RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15374
(205 letters)
>gnl|CDD|129685 TIGR00597, rad10, DNA repair protein rad10. All proteins in this
family for which functions are known are components in a
multiprotein endonuclease complex (usually made up of
Rad1 and Rad10 homologs). This complex is used primarily
for nucleotide excision repair but also for some aspects
of recombination repair. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 112
Score = 146 bits (369), Expect = 2e-45
Identities = 69/113 (61%), Positives = 86/113 (76%), Gaps = 6/113 (5%)
Query: 69 NAILVNPRQKGNPLLKHIGKVPWEYDDSIIPDYVMGRTTCALFLSIKYHALKPDYIADRI 128
N+ILVNPRQKGNPLLKH+ VPWEY D +IPDYV+G+ TCALFLS++YH L PDYI R+
Sbjct: 1 NSILVNPRQKGNPLLKHVRNVPWEYGD-VIPDYVLGQGTCALFLSLRYHNLHPDYIHRRL 59
Query: 129 KALGKLYKL-----QVDSKDPHHALKYLTRVCLLCDLTLMLAWSPEEAGEMIE 176
++LGK + L QVD K+P ALK L ++C+L D TL+LAWS EEA +E
Sbjct: 60 QSLGKNFNLRILLVQVDVKNPQQALKELAKMCILNDCTLILAWSFEEAARYLE 112
Score = 26.0 bits (57), Expect = 7.3
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 1 MLAWSPEEAGEMIE 14
+LAWS EEA +E
Sbjct: 99 ILAWSFEEAARYLE 112
>gnl|CDD|190768 pfam03834, Rad10, Binding domain of DNA repair protein Ercc1
(rad10/Swi10). Ercc1 and XPF (xeroderma pigmentosum
group F-complementing protein) are two
structure-specific endonucleases of a class of seven
containing an ERCC4 domain. Together they form an
obligate complex that functions primarily in nucleotide
excision repair (NER), a versatile pathway able to
detect and remove a variety of DNA lesions induced by UV
light and environmental carcinogens, and secondarily in
DNA interstrand cross-link repair and telomere
maintenance. This domain in fact binds simultaneously to
both XPF and single-stranded DNA; this ternary complex
explains the important role of Ercc1 in targeting its
catalytic XPF partner to the NER pre-incision complex.
Length = 68
Score = 116 bits (294), Expect = 2e-34
Identities = 45/69 (65%), Positives = 55/69 (79%), Gaps = 1/69 (1%)
Query: 69 NAILVNPRQKGNPLLKHIGKVPWEYDDSIIPDYVMGRTTCALFLSIKYHALKPDYIADRI 128
++ILV+PRQKGNPLLKH+ VPWEY D I+PDYV+G+T C LFLS+KYH L P+YI R+
Sbjct: 1 SSILVSPRQKGNPLLKHLKNVPWEYSD-IVPDYVVGKTRCVLFLSLKYHRLHPEYIYTRL 59
Query: 129 KALGKLYKL 137
K L K Y L
Sbjct: 60 KKLQKNYNL 68
>gnl|CDD|227566 COG5241, RAD10, Nucleotide excision repair endonuclease NEF1, RAD10
subunit [DNA replication, recombination, and repair].
Length = 224
Score = 115 bits (288), Expect = 6e-32
Identities = 48/164 (29%), Positives = 72/164 (43%), Gaps = 11/164 (6%)
Query: 41 NFDPVPAAQNSATSESVQPSRAGASKS---SNAILVNPRQKGNPLLKHIGKVPWEYDDSI 97
N DP A ++ ++GA + S I V+P QKGNP L W Y+ I
Sbjct: 3 NTDPTSFESILAGVAKLRKEKSGADTTGSQSLEIDVSPLQKGNPQLSRRINSNWVYNAFI 62
Query: 98 IPDYVMGRTTCALFLSIKYHALKPDYIADRIKALGKLYKLQ-----VDSKDPHHALKYLT 152
PD LFLS+++H+ +P+YI RI L K YK + VDS + +++ L
Sbjct: 63 KPDEWTDSKATDLFLSLRFHSTRPEYIVLRISKL-KSYKERPLLNHVDSTNWRASIQELV 121
Query: 153 RVCLLCDLTLMLAWSPEEAGEMIETYKVFENKPPDLIMEKQDVD 196
+ T+ L +S EE T + +I Q +D
Sbjct: 122 STTGIN--TIYLDYSVEERSRYFLTLTYHKLYSDYIIRRMQSLD 163
Score = 36.9 bits (85), Expect = 0.003
Identities = 8/33 (24%), Positives = 12/33 (36%)
Query: 2 LAWSPEEAGEMIETYKVFENKPPDLIMEKQDVD 34
L +S EE T + +I Q +D
Sbjct: 131 LDYSVEERSRYFLTLTYHKLYSDYIIRRMQSLD 163
>gnl|CDD|233916 TIGR02541, flagell_FlgJ, flagellar rod assembly protein/muramidase
FlgJ. The N-terminal region of this protein acts
directly in flagellar rod assembly. The C-terminal
region is a flagellum-specific muramidase (peptidoglycan
hydrolase) required for formation of the outer membrane
L ring.
