RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2704
(256 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 105 bits (265), Expect = 9e-30
Identities = 35/57 (61%), Positives = 43/57 (75%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
RR RTTF+ QLEELE+ F K YP REELA ++ LTE +V+VWFQNRRAKW++
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 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 = 93.8 bits (234), Expect = 4e-25
Identities = 33/59 (55%), Positives = 41/59 (69%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
RR RT F+ QLEELE+ F K YP REELA + LTE +V++WFQNRRAK ++ E
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 90.8 bits (226), Expect = 5e-24
Identities = 33/57 (57%), Positives = 43/57 (75%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
+RR RT+F+ QLEELE+ F K YP REELA ++ L+E +V+VWFQNRRAKW+
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 65.5 bits (160), Expect = 2e-13
Identities = 27/103 (26%), Positives = 48/103 (46%), Gaps = 1/103 (0%)
Query: 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169
G + R ++ QL LER F YP R +L+L +++ VQ+WFQN+RAK
Sbjct: 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKE 106
Query: 170 RKQEKLVSKQPQELFSSPL-QSPASPSPDLNVISVPAASPVPH 211
+K+ +Q + L + + + +++I S +
Sbjct: 107 KKKRSGKVEQRPGEEEADLAKIGSLSTGQISIIETLEFSRTSY 149
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 36.2 bits (83), Expect = 0.017
Identities = 31/169 (18%), Positives = 49/169 (28%), Gaps = 14/169 (8%)
Query: 42 DPLLSGFTLPISQMPPVIVTTLQQSCSANFQPVMKYNPSTSPQVSPSSP----------- 90
DPLL+G + TT QS +A +PV + P S V P+ P
Sbjct: 308 DPLLNGAPITEPVAVAAAATTATQSWAAPVEPVTQTPPVASVDVPPAQPTVAWQPVPGPQ 367
Query: 91 ---PTLCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREEL 147
P + +P P+ Q + + Q A P E
Sbjct: 368 TGEPVIAPAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQ 427
Query: 148 ALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQPQELFSSPLQSPASPSP 196
+ + + +Q+ + Q Q PA+ P
Sbjct: 428 PAQQPYYAPAPEQPVAGNAWQAEEQQSTFAPQSTYQTEQTYQQPAAQEP 476
Score = 27.7 bits (61), Expect = 7.1
Identities = 24/144 (16%), Positives = 52/144 (36%), Gaps = 17/144 (11%)
Query: 77 YNPSTSPQVSPSSPPTLCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKT 136
+ P P P P + Q ++ Q+ Q ++ +
Sbjct: 745 FTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQY 804
Query: 137 HYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQPQELF----------SS 186
P ++ +A + + + V Q ++++ ++ V+ QPQ+ S
Sbjct: 805 QQP----QQPVAPQPQYQQPQQPVAPQ---PQYQQPQQPVAPQPQDTLLHPLLMRNGDSR 857
Query: 187 PLQSPASPSPDLNVISVPAASPVP 210
PL P +P P L++++ P + P
Sbjct: 858 PLHKPTTPLPSLDLLTPPPSEVEP 881
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 32.8 bits (75), Expect = 0.12
Identities = 23/138 (16%), Positives = 46/138 (33%), Gaps = 31/138 (22%)
Query: 80 STSPQVSPSSPPTLCFSPTPTPESPPTQQT-------------------GKRKQRRYRTT 120
+ + +L + + +S ++ K+ QR+ +
Sbjct: 46 DSESSSNSVPSLSLSSTASSLSDSSTYSRSLKEVKLERQAQEAYENWLSAKQAQRQKKLQ 105
Query: 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQ--NRRAKWRKQEKLVSK 178
+ ++ ER REE LR L + + + W + ++A ++ K K
Sbjct: 106 KLLEEKQKQEREKE---------REEAELRQRLAKEKYEEWCRQKAQQAAKQRTPK-HKK 155
Query: 179 QPQELFSSPLQSPASPSP 196
+ E SS L A P
Sbjct: 156 EAAESASSSLSGSAKPER 173
>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein TraB;
Provisional.
