RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6673
(286 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 45.8 bits (109), Expect = 2e-07
Identities = 15/26 (57%), Positives = 17/26 (65%)
Query: 253 NLLIHERTHTDERPYSCDVCNKAFRR 278
NL H RTHT E+PY C VC K+F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 34.2 bits (79), Expect = 0.003
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 240 ICRFCSRHFTKSYNLLIHERTH 261
C C + F++ NL H RTH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 31.9 bits (73), Expect = 0.016
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 268 SCDVCNKAFRRQDHLRDHR 286
C C K+F R+ +L+ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHL 19
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 34.0 bits (78), Expect = 0.003
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 239 FICRFCSRHFTKSYNLLIHERTH 261
+ C C + F L H RTH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 32.8 bits (75), Expect = 0.009
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 267 YSCDVCNKAFRRQDHLRDH 285
Y C C K F+ + LR+H
Sbjct: 1 YRCPECGKVFKSKSALREH 19
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 33.4 bits (76), Expect = 0.006
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 239 FICRFCSRHFTKSYNLLIHERTH 261
F C C + F+ L H R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 32.2 bits (73), Expect = 0.017
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 267 YSCDVCNKAFRRQDHLRDHR 286
+ C +C K+F +D L+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHL 20
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 35.6 bits (82), Expect = 0.006
Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 238 QFICRFCSRHFTKSYNLLIHER--THTDERPYSCDVCNKAFRRQDHLRDH 285
++C C F+ S +L H R H+ C VC K FR D DH
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSK----VCPVCGKEFRNTDSTLDH 118
>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 = 30.6 bits (70), Expect = 0.063
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 267 YSCDVCNKAFRRQDHLRDH 285
+ C++CN F + L+ H
Sbjct: 1 FYCELCNVTFTSESQLKSH 19
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 30.3 bits (69), Expect = 0.075
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 267 YSCDVCNKAFRRQDHLRDHR 286
++C VC K F L H+
Sbjct: 2 HTCGVCGKTFSSLQALGGHK 21
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus, particularly
the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 28.3 bits (64), Expect = 0.38
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 238 QFICRFCSRHFTKSYNLLIHERT 260
QF C C ++F L H ++
Sbjct: 1 QFYCVACDKYFKSENALENHLKS 23
>gnl|CDD|215570 PLN03091, PLN03091, hypothetical protein; Provisional.
Length = 459
Score = 31.1 bits (70), Expect = 0.77
Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 2/78 (2%)
Query: 45 QRSLQNVALTLQTAMVSSLQQAALLPPNSPAAAALNLQALESYLTLH--RLSSTVNSPQR 102
+ A + LL ++ A + S ++ +L +S +
Sbjct: 136 EDKNPPTDDKSDKASSVVSNELNLLKADNSKPLAALQEKRSSSISPAGYQLEVESSSSSK 195
Query: 103 VSNSNNNNNNNNNTTTKT 120
++NSNNNN++N+N T T
Sbjct: 196 INNSNNNNHSNSNLMTPT 213
>gnl|CDD|206084 pfam13913, zf-C2HC_2, zinc-finger of a C2HC-type. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 25
Score = 27.2 bits (61), Expect = 0.97
Identities = 7/20 (35%), Positives = 8/20 (40%), Gaps = 1/20 (5%)
Query: 241 CRFCSRHFTKSYNLLIHERT 260
C C R F L HE+
Sbjct: 5 CPICGRKFAPDR-LAKHEKV 23
>gnl|CDD|214993 smart01047, C1_4, TFIIH C1-like domain. The carboxyl-terminal
region of TFIIH is essential for transcription activity.
This regions binds three zinc atoms through two
independent domain. The first contains a C4 zinc finger
motif, whereas the second is characterised by a
CX(2)CX(2-4)FCADCD motif. The solution structure of the
second C-terminal domain revealed homology with the
regulatory domain of protein kinase C.
Length = 49
Score = 27.3 bits (61), Expect = 1.4
Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 6/39 (15%)
Query: 235 PKKQFICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCN 273
++ C C + F ++ IHE H +C C
Sbjct: 17 TSSRYRCTKCKQVFCIDCDVFIHETLH------NCPGCE 49
>gnl|CDD|183017 PRK11177, PRK11177, phosphoenolpyruvate-protein phosphotransferase;
Provisional.
