSSALHSLMMETSSSNSKLHGSTSAAA 313
TT + L S + ++S S+ +HG T A
Sbjct: 44 TTGTTLMSKIAKSSGSSFSIHGITGLLA 71
>gnl|CDD|227603 COG5278, COG5278, Predicted periplasmic ligand-binding sensor
domain [Signal transduction mechanisms].
Length = 207
Score = 28.9 bits (65), Expect = 4.0
Identities = 18/113 (15%), Positives = 37/113 (32%), Gaps = 8/113 (7%)
Query: 58 RQREYENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITE 117
EY +E + + E++ T + LE IQ E + T
Sbjct: 74 GNDEYLEPYEEATEELDQKLEELRALTADDPELLESLDDLEPLIQWKLAEADE-----TI 128
Query: 118 ILEKRVTDSQQKENQRSNLVAARSKMNTLRNLRSELPNATDKRSVASSALTQE 170
L + + S+ + M+ +R E+ ++R + + Q+
Sbjct: 129 PLRRDGKLEAAVQIISSDQ--GKVLMDAIRQYLQEIEEEENER-LTQALAEQQ 178
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 29.3 bits (66), Expect = 4.0
Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 31 QSQNSLDQLQNKVNQFYQMAASMTPEQRQREYENLLQEYNKPMIDSEEKINLATQIQEFF 90
+ L++L+ +++ A +TPEQ ++ LL+ + + EEK +I+E
Sbjct: 116 ARELELEELEKQLDNELYRVAGLTPEQARKL---LLKLLDAEL--EEEKAQRVKKIEEEA 170
Query: 91 NKYTRKLEQDI 101
+ + Q+I
Sbjct: 171 DLEAERKAQNI 181
>gnl|CDD|219636 pfam07911, DUF1677, Protein of unknown function (DUF1677). The
sequences found in this family are all derived from
hypothetical plant proteins of unknown function. The
region features a number of highly conserved cysteine
residues.
Length = 91
Score = 27.3 bits (61), Expect = 4.3
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 10/37 (27%)
Query: 377 EWYHCECVGIAPDNPP----------KGKWYCPLCLE 403
E CEC G+ + P G+W C LC E
Sbjct: 3 ESVRCECCGLTEECTPEYIARVRARFGGRWVCGLCSE 39
>gnl|CDD|227847 COG5560, UBP12, Ubiquitin C-terminal hydrolase [Posttranslational
modification, protein turnover, chaperones].
Length = 823
Score = 29.5 bits (66), Expect = 4.7
Identities = 9/18 (50%), Positives = 9/18 (50%)
Query: 392 PKGKWYCPLCLEKMAASK 409
WYCP C E ASK
Sbjct: 692 LSDSWYCPGCKEFRQASK 709
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 29.1 bits (66), Expect = 4.7
Identities = 11/49 (22%), Positives = 19/49 (38%)
Query: 1 MLYLEDYIELVEILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQM 49
L D + L+E +EL+++ L L K+ Q Q+
Sbjct: 580 CYDLRDLLTLLEAQKKELQEKMESESAFLTGEYAHLIDLLEKMAQLLQL 628
>gnl|CDD|226837 COG4403, LcnDR2, Lantibiotic modifying enzyme [Defense mechanisms].
Length = 963
Score = 29.4 bits (66), Expect = 4.8
Identities = 18/117 (15%), Positives = 37/117 (31%), Gaps = 6/117 (5%)
Query: 16 QELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQR-QREYENLLQEYNKPMI 74
+ ++ +LD+ + K + T E + +E E N P
Sbjct: 352 GIKPEDQEKISILDVSGIS---GKGGKEYKLKVNINLNTDEMKIVKEPYMFESEKNLPTF 408
Query: 75 DSEEK--INLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGITEILEKRVTDSQQK 129
+ ++K ++ +I E F L I + K + + R T +
Sbjct: 409 NGKDKELLDYIKEITEGFRNMYLLLCSGISEIKEKNILAFEDCKIRVVFRNTSVYAE 465
>gnl|CDD|234493 TIGR04189, surface_SprA, cell surface protein SprA. SprA is a cell
surface protein widely distributed in the Bacteroidetes
lineage. In Flavobacterium johnsoniae, a species that
shows gliding motility, mutation disrupts gliding.