Length = 475
Score = 32.9 bits (75), Expect = 0.15
Identities = 26/172 (15%), Positives = 50/172 (29%), Gaps = 20/172 (11%)
Query: 96 SPTPTPESPPTQQTG------KRKQRRYRTTFSNFQLEELERAFHK-THYPDVFFREELA 148
+ P TG K R++ TT ++++ + + DV ++
Sbjct: 42 GEAVAEQEPVPDMTGVVDTTFDDKVRQHATTEMQVTAAQMQKQYEEIRRELDVLNKQRGD 101
Query: 149 LRIDLTEARVQVWFQNRRAKWRKQEKLVSKQPQELFSSPLQSPASPSPDLNVISVPAASP 208
+ + + A +Q K + P P+ + P P
Sbjct: 102 DQRRIEK------LGQDNAALAEQVKALGANPVTATGEPVPQMPASPPGPE--GEPQPGN 153
Query: 209 VPHFSPP-----VCSTSSFYLGMEWGGFMSYQGASTPQPQKESSDIISTDDK 255
P PP V ++FY G S P P + + ++
Sbjct: 154 TPVSFPPQGSVAVPPPTAFYPGNGVTPPPQVTYQSVPVPNRIQRKTFTYNEG 205
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 31.7 bits (72), Expect = 0.39
Identities = 14/70 (20%), Positives = 25/70 (35%), Gaps = 3/70 (4%)
Query: 37 PNQNGDPLLSGFTLPISQMPPVIVTTLQQSCSANFQPVMKYNPSTSPQVSPSSPPTLCFS 96
P Q+ P+ + P + P S S + P ++ Q + + P
Sbjct: 375 PKQHIKPVFTQ---PAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDP 431
Query: 97 PTPTPESPPT 106
P P +PP+
Sbjct: 432 PAAVPVNPPS 441
Score = 27.8 bits (62), Expect = 6.1
Identities = 9/38 (23%), Positives = 13/38 (34%)
Query: 72 QPVMKYNPSTSPQVSPSSPPTLCFSPTPTPESPPTQQT 109
QP PS + SPS + + P+S
Sbjct: 385 QPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAG 422
>gnl|CDD|115704 pfam07068, Gp23, Major capsid protein Gp23. This family contains a
number of major capsid Gp23 proteins approximately 500
residues long, from T4-like bacteriophages.
Length = 493
Score = 31.5 bits (71), Expect = 0.42
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 56 PPVIVTTLQQSCSANFQPVMKYNPSTSPQVSPSSPPTL 93
P V +T L+ S NFQPVM + V+P + +L
Sbjct: 444 PYVALTPLRGSDPKNFQPVMGFKTRYGIGVNPFAESSL 481
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 31.3 bits (71), Expect = 0.63
Identities = 24/102 (23%), Positives = 31/102 (30%), Gaps = 3/102 (2%)
Query: 35 NTPNQNGDPLLSGFTLPISQMPPVIVTTLQQSCSANFQPVMKYNPSTSPQVSPSSP--PT 92
P Q F QMPP QQ QP + P P P P
Sbjct: 235 QLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQ-QQPPQPQAQPPPQNQPTPHPGLPQGQN 293
Query: 93 LCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFH 134
P P+ P Q + +QR + QL + +R
Sbjct: 294 APLPPPQQPQLLPLVQQPQGQQRGPQFREQLVQLSQQQREAL 335
>gnl|CDD|180917 PRK07279, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1034
Score = 31.2 bits (71), Expect = 0.63
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 5/20 (25%)
Query: 124 FQLEELERAFHKTHYPDVFF 143
FQL A+ K HYP VF+
Sbjct: 693 FQL-----AYFKAHYPAVFY 707
>gnl|CDD|182059 PRK09752, PRK09752, adhesin; Provisional.
Length = 1250
Score = 30.4 bits (68), Expect = 1.1
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 4/26 (15%)
Query: 82 SPQVSPSSPPTLCFSPTPTPESPPTQ 107
S +V+P SPP P PTP+ PT
Sbjct: 915 SQEVTPPSPP----DPDPTPDPDPTP 936
>gnl|CDD|225468 COG2916, Hns, DNA-binding protein H-NS [General function prediction
only].
Length = 128
Score = 28.2 bits (63), Expect = 2.1
Identities = 18/72 (25%), Positives = 24/72 (33%), Gaps = 5/72 (6%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
R R LE LE K +EE A I E R Q + R+
Sbjct: 6 RTLRAMARETYLELLEEMLEKEEQVVQERQEEEAAAIAEIEER-----QEKYGTIRELLI 60
Query: 175 LVSKQPQELFSS 186
P+EL ++
Sbjct: 61 KDGITPEELLNT 72
>gnl|CDD|227678 COG5388, COG5388, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 209
Score = 29.0 bits (65), Expect = 2.2
Identities = 16/62 (25%), Positives = 21/62 (33%), Gaps = 13/62 (20%)
Query: 97 PTPTPESPPTQQTGKRKQRRYRTTFSNFQL-EELERAFH------------KTHYPDVFF 143
TP P SP + +R + R R + F L K+ PDVF
Sbjct: 3 STPWPMSPSKPRAVERSKMRSRQGITIFHYWNRLRGGRALPRREDIDPAKLKSLLPDVFI 62
Query: 144 RE 145
E
Sbjct: 63 LE 64
>gnl|CDD|221839 pfam12898, Stc1, Stc1 domain. The domain contains 8 conserved
cysteines that may bind to zinc. In S. pombe this
protein acts as a protein linker which links the
chromatin modifying CLRC complex to RNAi by tethering it
to the RITS complex. The region is reported as a LIM
domain here, but has a slightly different arrangement of
its CxxC pairs from the Pfam LIM domain pfam00412, hence
why it is not part of that family. The tandem
zinc-finger structure could mediate protein-protein
interactions.