Length = 575
Score = 30.0 bits (68), Expect = 1.8
Identities = 26/59 (44%), Positives = 31/59 (52%), Gaps = 8/59 (13%)
Query: 145 KTALALADIDALGNIEDEV---PDDLLETSSPETADLNLKTSLEFPA-FPGETSYPSLL 199
K L L ID L I++EV DL T S ETA LNLK L F G TS+ S++
Sbjct: 139 KNILGLKIID-LSAIQEEVILVAADL--TPS-ETAQLNLKKVLGFITDIGGRTSHTSIM 193
>gnl|CDD|222704 pfam14353, CpXC, CpXC protein. This presumed domain is
functionally uncharacterized. This domain is found in
bacteria and archaea, and is typically between 122 and
134 amino acids in length. It contains four conserved
cysteines forming two CpXC motifs.
Length = 128
Score = 28.5 bits (64), Expect = 2.2
Identities = 8/46 (17%), Positives = 13/46 (28%), Gaps = 9/46 (19%)
Query: 241 CRFCSRHFTKSYNLLIHERTHTDERP---------YSCDVCNKAFR 277
C C F ++ + R ++C C FR
Sbjct: 4 CPSCGHEFEAEVWTSVNADEDPELREAILDGTLFTFTCPSCGHEFR 49
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 29.6 bits (66), Expect = 2.3
Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 5/50 (10%)
Query: 240 ICRFCSRHFTKSYNLLIHERTHTDERPYSCDVCNKA----FRRQDHLRDH 285
+C FC +F L H R E + CD+ F+ + L H
Sbjct: 222 LCIFCKIYFYDDDELRRHCRLR-HEACHICDMVGPIRYQYFKSYEDLEAH 270
>gnl|CDD|149709 pfam08734, GYD, GYD domain. This protein is found in a range of
bacteria. It is usually less than 100 amino acids in
length. The function of the protein is unknown. It may
belong to the dimeric alpha/beta barrel superfamily.
Length = 91
Score = 27.2 bits (61), Expect = 3.2
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 136 EVPDDLSTTKTALALADIDALGNIEDE 162
E PDD S LA+A A GN+ E
Sbjct: 53 EAPDDASAAALGLAIA---AAGNVRTE 76
>gnl|CDD|184656 PRK14389, PRK14389, hypothetical protein; Provisional.
Length = 98
Score = 27.2 bits (60), Expect = 3.8
Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 7/28 (25%)
Query: 74 PAAAALNLQALE-------SYLTLHRLS 94
P +A +LQALE SYLTL RL+
Sbjct: 29 PTCSAYSLQALEQHGAAAGSYLTLRRLA 56
>gnl|CDD|225248 COG2373, COG2373, Large extracellular alpha-helical protein [General
function prediction only].
Length = 1621
Score = 28.5 bits (64), Expect = 4.7
Identities = 18/88 (20%), Positives = 29/88 (32%), Gaps = 1/88 (1%)
Query: 21 DVLALPDAGNIVKSLQTTLQEELLQRSLQNVALTLQTAMVSSLQQAALLPPNSPAAAALN 80
+LAL ++ ++Q TL L L+ Q L AL A +N
Sbjct: 1369 LMLALAAELKLLPAIQPTLLRALALEWFDKRYLSTQEQAALLLAARALQAGKWVAQKQVN 1428
Query: 81 LQAL-ESYLTLHRLSSTVNSPQRVSNSN 107
+ L +S +P N+
Sbjct: 1429 GEELTGWKGLRRNGNSLQLAPLVFVNTG 1456
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 28.1 bits (62), Expect = 5.1
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 263 DERPYSCDV--CNKAFRRQDHLRDHR 286
D +PY C V CNK ++ Q+ L+ H
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHM 371
>gnl|CDD|225148 COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain)
[Inorganic ion transport and metabolism].
Length = 451
Score = 28.4 bits (64), Expect = 5.5
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 11/72 (15%)
Query: 126 DIDALGNIEDEVPDDL------STTKTALALADIDALGNIEDEVPDD----LLETSSPET 175
+ LG ++DEV +++ A+ DID ++ DE+PD+ LL PE
Sbjct: 60 AAEVLGELDDEVREEIIEALSDEELAAAIEELDIDDAADLLDELPDEVRDELLSLLDPEE 119
Query: 176 ADLNLKTSLEFP 187
++ L +P
Sbjct: 120 RAR-VRQLLSYP 130
>gnl|CDD|240427 PTZ00470, PTZ00470, glycoside hydrolase family 47 protein;
Provisional.
