RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2181
(490 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 72.1 bits (178), Expect = 4e-16
Identities = 24/45 (53%), Positives = 32/45 (71%)
Query: 109 RNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
R RT+FT EQ++ LEKEFE+ YP RE LA K+GL E +++V
Sbjct: 2 RKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKV 46
Score = 47.5 bits (114), Expect = 2e-07
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 227 KEFERTHYPDVFARERLADKIGLPEARIQV 256
KEFE+ YP RE LA K+GL E +++V
Sbjct: 17 KEFEKNRYPSAEEREELAKKLGLTERQVKV 46
Score = 37.1 bits (87), Expect = 9e-04
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 339 QVWFSNRRAKWRR 351
+VWF NRRAKW+R
Sbjct: 45 KVWFQNRRAKWKR 57
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 64.6 bits (158), Expect = 1e-13
Identities = 24/46 (52%), Positives = 33/46 (71%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
+R RTSFT EQ++ LEKEF++ YP RE LA K+GL E +++V
Sbjct: 2 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKV 47
Score = 42.2 bits (100), Expect = 1e-05
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 227 KEFERTHYPDVFARERLADKIGLPEARIQV 256
KEF++ YP RE LA K+GL E +++V
Sbjct: 18 KEFQKNPYPSREEREELAKKLGLSERQVKV 47
Score = 32.2 bits (74), Expect = 0.044
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 339 QVWFSNRRAKWR 350
+VWF NRRAKW+
Sbjct: 46 KVWFQNRRAKWK 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in
the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 63.0 bits (154), Expect = 6e-13
Identities = 22/45 (48%), Positives = 31/45 (68%)
Query: 109 RNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
R RT FT EQ++ LEKEFE+ YP RE LA ++GL E ++++
Sbjct: 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKI 46
Score = 42.6 bits (101), Expect = 1e-05
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 227 KEFERTHYPDVFARERLADKIGLPEARIQV 256
KEFE+ YP RE LA ++GL E ++++
Sbjct: 17 KEFEKNPYPSREEREELAKELGLTERQVKI 46
Score = 34.5 bits (80), Expect = 0.008
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 339 QVWFSNRRAKWRREE 353
++WF NRRAK +R E
Sbjct: 45 KIWFQNRRAKLKRSE 59
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 40.5 bits (95), Expect = 5e-04
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 14/78 (17%)
Query: 77 KEHESTSDI-NSEPNSSADEDSQMRLRLKRKLQRNRTSFTNEQIDSLEKEFERTHYPDVF 135
+ +S + + SS + + R T+EQ+ LE+EFE YP
Sbjct: 33 EAADSEMKLERKQDGSSPPKSKRRRT-------------TDEQLMVLEREFEINPYPSSI 79
Query: 136 ARERLADKIGLPEARIQV 153
R +L+ + +P +Q+
Sbjct: 80 TRIKLSLLLNMPPKSVQI 97
Score = 30.9 bits (70), Expect = 0.77
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 227 KEFERTHYPDVFARERLADKIGLPEARIQV 256
+EFE YP R +L+ + +P +Q+
Sbjct: 68 REFEINPYPSSITRIKLSLLLNMPPKSVQI 97
Score = 27.8 bits (62), Expect = 7.6
Identities = 10/39 (25%), Positives = 21/39 (53%)
Query: 339 QVWFSNRRAKWRREEKLRNQRRGSTGSVNSANTTTSTTA 377
Q+WF N+RAK +++ + ++R + A + +T
Sbjct: 96 QIWFQNKRAKEKKKRSGKVEQRPGEEEADLAKIGSLSTG 134
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 34.7 bits (80), Expect = 0.12
Identities = 16/108 (14%), Positives = 33/108 (30%), Gaps = 8/108 (7%)
Query: 95 EDSQMRLRLKRKLQRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIG--------L 146
+ L + RN +I+SLE+ ER +E L + L
Sbjct: 382 REELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTEL 441
Query: 147 PEARIQVSSINRVLRNLAAQKEQQASAHNQTSETVYDKLRMFNGQPGW 194
E ++ + L L + ++ + E + + +
Sbjct: 442 EELNEELEELEEQLEELRDRLKELERELAELQEELQRLEKELSSLEAR 489
>gnl|CDD|132333 TIGR03290, CoB_CoM_SS_C, CoB--CoM heterodisulfide reductase,
subunit C. The last step in methanogenesis leaves two
coenzymes of methanogenesis, CoM and CoB, linked by a
disulfide bond. Members of this protein family are the
C subunit of the enzyme that reduces the
heterodisulfide to CoB-SH and CoM-SH. Similar enzyme
complex subunits are found in various other species,
but likely act on a different substrate.
