RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8148
(390 letters)
>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 = 61.1 bits (149), Expect = 2e-12
Identities = 18/55 (32%), Positives = 32/55 (58%)
Query: 269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 323
F L++ ++KN YP+ +E+ +L++ GLT QV WF+NRR + + +
Sbjct: 5 TRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59
Score = 59.9 bits (146), Expect = 6e-12
Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 6/64 (9%)
Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
R++ TP+Q L++ ++KN YP+ +E+ +L++ GLT QV WF+NRR +
Sbjct: 2 RKRTRFTPEQLEE------LEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKL 55
Query: 375 RTPQ 378
+ +
Sbjct: 56 KRSE 59
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 58.4 bits (142), Expect = 2e-11
Identities = 17/50 (34%), Positives = 30/50 (60%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
F L++ + KN YP+ +E+ +L++ GL+ QV WF+NRR + +
Sbjct: 8 FTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
Score = 58.4 bits (142), Expect = 2e-11
Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 7/63 (11%)
Query: 314 NRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQ 372
RR+R TP+Q L++ + KN YP+ +E+ +L++ GL+ QV WF+NRR
Sbjct: 1 KRRKRTSFTPEQLEE------LEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRA 54
Query: 373 RDR 375
+ +
Sbjct: 55 KWK 57
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 55.6 bits (135), Expect = 2e-10
Identities = 24/62 (38%), Positives = 39/62 (62%), Gaps = 7/62 (11%)
Query: 315 RRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
RR+R TP+Q L++ ++KNRYP+ +E+ +L++ GLT QV WF+NRR +
Sbjct: 1 RRKRTTFTPEQL------EELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAK 54
Query: 374 DR 375
+
Sbjct: 55 WK 56
Score = 54.4 bits (132), Expect = 6e-10
Identities = 19/51 (37%), Positives = 32/51 (62%)
Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
F L++ ++KNRYP+ +E+ +L++ GLT QV WF+NRR + +
Sbjct: 6 TFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWK 56
>gnl|CDD|203350 pfam05920, Homeobox_KN, Homeobox KN domain. This is a homeobox
transcription factor KN domain conserved from fungi to
human and plants.
Length = 40
Score = 49.8 bits (120), Expect = 2e-08
Identities = 16/34 (47%), Positives = 23/34 (67%)
Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
N YP+ +EK +L+ TGL+ Q+ NWF N R+R
Sbjct: 7 HNPYPSEEEKSELARQTGLSRKQIDNWFINARRR 40
Score = 49.8 bits (120), Expect = 2e-08
Identities = 16/34 (47%), Positives = 23/34 (67%)
Query: 340 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
N YP+ +EK +L+ TGL+ Q+ NWF N R+R
Sbjct: 7 HNPYPSEEEKSELARQTGLSRKQIDNWFINARRR 40
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 46.3 bits (110), Expect = 3e-06
Identities = 18/95 (18%), Positives = 41/95 (43%), Gaps = 14/95 (14%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECY 338
L+ ++ N YP+ + +LS + + V WF+N+R +++ + +++
Sbjct: 66 LEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQR-------- 117
Query: 339 DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
+E+ L++I L+ Q+S R
Sbjct: 118 ------PGEEEADLAKIGSLSTGQISIIETLEFSR 146
Score = 40.5 bits (95), Expect = 3e-04
Identities = 14/71 (19%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
++R T +Q + L+ ++ N YP+ + +LS + + V WF+N+R ++
Sbjct: 53 SKRRRTTDEQLMV------LEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKE 106
Query: 375 RTPQQRAKNRT 385
+ + +
Sbjct: 107 KKKRSGKVEQR 117
>gnl|CDD|180933 PRK07329, PRK07329, hypothetical protein; Provisional.
Length = 246
Score = 31.9 bits (73), Expect = 0.45
Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 2/76 (2%)
Query: 100 RGRDLGYSSDDSSPVLYETNAHDFNKHYLEIQQKAQ-EYLN-MKKLNPNMSFTPEQIDCL 157
+G ++GY + +L DF+ L + +YL+ E + +
Sbjct: 71 KGIEIGYFAPREDDILDFLANKDFDLKLLSVHHNGVYDYLDDEVADMDKKELLQEYFEKM 130
Query: 158 CEAMQQSGDFDKLAMF 173
EA+ + D D LA F
Sbjct: 131 EEAIGRVHDADVLAHF 146
>gnl|CDD|172552 PRK14061, PRK14061, unknown domain/lipoate-protein ligase A fusion
protein; Provisional.
Length = 562
Score = 32.0 bits (72), Expect = 0.66
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 303 LTLTQVSNWFKNRRQRDRTPQQRSIQRS--RNALKECYDKNRYPNPDEKRQLSEITGLT 359
+ L Q ++WF QR R PQ + R+ R R +PDEKR + + LT
Sbjct: 24 VALMQGASWFSQNHQRQRNPQLEELARTLARQVTLNVAPLMRTDSPDEKRIQAILDQLT 82
>gnl|CDD|213249 cd03282, ABC_MSH4_euk, ATP-binding cassette domain of eukaryotic
MutS4 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family possess C-terminal domain with a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 204
Score = 30.8 bits (70), Expect = 0.92
Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 1/68 (1%)
Query: 187 ESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAV 246
E +++ + V + H F ++ AIL + + H + Q + G + + G
Sbjct: 135 ECLIKKESTVFFATH-FRDIAAILGNKSCVVHLHMKAQSINSNGIEMAYKLVLGLYRIVD 193
Query: 247 DKYRIRKK 254
D R +
Sbjct: 194 DGIRFVRV 201
Score = 28.1 bits (63), Expect = 5.6
Identities = 11/55 (20%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 48 ESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGR 102
E +++ + V + H F ++ AIL + + H + Q + G + + G
Sbjct: 135 ECLIKKESTVFFATH-FRDIAAILGNKSCVVHLHMKAQSINSNGIEMAYKLVLGL 188
>gnl|CDD|236309 PRK08599, PRK08599, coproporphyrinogen III oxidase; Provisional.