Length = 84
Score = 27.4 bits (61), Expect = 2.5
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 112 RKQRRYRTTFSNFQLEELERA 132
K+ R R+ FS QLE+L +A
Sbjct: 5 CKKIRPRSAFSKRQLEKLRKA 25
>gnl|CDD|147812 pfam05858, BIV_Env, Bovine immunodeficiency virus surface protein
(SU). The bovine lentivirus also known as the bovine
immunodeficiency-like virus (BIV) has conserved and
hypervariable regions in the surface envelope gene. This
family corresponds to the SU surface protein.
Length = 548
Score = 28.9 bits (64), Expect = 2.7
Identities = 22/67 (32%), Positives = 27/67 (40%), Gaps = 3/67 (4%)
Query: 86 SPSSPPTLCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHY-PDVFFR 144
S P CFS P P +Q GK Q + T +E E+ T PD+F
Sbjct: 295 DTSKAPWFCFSNAPIPSCRSSQWGGKYFQEKVNQTVVEQVMELAEKHSRATWIEPDLFEE 354
Query: 145 E--ELAL 149
ELAL
Sbjct: 355 VIYELAL 361
>gnl|CDD|215145 PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED.
Length = 590
Score = 28.9 bits (65), Expect = 2.8
Identities = 10/62 (16%), Positives = 19/62 (30%), Gaps = 1/62 (1%)
Query: 55 MPPVIVTTLQQSCSANFQPVMKYNPSTSPQVSPSSPPTLCFSPTPTPESPPTQQTGKRKQ 114
+ S + +P + PS S + S L +P+P S +
Sbjct: 16 SSSSSSSQSSPPSSTSPRPRRR-KPSASSLLHTPSILPLPKLSSPSPPSVTLPPAATTQT 74
Query: 115 RR 116
+
Sbjct: 75 PQ 76
>gnl|CDD|213232 cd03265, ABC_DrrA, Daunorubicin/doxorubicin resistance ATP-binding
protein. DrrA is the ATP-binding protein component of a
bacterial exporter complex that confers resistance to
the antibiotics daunorubicin and doxorubicin. In
addition to DrrA, the complex includes an integral
membrane protein called DrrB. DrrA belongs to the ABC
family of transporters and shares sequence and
functional similarities with a protein found in cancer
cells called P-glycoprotein. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region in
addition to the Walker A motif/P-loop and Walker B motif
commonly found in a number of ATP- and GTP-binding and
hydrolyzing proteins.
Length = 220
Score = 28.1 bits (63), Expect = 3.7
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVW 161
R T+S LE A H P+V F +E + +D + R VW
Sbjct: 127 RLVKTYSGGMRRRLEIARSLVHRPEVLFLDEPTIGLD-PQTRAHVW 171
>gnl|CDD|215298 PLN02542, PLN02542, fructose-1,6-bisphosphatase.
Length = 412
Score = 28.3 bits (63), Expect = 3.9
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 80 STSPQVSPSSPPTLCFSPTPTPESPPTQQTGKRKQ 114
S+S V+P+S L + T S P K+
Sbjct: 12 SSSRSVAPASQCQLSSFDSLTLNSFPRSPGSKKHH 46
>gnl|CDD|139494 PRK13335, PRK13335, superantigen-like protein; Reviewed.
Length = 356
Score = 28.2 bits (62), Expect = 4.5
Identities = 22/102 (21%), Positives = 39/102 (38%), Gaps = 8/102 (7%)
Query: 37 PNQNGDPLLSGFTLPISQMPPVIVTTLQQSC-SANFQPVMKYNP-STSPQVSPSSPPT-- 92
PN N + + ISQ +L S A Q + ST+P+ ++PP+
Sbjct: 80 PNTNEEKTSASKIEKISQPKQEEQKSLNISATPAPKQEQSQTTTESTTPKTKVTTPPSTN 139
Query: 93 ----LCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELE 130
+ + + TP+SP +Q +Y + + E
Sbjct: 140 TPQPMQSTKSDTPQSPTIKQAQTDMTPKYEDLRAYYTKPSFE 181
>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106). This
family of proteins are found in large numbers in the
Trichomonas vaginalis proteome. The function of this
protein is unknown.