Length = 294
Score = 30.2 bits (68), Expect = 0.75
Identities = 15/55 (27%), Positives = 22/55 (40%)
Query: 35 PHSKTWNFDPVPAAQNSATSESVQPSRAGASKSSNAILVNPRQKGNPLLKHIGKV 89
P DP P A ESV+ SR + ++ +P+ N +L H K
Sbjct: 108 PLVYRPRLDPKPRRIVKALIESVELSRPRGRSHAESVPGHPKSFVNSMLPHARKA 162
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 28.1 bits (63), Expect = 4.0
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 156 LLCDLTLMLAWS---PEEAGEMIETYKVFENKPPDLIMEKQDVDPH 198
LL +L ++ PEE ++ VFE K D E ++ P
Sbjct: 884 LLTELIFSGEFNDLEPEELAALLSA-FVFEEKTDDGTAEAPEITPA 928
>gnl|CDD|218891 pfam06090, Ins_P5_2-kin, Inositol-pentakisphosphate 2-kinase. This
is a family of inositol-pentakisphosphate 2-kinases (EC
2.7.1.158) (also known as inositol
1,3,4,5,6-pentakisphosphate 2-kinase, Ins(1,3,4,5,6)P5
2-kinase) and InsP5 2-kinase). This enzyme
phosphorylates Ins(1,3,4,5,6)P5 to form
Ins(1,2,3,4,5,6)P6 (also known as InsP6 or phytate).
InsP6 is involved in many processes such as mRNA export,
nonhomologous end-joining, endocytosis and ion channel
regulation.
Length = 301
Score = 27.7 bits (62), Expect = 4.7
Identities = 16/64 (25%), Positives = 23/64 (35%), Gaps = 9/64 (14%)
Query: 122 DYIADRIKALGKLYKLQV------DSKDPHHALKYLTRVCL---LCDLTLMLAWSPEEAG 172
+Y+ L KL LQ D L L L D +L + +S +E G
Sbjct: 214 EYLLKDNSVLQKLLDLQKLLLSAEDGVGLESLLDVSRDFLLAMTLRDCSLFIRFSRDEQG 273
Query: 173 EMIE 176
+E
Sbjct: 274 FSVE 277
>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P. syringae 6; Provisional.
Length = 1153
Score = 27.5 bits (61), Expect = 5.5
Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 13/74 (17%)
Query: 122 DYIADRIKALGKLYKLQVDSKDPH----HALKYLTRVCLLCDLTLMLAWSPEEAGEMIET 177
D +A + + G ++ V +KD H H + ++ VCL S E A EM
Sbjct: 312 DALAGQTQWFGSGSRIIVITKDKHFLRAHGIDHIYEVCLP---------SNELALEMFCR 362
Query: 178 YKVFENKPPDLIME 191
+N PPD ME
Sbjct: 363 SAFKKNSPPDGFME 376
>gnl|CDD|238247 cd00433, Peptidase_M17, Cytosol aminopeptidase family, N-terminal
and catalytic domains. Family M17 contains zinc- and
manganese-dependent exopeptidases ( EC 3.4.11.1),
including leucine aminopeptidase. They catalyze removal
of amino acids from the N-terminus of a protein and play
a key role in protein degradation and in the metabolism
of biologically active peptides. They do not contain
HEXXH motif (which is used as one of the signature
patterns to group the peptidase families) in the
metal-binding site. The two associated zinc ions and the
active site are entirely enclosed within the C-terminal
catalytic domain in leucine aminopeptidase. The enzyme
is a hexamer, with the catalytic domains clustered
around the three-fold axis, and the two trimers related
to one another by a two-fold rotation. The N-terminal
domain is structurally similar to the ADP-ribose binding
Macro domain. This family includes proteins from
bacteria, archaea, animals and plants.