Length = 2315
Score = 29.3 bits (66), Expect = 4.9
Identities = 26/147 (17%), Positives = 51/147 (34%), Gaps = 15/147 (10%)
Query: 106 LELEADNSGITEILEKRVTDSQQKENQRSNLVAARSKMNTLRNLRSELPNATDKRSVASS 165
+ A N +T + + Q+ +Q L A + + L+ +L A +
Sbjct: 1920 RDEAARNGWLTT-FQSFNSQYTQRFSQNLQLRA---NLEPIPGLKIDL-TANRTYTR--- 1971
Query: 166 ALTQEYKYSNFNSGVASSAGNNAINYSLSNIGAGGMAITAAASQAIAATQQMKQGR---- 221
+Y+Y+N S N + N+S+S I G + + A ++ ++ R
Sbjct: 1972 --RTQYRYNNVTGVYQSMTPNTSGNFSISTIAIGTAFWNSNDGNSSEAFEKFRENRLTIA 2029
Query: 222 -RTASLKASYEAIHGGAGSSADIISKE 247
R A G S++
Sbjct: 2030 NRLAEQYGGTVYPSDDGGIGYGKNSQD 2056
>gnl|CDD|153408 cd07375, Anticodon_Ia_like, Anticodon-binding domain of class Ia
aminoacyl tRNA synthetases and similar domains. This
domain is found in a variety of class Ia aminoacyl tRNA
synthetases, C-terminal to the catalytic core domain.
It recognizes and specifically binds to the anticodon
of the tRNA. Aminoacyl tRNA synthetases catalyze the
transfer of cognate amino acids to the 3'-end of their
tRNAs by specifically recognizing cognate from
non-cognate amino acids. Members include valyl-,
leucyl-, isoleucyl-, cysteinyl-, arginyl-, and
methionyl-tRNA synthethases. This superfamily also
includes a domain from MshC, an enzyme in the mycothiol
biosynthetic pathway.
Length = 117
Score = 27.9 bits (62), Expect = 5.1
Identities = 13/58 (22%), Positives = 23/58 (39%)
Query: 34 NSLDQLQNKVNQFYQMAASMTPEQRQREYENLLQEYNKPMIDSEEKINLATQIQEFFN 91
L + + + E+ RE LQE+ K ++ E ++ T +QE F
Sbjct: 16 RLLSFFRKALGGTQPKWDNELLEEADRELLARLQEFIKRTTNALEALDPTTAVQELFK 73
>gnl|CDD|225336 COG2715, SpmA, Uncharacterized membrane protein, required for spore
maturation in B.subtilis. [General function prediction
only].
Length = 206
Score = 28.6 bits (64), Expect = 5.2
Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 22/97 (22%)
Query: 185 GNNAINYSLSNIGAGGMAITAAAS----QAIAATQQMKQGRRTAS--------------- 225
G+ A+ Y L N+ A + + AA+ +A+ Q++ + TAS
Sbjct: 85 GHPAMGYILMNMSANMLGLGNAATPLGLKAMEELQEINPNKSTASNAMIMFLVINTASIT 144
Query: 226 -LKASYEAIHGGAGSS--ADIISKELAGAAQTAIAAI 259
+ + +I GS DI + + IA I
Sbjct: 145 LIPTTVISIRMAYGSKNPTDIFLPTILATVCSTIAGI 181
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 28.4 bits (64), Expect = 5.3
Identities = 27/110 (24%), Positives = 45/110 (40%), Gaps = 11/110 (10%)
Query: 3 YLEDYIELVEILPQELRDRFTEMR--LLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQR 60
YL D E LP EL+ E++ L +LQ Q + Q +N+ + E+ Q+
Sbjct: 57 YLSDTPSARERLP-ELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQK 115
Query: 61 EYENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEA 110
E + Q + EE L ++ E L+Q+ + + E E
Sbjct: 116 ELARIKQLSANAIELDEENRELREELAE--------LKQENEALEAENER 157
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 140
Score = 27.9 bits (63), Expect = 5.6
Identities = 13/71 (18%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 37 DQLQNKVNQFYQMAASMTPEQR---QREYENLLQEYNKPMIDSEEKINLATQIQEFFNKY 93
+LQ + + AA+++ R ++E + +QE+ + ++ + QE K
Sbjct: 39 KELQKLKEKLQKDAATLSEAAREKKEKELQKKVQEFQRKQQKLQQDLQKRQ--QEELQKI 96
Query: 94 TRKLEQDIQKF 104
K+ + I++
Sbjct: 97 LDKINKAIKEV 107
>gnl|CDD|221997 pfam13233, Complex1_LYR_2, Complex1_LYR-like. This is a family
of proteins carrying the LYR motif of family
Complex1_LYR, pfam05347, likely to be involved in Fe-S
cluster biogenesis in mitochondria.