Length = 522
Score = 28.2 bits (63), Expect = 6.0
Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 4/67 (5%)
Query: 82 QALESYLTLHRLS-STVNSPQRVSNSNNNNNNNNNTTTKTALALADIDALG---NIEDEV 137
L +L++H + N+ +N N+NN NNN + + N DEV
Sbjct: 2 VNLREHLSVHNNADDNYNNNNNNNNQINSNNPNNNGNNQASKLPRGKKKQENPFNKIDEV 61
Query: 138 PDDLSTT 144
Sbjct: 62 YYQNEKL 68
>gnl|CDD|214933 smart00953, RES, RES domain. This presumed protein contains 3
highly conserved polar groups that could form an active
site. These are an arginine, glutamate and serine, hence
the RES domain. RES is found widely distributed in
bacteria, it has about 150 residues in length.
Length = 121
Score = 26.6 bits (59), Expect = 7.5
Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 6/67 (8%)
Query: 116 TTTKTALA--LADIDALGNIEDEVPDDLS----TTKTALALADIDALGNIEDEVPDDLLE 169
+ +TALA L + +P D + LAL + ++PDD L+
Sbjct: 22 ESPETALAEVLYHRERFLAASPGLPRDYTLFRVLVADDLALVALLLDIPPAADLPDDWLD 81
Query: 170 TSSPETA 176
A
Sbjct: 82 PEDDYPA 88
>gnl|CDD|236923 PRK11530, PRK11530, hypothetical protein; Provisional.
Length = 183
Score = 27.3 bits (61), Expect = 7.7
Identities = 15/61 (24%), Positives = 27/61 (44%)
Query: 38 TLQEELLQRSLQNVALTLQTAMVSSLQQAALLPPNSPAAAALNLQALESYLTLHRLSSTV 97
TL +E+ Q + Q VA+ Q + ++ L P + A L Q ++L ++
Sbjct: 35 TLNQEMTQLTQQAVAIEQQNRLNANSTSGVYLLPAAKTPARLESQIGTLRMSLSNITPEA 94
Query: 98 N 98
N
Sbjct: 95 N 95
>gnl|CDD|227443 COG5112, UFD2, U1-like Zn-finger-containing protein [General
function prediction only].
Length = 126
Score = 26.6 bits (58), Expect = 8.5
Identities = 14/52 (26%), Positives = 21/52 (40%)
Query: 214 IVTDSISKPVQKSTPVASTARPKKQFICRFCSRHFTKSYNLLIHERTHTDER 265
I D +K QK P Q C C+R+F L+ H++ +R
Sbjct: 31 IKNDLSTKESQKKLPYDPELPGLGQHYCIECARYFITEKALMEHKKGKVHKR 82
>gnl|CDD|233339 TIGR01278, DPOR_BchB, light-independent protochlorophyllide
reductase, B subunit. Alternate name: dark
protochlorophyllide reductase This enzyme describes the
B subunit of the dark form protochlorophyllide
reductase, a nitrogenase-like enzyme. This subunit shows
homology to the nitrogenase molybdenum-iron protein. It
catalyzes a step in bacteriochlorophyll biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Chlorophyll and bacteriochlorphyll].
Length = 511
Score = 27.5 bits (61), Expect = 9.5
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 6/48 (12%)
Query: 42 ELLQRSLQNVALTLQTAMVSSLQQAALLPPNSPAAAALNLQALESYLT 89
LLQ L N+A L ++ ++ + A QA + LT
Sbjct: 98 SLLQEDLGNLAAAAG------LDKSKVIVADVNAYRRKENQAADRTLT 139
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 27.3 bits (61), Expect = 9.9
Identities = 15/47 (31%), Positives = 23/47 (48%)
Query: 123 ALADIDALGNIEDEVPDDLSTTKTALALADIDALGNIEDEVPDDLLE 169
AL ++ A ++E DL + ALAD DAL V +++L
Sbjct: 16 ALEELLAAYDVEVPDGPDLDEEELLEALADADALIVSVTPVTEEVLA 62
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
0.309 0.124 0.337
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,755,936
Number of extensions: 1260653
Number of successful extensions: 1179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1137
Number of HSP's successfully gapped: 49
Length of query: 286
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 190
Effective length of database: 6,679,618
Effective search space: 1269127420
Effective search space used: 1269127420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 58 (26.2 bits)