Length = 144
Score = 32.4 bits (74), Expect = 0.24
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 1 MKVSSINRVLRNLAAQKEQQASAHNQTSETVY 32
+K++ I + LRNLAA+K A AH +T+ V
Sbjct: 62 VKITDIIKALRNLAAKKGFMAKAHRKTASFVL 93
Score = 32.0 bits (73), Expect = 0.29
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 151 IQVSSINRVLRNLAAQKEQQASAHNQTSETVY 182
++++ I + LRNLAA+K A AH +T+ V
Sbjct: 62 VKITDIIKALRNLAAKKGFMAKAHRKTASFVL 93
Score = 32.0 bits (73), Expect = 0.29
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 254 IQVSSINRVLRNLAAQKEQQASAHNQTSETVY 285
++++ I + LRNLAA+K A AH +T+ V
Sbjct: 62 VKITDIIKALRNLAAKKGFMAKAHRKTASFVL 93
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 33.4 bits (76), Expect = 0.31
Identities = 21/78 (26%), Positives = 26/78 (33%), Gaps = 9/78 (11%)
Query: 363 TGSVNSANTTTSTTALDHVPPTSQSPPPSSRLPLNPGGFNPSS---------MYSSIPQP 413
T V T + AL+H TS S P G SS Y+ P
Sbjct: 137 TERVKEDTPATPSRALNHYISTSGRQRVKSYTPKPRGEVKSSSPTQTREKVRKYTPSPLG 196
Query: 414 AGMDSYNPSCLQQAAREH 431
++SY PS R H
Sbjct: 197 RMVNSYAPSTFMTMPRSH 214
>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 = 32.7 bits (75), Expect = 0.50
Identities = 18/100 (18%), Positives = 38/100 (38%), Gaps = 14/100 (14%)
Query: 94 DEDSQMRLRLKRKLQRNRTSFT--NEQIDSLEKEFER---------THYPDVF-ARERLA 141
+E L +L E+++SLE E E + ++ E L
Sbjct: 326 EELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLR 385
Query: 142 DKIGLPEARIQVSSINRVLRNLAAQKEQQASAHNQTSETV 181
K+ + +Q++S+N + L A+ E+ + + +
Sbjct: 386 SKVA--QLELQIASLNNEIERLEARLERLEDRRERLQQEI 423
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 31.6 bits (72), Expect = 1.1
Identities = 18/100 (18%), Positives = 37/100 (37%), Gaps = 13/100 (13%)
Query: 100 RLRLKRKLQRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINRV 159
L K + Q+++ + +Q+ SLE E + + L + R Q++ +N
Sbjct: 49 ALEKKIREQQDQRAKLEKQLKSLETEIASL------EAQLIETADDLKKLRKQIADLNAR 102
Query: 160 LRNLAAQKEQQA-------SAHNQTSETVYDKLRMFNGQP 192
L L Q+ +Q +A ++ L +
Sbjct: 103 LNALEVQEREQRRRLAEQLAALQRSGRNPPPALLVSPEDA 142
>gnl|CDD|238706 cd01418, Ribosomal_L19e_A, Ribosomal protein L19e, archaeal. L19e
is found in the large ribosomal subunit of eukaryotes
and archaea. L19e is distinct from the ribosomal subunit
L19, which is found in prokaryotes. It consists of two
small globular domains connected by an extended segment.