Length = 97
Score = 27.0 bits (60), Expect = 6.1
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 57 QRQREYENLLQEYNKPM-IDSEEKINLATQIQEF 89
+ QR Y LL+ YN + + EEK+
Sbjct: 63 KAQRHYLELLERYNPGLDMSEEEKVRQTANRVGL 96
>gnl|CDD|193205 pfam12729, 4HB_MCP_1, Four helix bundle sensory module for signal
transduction. This family is a four helix bundle that
operates as a ubiquitous sensory module in prokaryotic
signal-transduction. The 4HB_MCP is always found between
two predicted transmembrane helices indicating that it
detects only extracellular signals. In many cases the
domain is associated with a cytoplasmic HAMP domain
suggesting that most proteins carrying the bundle might
share the mechanism of transmembrane signalling which is
well-characterized in E coli chemoreceptors.
Length = 181
Score = 28.0 bits (63), Expect = 6.4
Identities = 20/94 (21%), Positives = 36/94 (38%), Gaps = 19/94 (20%)
Query: 16 QELRDRFTEMR-----LLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQREYENLLQEYN 70
E+R E+R L+ D+L + + + E + LL++Y
Sbjct: 52 GEIRSNLREIRANLLELILTTDPAERDELLKDIEEL------------RAEIDKLLKKYE 99
Query: 71 KPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKF 104
K ++ EEK L + +E Y RK+ +
Sbjct: 100 KTILTEEEK-KLFNEFKEQLKAY-RKVRNKVLDL 131
>gnl|CDD|213032 cd11672, ADDz, ADDz for ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger
domain. The ADDz zinc finger domain is present in the
chromatin-associated proteins
cytosine-5-methyltransferase 3 (Dnmt3) and ATRX, a SNF2
type transcription factor protein. The Dnmt3 family
includes two active DNA methyltransferases, Dnmt3a and
-3b, and one regulatory factor Dnmt3l. DNA methylation
is an important epigenetic mechanism involved in diverse
biological processes such as embryonic development, gene
expression, and genomic imprinting. The ADDz domain is a
PHD-like zinc finger motif that contains two parts, a
C2-C2 and a PHD-like zinc finger. PHD zinc finger
domains have been identified in more than 40 proteins
that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional zinc
finger C2-C2 like motif is located about twenty residues
upstream of the C4-C-C3 motif.
Length = 120
Score = 27.6 bits (62), Expect = 6.5
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 25/66 (37%)
Query: 351 YNFY-TIFCSQVAFGVMVACDSKNCP--YEWYHC-EC----VG------IAPDNPPKGKW 396
Y Y TI C G ++ CD+++C Y C C VG + ++P W
Sbjct: 46 YQSYCTICCGG---GEVILCDNESCCRVY----CTACLDFLVGPGTYDKVLDEDP----W 94
Query: 397 YCPLCL 402
C LCL
Sbjct: 95 SCYLCL 100
>gnl|CDD|237076 PRK12362, PRK12362, germination protease; Provisional.