Length = 422
Score = 28.1 bits (62), Expect = 5.2
Identities = 15/71 (21%), Positives = 21/71 (29%), Gaps = 4/71 (5%)
Query: 51 PISQMPPVIVTTLQQSCSANFQPVMKYNPSTSPQVSPSSPPTLCFSPTPTPESPPTQQTG 110
P P + QQ N + P P P P + P T+Q
Sbjct: 201 PKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTP----QNPAQQPPQTEQGH 256
Query: 111 KRKQRRYRTTF 121
KR + + F
Sbjct: 257 KRSREQGNQEF 267
>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 559
Score = 28.0 bits (62), Expect = 5.3
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 171 KQEKLVSKQPQELFSSPLQSPASPSPDLNVISVPAASPVP 210
+QE +S P++LF+ L + P + V A +PVP
Sbjct: 154 RQEHALSAVPEQLFADFLTTAPVPRAPVQAPVVAAPAPVP 193
>gnl|CDD|116209 pfam07590, DUF1556, Protein of unknown function (DUF1556).
Length = 94
Score = 26.1 bits (57), Expect = 6.9
Identities = 14/39 (35%), Positives = 18/39 (46%)
Query: 80 STSPQVSPSSPPTLCFSPTPTPESPPTQQTGKRKQRRYR 118
S +P SSPP + S P P S + T R + R R
Sbjct: 37 SVNPLPPNSSPPNVVRSKRPRPASLASTPTLLRVRERRR 75
>gnl|CDD|218940 pfam06209, COBRA1, Cofactor of BRCA1 (COBRA1). This family
consists of several cofactor of BRCA1 (COBRA1) like
proteins. It is thought that COBRA1 along with BRCA1 is
involved in chromatin unfolding. COBRA1 is recruited to
the chromosome site by the first BRCT repeat of BRCA1,
and is itself sufficient to induce chromatin unfolding.
BRCA1 mutations that enhance chromatin unfolding also
increase its affinity for, and recruitment of, COBRA1.
It is thought that that reorganisation of higher levels
of chromatin structure is an important regulated step in
BRCA1-mediated nuclear functions.
Length = 475
Score = 27.5 bits (61), Expect = 8.3
Identities = 14/36 (38%), Positives = 16/36 (44%)
Query: 173 EKLVSKQPQELFSSPLQSPASPSPDLNVISVPAASP 208
LV K SSP P +PS D + SVP P
Sbjct: 439 ALLVDKIEASRKSSPAPEPETPSSDSPLHSVPTPPP 474
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 27.3 bits (60), Expect = 9.2
Identities = 24/94 (25%), Positives = 36/94 (38%), Gaps = 3/94 (3%)
Query: 17 RLPIVTVPNNAYSISGLLNTPNQNGDPLLSGFTLPISQMPPV--IVTTLQQSCSANFQPV 74
++ + N + GL P Q G P + P+ Q+ + Q S + P
Sbjct: 382 QMVALGYLNIQGNQGGLGANPMQQGQPGMMSSPSPVPQVQTNQSMPQPPQPSVPSPGGPG 441
Query: 75 MKYNPSTSPQVSPSSPPTLCFSPTPTPESPPTQQ 108
+ S S + PS PP L SP+P P Q
Sbjct: 442 SQPPQSVSGGMIPS-PPALMPSPSPQMSQSPASQ 474
>gnl|CDD|165564 PHA03309, PHA03309, transcriptional regulator ICP4; Provisional.
Length = 2033
Score = 27.5 bits (60), Expect = 9.3
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 66 SCSANFQPVMKYNPSTSPQVSPSSPPTLCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQ 125
S S++ +PS+ P S S+ P+L SP+P +P + R++ R R + + F+
Sbjct: 1818 SSSSSSSSSSSSSPSSRP--SRSATPSLSPSPSPPRRAPVDRSRSGRRRERDRPSANPFR 1875
Query: 126 LEELERAFHKTHYPD 140
+R+ H PD
Sbjct: 1876 WAPRQRS-RADHSPD 1889
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
0.315 0.130 0.391
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: 13,232,853
Number of extensions: 1233810
Number of successful extensions: 1441
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1375
Number of HSP's successfully gapped: 88
Length of query: 256
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 161
Effective length of database: 6,723,972
Effective search space: 1082559492
Effective search space used: 1082559492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 58 (26.1 bits)