It is located toward the surface of the large subunit,
with one exposed end involved in forming the
intersubunit bridge with the small subunit. The other
exposed end is involved in forming the translocon
binding site, along with L22, L23, L24, L29, and L31e
subunits.
Length = 145
Score = 30.0 bits (68), Expect = 1.5
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 324 ISRDDAKGLVQQSARQV----WFSNRRAKWRREEKLRNQRRGSTGSV 366
I+RDD + L+++ + S R K R E++ + +RRG GS
Sbjct: 33 ITRDDIRALIKEGVIKAKPKKGISRGRLKERHEKRKKGRRRGP-GSR 78
>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain. This
family represents the C-terminus (approximately 300
residues) of proteins that are involved as binding
partners for Prp19 as part of the nuclear pore complex.
The family in Drosophila is necessary for pre-mRNA
splicing, and the human protein has been found in
purifications of the spliceosome. In the past this
family was thought, erroneously, to be associated with
microfibrillin.
Length = 277
Score = 30.3 bits (68), Expect = 2.1
Identities = 25/118 (21%), Positives = 39/118 (33%), Gaps = 3/118 (2%)
Query: 72 SRDDAKEHESTSDINSEPNSSADEDSQMRLRLKRKLQRNRTSFTNEQIDSL---EKEFER 128
++ E + SE D + M RLK R + T ++ + EK E
Sbjct: 6 ELEEEDESGEEEEEESEEEEETDSEDDMEPRLKPVFTRKKDRITIQEREREAAKEKALEE 65
Query: 129 THYPDVFARERLADKIGLPEARIQVSSINRVLRNLAAQKEQQASAHNQTSETVYDKLR 186
R+R KI E + ++ R A + N+ E KLR
Sbjct: 66 EAKRKAEERKRETLKIVEEEVKKELELKKRNTLLEANIDDVDTDDENEEEEYEAWKLR 123
>gnl|CDD|151954 pfam11517, Nab2, Nuclear abundant poly(A) RNA-bind protein 2
(Nab2). Nab2 is a yeast heterogeneous nuclear
ribonucleoprotein that modulates poly(A) tail length and
mRNA. This is the N terminal domain of the protein which
mediates interactions with the C-terminal globular
domain, Myosin-like protein 1 and the mRNA export
factor, Gfd1.The N-terminal domain of Nab2 shows a
structure of a helical fold. The N terminal domain of
Nab2 is thought to mediate protein protein interactions
that facilitate the nuclear export of mRNA. An essential
hydrophobic Phe73 patch on the N terminal domain is
thought to be a important component of the interface
between Nab2 and Mlp1.
Length = 107
Score = 28.7 bits (64), Expect = 2.6
Identities = 12/35 (34%), Positives = 14/35 (40%), Gaps = 5/35 (14%)
Query: 170 QASAHNQTSETVYDKLRMFNGQPGWAWYPGSTPTP 204
+ ETVY KLRM QP S P+
Sbjct: 78 ELLQQGDDLETVYSKLRMMASQP-----SSSAPSA 107
Score = 28.7 bits (64), Expect = 2.6
Identities = 12/35 (34%), Positives = 14/35 (40%), Gaps = 5/35 (14%)
Query: 273 QASAHNQTSETVYDKLRMFNGQPGWAWYPGSTPTP 307
+ ETVY KLRM QP S P+
Sbjct: 78 ELLQQGDDLETVYSKLRMMASQP-----SSSAPSA 107
>gnl|CDD|129317 TIGR00213, GmhB_yaeD, D,D-heptose 1,7-bisphosphate phosphatase.