Length = 318
Score = 28.7 bits (65), Expect = 6.6
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 36 LDQLQNKVN---QFYQMAASMTPEQRQREYENLLQEYNKPMI 74
LD+L N+ +FY M S+ E++Q+ + +L Y +I
Sbjct: 246 LDELINQSEEGSEFYNMLKSLNQEEKQQLIKEVLSPYVGNLI 287
>gnl|CDD|236781 PRK10869, PRK10869, recombination and repair protein; Provisional.
Length = 553
Score = 28.7 bits (65), Expect = 6.6
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 12 EILPQELRDRFTEMRLLDLQSQNSLDQLQNKVNQFYQMA---ASMTPEQRQR 60
E LPQ + E + LD ++ L+ L V + +Q A A + RQR
Sbjct: 320 EELPQHHQQLLEEQQQLD-DQEDDLETLALAVEKHHQQALETAQKLHQSRQR 370
>gnl|CDD|232981 TIGR00456, argS, arginyl-tRNA synthetase. This model recognizes
arginyl-tRNA synthetase in every completed genome to
date. An interesting feature of the alignment of all
arginyl-tRNA synthetases is a fairly deep split between
two families. One family includes archaeal, eukaryotic
and organellar, spirochete, E. coli, and Synechocystis
sp. The second, sharing a deletion of about 25 residues
in the central region relative to the first, includes
Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and
Mycobacteria, and the Gram-negative bacterium
Helicobacter pylori [Protein synthesis, tRNA
aminoacylation].
Length = 566
Score = 28.8 bits (65), Expect = 6.8
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 3/79 (3%)
Query: 43 VNQFYQMAASMTPEQRQREYENLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQ 102
V +F + ++ E E NK EE L + +E F K E+ I+
Sbjct: 172 VEKFGNEKLNEAVKKPDHGLEGFYVEINK---RLEENEELEEEARELFVKLESGDEEAIK 228
Query: 103 KFKLELEADNSGITEILEK 121
+K +E GI E L +
Sbjct: 229 LWKRLVEYSLEGIKETLAR 247
>gnl|CDD|236101 PRK07803, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 626
Score = 28.5 bits (64), Expect = 7.4
Identities = 18/62 (29%), Positives = 24/62 (38%), Gaps = 25/62 (40%)
Query: 196 IGAGGMAITAAASQAIAATQQMKQGRRTASLKASYEAIHGGAGSSADIISKELAGAAQTA 255
IGAGG + AA I A ++ G R A ++ K L G A T
Sbjct: 14 IGAGGAGLRAA----IEARER---GLRVA------------------VVCKSLFGKAHTV 48
Query: 256 IA 257
+A
Sbjct: 49 MA 50
>gnl|CDD|140213 PTZ00186, PTZ00186, heat shock 70 kDa precursor protein;
Provisional.
Length = 657
Score = 28.5 bits (63), Expect = 7.7
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 121 KRVTDSQQKENQRSNLVAARSKMNTLRNLRSELPNATDK--RSVASSALTQEYKYSNFNS 178
K V+D++ KEN ++ + R M + +L ATDK ++V T+ + + NS
Sbjct: 574 KYVSDAE-KENVKTLVAELRKAMENPNVAKDDLAAATDKLQKAVMECGRTEYQQAAAANS 632
Query: 179 GVASSAGNNA 188
G +S++G
Sbjct: 633 GSSSNSGEQQ 642
>gnl|CDD|220629 pfam10199, Adaptin_binding, Alpha and gamma adaptin binding
protein p34. p34 is a protein involved in membrane
trafficking. It is known to interact with both alpha
and gamma adaptin. It has been speculated that p34 may
play a chaperone role such as preventing the soluble
adaptors from co-assembling with soluble clathrin, or
helping to remove the adaptors from the coated vesicle.
Another possible function is in aiding the recruitment
of soluble adaptors onto the membrane.