Length = 377
Score = 30.6 bits (70), Expect = 1.3
Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 21/72 (29%)
Query: 122 DFNKHYLEIQQKAQEYLNM---------KKLNPNM-----------SFTPEQIDCLCEAM 161
DFNK +++ Q EYL+ + + + + EQ++ L A+
Sbjct: 19 DFNKVFIK-NQPVDEYLDALIKEMNTYAIRPFDKLKTIYIGGGTPTALSAEQLERLLTAI 77
Query: 162 QQSGDFDKLAMF 173
++ L F
Sbjct: 78 HRNLPLSGLEEF 89
>gnl|CDD|217827 pfam03979, Sigma70_r1_1, Sigma-70 factor, region 1.1. Region 1.1
modulates DNA binding by region 2 and 4 when sigma is
unbound by the core RNA polymerase. Region 1.1 is also
involved in promoter binding.
Length = 79
Score = 28.0 bits (63), Expect = 2.2
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 131 QQKAQEYLNMKKLN---PNMSFTPEQIDCLCE 159
Q K + YL ++N P EQID +
Sbjct: 15 QGKKRGYLTYDEINEALPPDDVDSEQIDDIIS 46
>gnl|CDD|222122 pfam13429, TPR_15, Tetratricopeptide repeat.
Length = 279
Score = 29.2 bits (66), Expect = 3.5
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 20 EAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKR 61
++GD+ ++ L SL P+EA L ARA +
Sbjct: 117 YLYTRAGDYKRIVDLLASLTPEEAAEQSAGFLSARAEYYRQT 158
Score = 29.2 bits (66), Expect = 3.5
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 159 EAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKR 200
++GD+ ++ L SL P+EA L ARA +
Sbjct: 117 YLYTRAGDYKRIVDLLASLTPEEAAEQSAGFLSARAEYYRQT 158
>gnl|CDD|130767 TIGR01706, NAPA, periplasmic nitrate reductase, large subunit.
This model represents the large subunit of a family of
nitrate reductases found in proteobacteria which are
localized to the periplasm. This subunit binds
molybdopterin and contains a twin-arginine motif at the
N-terminus. The protein associates with NapB, a soluble
heme-containing protein and NapC, a membrane-bound
cytochrome c. The periplasmic nitrate reductases are not
involved in the assimilation of nitrogen, and are not
directly involved in the formation of electrochemical
gradients (i.e. respiration) either. Rather, the purpose
of this enzyme is either dissimilatory (i.e. to dispose
of excess reductive equivalents) or indirectly
respiratory by virtue of the consumption of electrons
derived from NADH via the proton translocating NADH
dehydrogenase. The enzymes from Alicagenes eutrophus and
Paracoccus pantotrophus have been characterized. In E.
coli (as well as other organisms) this gene is part of a
large nitrate reduction operon (napFDAGHBC) [Energy
metabolism, Aerobic, Energy metabolism, Electron
transport, Central intermediary metabolism, Nitrogen
metabolism].
Length = 830
Score = 29.1 bits (65), Expect = 4.5
Identities = 23/87 (26%), Positives = 36/87 (41%), Gaps = 2/87 (2%)
Query: 208 AILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEET 267
A +S N +S Q + Y + + G DL D Y + P + +G+ET
Sbjct: 611 ANAKSLNAESTAFGFYVQKGLFEEYAKFGRGHGHDLAPFDTYHKVRGLRWP--VVNGKET 668
Query: 268 VYCFKERSRNALKECYDKNRYPNPDEK 294
+ ++E S +K Y NPD K
Sbjct: 669 QWRYREGSDPYVKAGAGFQFYGNPDGK 695
>gnl|CDD|217838 pfam04004, Leo1, Leo1-like protein. Members of this family are
part of the Paf1/RNA polymerase II complex. The Paf1
complex probably functions during the elongation phase
of transcription. The Leo1 subunit of the yeast
Paf1-complex binds RNA and contributes to complex
recruitment. The subunit acts by co-ordinating
co-transcriptional chromain modifications and helping
recruitment of mRNA 3prime-end processing factors.
Length = 312
Score = 28.3 bits (63), Expect = 6.9
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLS 353
+R+R++ +Q+ R R +E KN+ PN S
Sbjct: 239 KREREKKEEQKLRARRRRQNRE-KMKNKPPNRPGHGSGS 276
>gnl|CDD|227584 COG5259, RSC8, RSC chromatin remodeling complex subunit RSC8
[Chromatin structure and dynamics / Transcription].
Length = 531
Score = 28.3 bits (63), Expect = 8.9
Identities = 15/79 (18%), Positives = 29/79 (36%)
Query: 288 YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPD 347
P + + ++ E+ + S+ + T N+ ECYD+ R+P+
Sbjct: 204 SPKKESQGKVDELKDHSEKHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYDQGRFPSEF 263
Query: 348 EKRQLSEITGLTLTQVSNW 366
+T L + NW
Sbjct: 264 TSSDFKPVTISLLIRDKNW 282
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
0.319 0.133 0.406
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: 20,368,626
Number of extensions: 1957342
Number of successful extensions: 1788
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1787
Number of HSP's successfully gapped: 33
Length of query: 390
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 291
Effective length of database: 6,546,556
Effective search space: 1905047796
Effective search space used: 1905047796
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.8 bits)