Length = 468
Score = 27.5 bits (62), Expect = 5.7
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 121 PDYIADRIKALGKLYKLQVDSKD 143
P Y+A+ K L K ++V+ D
Sbjct: 173 PTYLAEEAKELAKELGVKVEVLD 195
>gnl|CDD|240272 PTZ00109, PTZ00109, DNA gyrase subunit b; Provisional.
Length = 903
Score = 27.5 bits (61), Expect = 6.1
Identities = 17/67 (25%), Positives = 31/67 (46%)
Query: 17 KVFENKPPDLIMEKQDVDPHSKTWNFDPVPAAQNSATSESVQPSRAGASKSSNAILVNPR 76
KVFEN L++ + + TW + ++ ESVQ + + +K N++ P
Sbjct: 619 KVFENSEIKLLITSIGLSVNPVTWRQYDLSHGTKASKDESVQNNNSTLTKKKNSLFDTPL 678
Query: 77 QKGNPLL 83
+ G +L
Sbjct: 679 RYGKIIL 685
>gnl|CDD|237002 PRK11857, PRK11857, dihydrolipoamide acetyltransferase; Reviewed.
Length = 306
Score = 27.1 bits (60), Expect = 6.7
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 24 PDLIMEKQDVDPHSKTWNFDPVPAAQNSATSESVQPSRAGASKSSNAILVNPRQKGNPLL 83
D + +DV+ K+ P PA S +S + Q ++ A ++ L R+K P+
Sbjct: 27 RDGKILAEDVENFIKSLKSAPTPAEAASVSS-AQQAAKTAAPAAAPPKLEGKREKVAPIR 85
Query: 84 KHIGK 88
K I +
Sbjct: 86 KAIAR 90
>gnl|CDD|232869 TIGR00197, yjeF_nterm, yjeF N-terminal region. The protein region
corresponding to This model shows no clear homology to
any protein of known function. This model is built on
yeast protein YNL200C and the N-terminal regions of E.
coli yjeF and its orthologs in various species. The
C-terminal region of yjeF and its orthologs shows
similarity to hydroxyethylthiazole kinase (thiM) and
other enzymes involved in thiamine biosynthesis. Yeast
YKL151C and B. subtilis yxkO match the yjeF C-terminal
domain but lack this region [Unknown function, General].
Length = 205
Score = 26.6 bits (59), Expect = 8.9
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 112 LSIKYHALKPDYIADRIKALGKLY 135
L+I +HA KP + DR + G+LY
Sbjct: 174 LTITFHAPKPGLLHDRAEVTGELY 197
>gnl|CDD|234863 PRK00913, PRK00913, multifunctional aminopeptidase A; Provisional.
Length = 483
Score = 26.7 bits (60), Expect = 8.9
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 121 PDYIADRIKALGKLYKLQVD 140
P Y+A+R K L K Y L+V+
Sbjct: 190 PAYLAERAKELAKEYGLEVE 209
>gnl|CDD|150796 pfam10170, C6_DPF, Cysteine-rich domain. This is the N-terminal
approximately 100 amino acids of a family of proteins
found from nematodes to humans. It contains between six
and eight highly conserved cysteine residues and a
characteristic DPF sequence motif. One member is
putatively named as receptor for egg jelly protein but
this could not confirmed.
Length = 97
Score = 25.5 bits (56), Expect = 9.5
Identities = 10/33 (30%), Positives = 15/33 (45%)
Query: 142 KDPHHALKYLTRVCLLCDLTLMLAWSPEEAGEM 174
P +L Y R CL C + A+ PE ++
Sbjct: 61 VGPECSLFYTKRFCLPCVKENLKAFPPEIQQDL 93
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
0.316 0.133 0.410
Gapped
Lambda K H
0.267 0.0650 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,584,868
Number of extensions: 949242
Number of successful extensions: 802
Number of sequences better than 10.0: 1
Number of HSP's gapped: 798
Number of HSP's successfully gapped: 22
Length of query: 205
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 113
Effective length of database: 6,857,034
Effective search space: 774844842
Effective search space used: 774844842
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: 41 (21.6 bits)
S2: 57 (25.9 bits)