Length = 101
Score = 27.0 bits (60), Expect = 7.9
Identities = 8/32 (25%), Positives = 15/32 (46%)
Query: 34 NSLDQLQNKVNQFYQMAASMTPEQRQREYENL 65
+ L K+ Q M AS+ E+R++ +
Sbjct: 67 EDFENLLTKLQQARDMTASLPDEERKKFAAKV 98
>gnl|CDD|151608 pfam11166, DUF2951, Protein of unknown function (DUF2951). This
family of proteins has no known function. It has a
highly conserved sequence.
Length = 97
Score = 26.7 bits (59), Expect = 8.1
Identities = 24/84 (28%), Positives = 34/84 (40%), Gaps = 20/84 (23%)
Query: 56 EQRQREYE---NLLQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADN 112
E QRE E L+E +K + +S ++I QE N QK L L+
Sbjct: 2 ESYQRETERRIQRLEENDKTIFESLDEIKDGQHTQELVN----------QKMDLTLD--- 48
Query: 113 SGITEILEKRVTDSQQKENQRSNL 136
I +R D + KE R N+
Sbjct: 49 ----SINRERELDKENKEENRKNI 68
>gnl|CDD|240578 cd12951, RRP7_Rrp7A, RRP7 domain ribosomal RNA-processing protein 7
homolog A (Rrp7A) and similar proteins. The family
corresponds to the RRP7 domain of Rrp7A, also termed
gastric cancer antigen Zg14, and similar proteins which
are yeast ribosomal RNA-processing protein 7 (Rrp7p)
homologs mainly found in Metazoans. The cellular
function of Rrp7A remains unclear currently. Rrp7A
harbors an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RRP7
domain.
Length = 129
Score = 27.2 bits (61), Expect = 8.1
Identities = 21/107 (19%), Positives = 42/107 (39%), Gaps = 33/107 (30%)
Query: 66 LQEYNKPMIDSEEKINLATQIQEFFNKYTRKLEQDIQKFKLELEADNSGIT--------- 116
++EYN + D E L ++I E+ +Y ++ E++ ++ + E E D G
Sbjct: 6 VEEYNASIPDPAE---LQSEIDEYMEEYDKEEEEEKEEKEKEAEPDEDGWVTVTKKGRRP 62
Query: 117 -----EILEKRVTDS----------------QQKENQRSNLVAARSK 142
E + + + Q +E++R+ L R K
Sbjct: 63 KTARKESVAAKAAEKEKKKKKKKELKNFYRFQIRESKRNELAELRKK 109
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 28.7 bits (65), Expect = 8.4
Identities = 27/167 (16%), Positives = 65/167 (38%), Gaps = 14/167 (8%)
Query: 5 EDYIELVEILPQELR---DRFTEMRLLDLQSQNSLDQLQNKVNQFYQMAASMTPEQRQRE 61
ED+ E L Q D + + + L + N+ + A +P
Sbjct: 55 EDFKLFKEKLKQSFSHIADIKVTFSIEVENITFTEELLLDYWNEIIEKAKKNSPL----- 109
Query: 62 YENLLQEYNKPMIDSEEKINLATQI--QEFFNKYTRKLEQDIQKF---KLELEADNSGIT 116
+++LL++ + ++ I + +I K+ KL + +KF L+++ +
Sbjct: 110 FKSLLKKQKVEVEGNKLIIKVNNEIERDHLKKKHLPKLIKQYEKFGFGILKIDFEIDDSK 169
Query: 117 EILEKRVTDSQQKENQRS-NLVAARSKMNTLRNLRSELPNATDKRSV 162
E LEK ++++ + + + A K+ + +S+ + +
Sbjct: 170 EELEKFEAQKEEEDEKLAKEALEAMKKLEAEKKKQSKNFDPKEGPVQ 216
>gnl|CDD|171679 PRK12717, flgL, flagellar hook-associated protein FlgL;
Provisional.