This family of proteins formerly designated yaeD
resembles the histidinol phosphatase domain of the
bifunctional protein HisB. The member from E. coli has
been characterized as D,D-heptose 1,7-bisphosphate
phosphatase, GmhB, involved in inner core LPS assembly
(PMID:11751812) [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 176
Score = 29.5 bits (66), Expect = 2.9
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 9/61 (14%)
Query: 400 GFNPSSMYSSIPQPAGMDSYNPSC---------LQQAAREHHHHSSYSYMFHDSLHSLQS 450
+ +Y P G++ + C L QA +E H + SYM D L +Q+
Sbjct: 79 DVDLDGIYYCPHHPEGVEEFRQVCDCRKPKPGMLLQARKELHIDMAQSYMVGDKLEDMQA 138
Query: 451 A 451
Sbjct: 139 G 139
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 29.7 bits (67), Expect = 4.5
Identities = 33/125 (26%), Positives = 48/125 (38%), Gaps = 37/125 (29%)
Query: 88 EPNSSADEDSQMRLRLKRKLQ------------RNRTSFTNEQIDSLEKEFERTHYPDVF 135
P+S E + LK + + RN ++SLEK+F R+ D+F
Sbjct: 203 LPSSILSEIEALEAELKEQSEKYEDLAQEIAHLRNELEEAQRSLESLEKKF-RSEGGDLF 261
Query: 136 A-RERLADKIGLPEARIQVSSINRV-LRNLAA-------------------QKEQQASAH 174
RE+L ++ EA NR LR LAA QKE+Q+ +
Sbjct: 262 EEREQLERQLKEIEAA---RKANRAQLRELAADPLPLLLIPNLLDSTKAQLQKEEQSQQN 318
Query: 175 NQTSE 179
T E
Sbjct: 319 QLTQE 323
>gnl|CDD|222449 pfam13908, Shisa, Wnt and FGF inhibitory regulator. Shisa is a
transcription factor-type molecule that physically
interacts with immature forms of the Wnt receptor
Frizzled and the FGF receptor within the endoplasmic
reticulum to inhibit their post-translational maturation
and trafficking to the cell surface.
Length = 177
Score = 28.6 bits (64), Expect = 5.3
Identities = 15/74 (20%), Positives = 21/74 (28%), Gaps = 11/74 (14%)
Query: 351 REEKLRNQRRGSTGSVNSANTTTSTTALDHVPP--------TSQSPPPSSRLPLNPGGFN 402
E+ R QR T + ++ TT P PP +P P
Sbjct: 103 LEKACRPQRPVMTRATSTTVQTTPLPQPPSTAPSYPGPQYQGYHPMPPQPGMPAPPYSLQ 162
Query: 403 ---PSSMYSSIPQP 413
P + P P
Sbjct: 163 YPPPGLLQPQGPPP 176
>gnl|CDD|240286 PTZ00139, PTZ00139, Succinate dehydrogenase [ubiquinone]
flavoprotein subunit; Provisional.
Length = 617
Score = 28.6 bits (64), Expect = 9.5
Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 65 PGSVTPISRDDAKEHESTSDINSEPNSSAD-EDSQMRLRLKRKLQRNRTSFTNEQIDSLE 123
PG P DA E S + ++ ++ D +Q+R R++R +Q++ F +SL+
Sbjct: 447 PGRPQPDLPKDAGE-ASIARLDKIRHNKGDISTAQIRKRMQRTMQKHAAVFRIG--ESLQ 503
Query: 124 KEFER-----THYPDVFARER 139
+ E+ + + DV +++
Sbjct: 504 EGVEKIKEIYSDFKDVKIKDK 524
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 0.376
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,913,175
Number of extensions: 2370067
Number of successful extensions: 2669
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2634
Number of HSP's successfully gapped: 83
Length of query: 490
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 389
Effective length of database: 6,457,848
Effective search space: 2512102872
Effective search space used: 2512102872
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 (21.8 bits)
S2: 61 (27.2 bits)