Length = 523
Score = 28.6 bits (64), Expect = 8.6
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 6/70 (8%)
Query: 140 RSKMNTLRNLRSELPNATDKRSVASSALTQEYKYSNFNSGVAS-SAGNNAINYSLSNIGA 198
++ ++TL LR L TD A AL S + + ++ + ++ + S+IGA
Sbjct: 405 QNILDTLSQLRKALSTPTDGDPAARQALRAA-----LASALGNLASAIDQVDTARSSIGA 459
Query: 199 GGMAITAAAS 208
G A+ +
Sbjct: 460 RGNALDIQGT 469
>gnl|CDD|217036 pfam02442, L1R_F9L, Lipid membrane protein of large eukaryotic DNA
viruses. The four families of large eukaryotic DNA
viruses, Poxviridae, Asfarviridae, Iridoviridae, and
Phycodnaviridae, referred to collectively as
nucleocytoplasmic large DNA viruses or NCLDV, have all
been shown to have a lipid membrane, in spite of the
major differences in virion structure. The paralogous
genes L1R and F9L encode membrane proteins that have a
conserved domain architecture, with a single, C-terminal
transmembrane helix, and an N-terminal,
multiple-disulfide-bonded domain. The conservation of
the myristoylated, disulfide-bonded protein L1R/F9L in
most of the NCLDV correlates with the conservation of
the thiol-disulfide oxidoreductase E10R which, in
vaccinia virus, is required for the formation of
disulfide bonds in L1R and F9L.
Length = 203
Score = 27.7 bits (62), Expect = 9.4
Identities = 13/92 (14%), Positives = 33/92 (35%), Gaps = 7/92 (7%)
Query: 124 TDSQQKENQRSNLVAARSKMNT-LRNLRSELPNATDKRSVASSALTQEYKYSNFNSGVAS 182
+ + Q++ + A +++ + + + + AS+ +T N + G
Sbjct: 75 VLNNLPQEQKAAVATAANEIGIDINAVVKDFVTELIQTCKASAVVTNSIDVQNIDIGECY 134
Query: 183 SAGNNAINYSLSNIGAGGMAITAAASQAIAAT 214
+ G + N G +A A+ + A
Sbjct: 135 APGGVITDLQFVNSG------SAEANCGLKAV 160
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil motif
at the N terminus region. Yeast cells with mutant Atg14
are defective not only in autophagy but also in sorting
of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically required
for the function of Apg6/Vps30p through the autophagic
pathway. There are 17 auto-phagosomal component proteins
which are categorized into six functional units, one of
which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The
AS-PI3K complex and the Atg2-Atg18 complex are essential
for nucleation, and the specific function of the AS-PI3K
apparently is to produce phosphatidylinositol
3-phosphate (PtdIns(3)P) at the pre-autophagosomal
structure (PAS). The localisation of this complex at the
PAS is controlled by Atg14. Autophagy mediates the
cellular response to nutrient deprivation, protein
aggregation, and pathogen invasion in humans, and
malfunction of autophagy has been implicated in multiple
human diseases including cancer. This effect seems to be
mediated through direct interaction of the human Atg14
with Beclin 1 in the human phosphatidylinositol 3-kinase
class III complex.
Length = 307
Score = 28.1 bits (63), Expect = 9.5
Identities = 17/83 (20%), Positives = 28/83 (33%), Gaps = 6/83 (7%)
Query: 96 KLEQDIQKFKLELEADNSGITEILEKRVTDSQQKENQRSNLVAARSKMNT------LRNL 149
+L D+ + LE E + E LE + + L AR K + L
Sbjct: 24 ELRLDLARLLLENEELKQKVEEALEGATNEDGKLAADLLKLEVARKKERLNQIRARISQL 83
Query: 150 RSELPNATDKRSVASSALTQEYK 172
+ E+ ++ AL Q
Sbjct: 84 KEEIEQKRERIEELKRALAQRRS 106
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
0.311 0.125 0.348
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,136,645
Number of extensions: 1860047
Number of successful extensions: 2118
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2078
Number of HSP's successfully gapped: 179
Length of query: 422
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 323
Effective length of database: 6,546,556
Effective search space: 2114537588
Effective search space used: 2114537588
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 60 (26.8 bits)