RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6751
(392 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 38.9 bits (91), Expect = 9e-05
Identities = 14/25 (56%), Positives = 20/25 (80%)
Query: 315 HLNRHMLVHTGDRPHECSVCGKRFA 339
+L RHM HTG++P++C VCGK F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 30.4 bits (69), Expect = 0.097
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 231 ALLVHVGMHSGIHPFTCHFCNKSFTQ 256
L H+ H+G P+ C C KSF+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 30.4 bits (69), Expect = 0.099
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 260 LVKHLNIHNGTKKYQCHLCGKGF 282
L +H+ H G K Y+C +CGK F
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSF 24
Score = 28.1 bits (63), Expect = 0.64
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 203 ELNAHIQTHSDLRPFVCEICGQGYK 227
L H++TH+ +P+ C +CG+ +
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 25.8 bits (57), Expect = 4.4
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 287 SYKFHQLVHSGERNVKCDICG 307
+ + H H+GE+ KC +CG
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCG 21
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 38.9 bits (90), Expect = 0.004
Identities = 31/199 (15%), Positives = 58/199 (29%), Gaps = 16/199 (8%)
Query: 151 KCFICDAQLTTETSYSVFYTMLSQSGVLLSERACMPLIHECPTCGKKWRTVSELNAHIQT 210
+ + S S + S + + L + +
Sbjct: 259 ESPRSSLPTASSQSSSPNESDSSSEKGFSL-PIKSKQCNISFSRSSPLTR--HLRSVNHS 315
Query: 211 HSDLRPFVC--EICGQGYKMKKALLVHVGMHSGIHPFTCHF--CNKSFTQKIG------L 260
L+PF C +CG+ + AL H+ +H+ I P + F+ + L
Sbjct: 316 GESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSL 375
Query: 261 VKHLNIHNGTKKYQCHLCGKGFI---HHTSYKFHQLVHSGERNVKCDICGLALTTKSHLN 317
++ ++ N K + S + N K C + +L
Sbjct: 376 QQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLI 435
Query: 318 RHMLVHTGDRPHECSVCGK 336
H +HT P CS+
Sbjct: 436 PHKKIHTNHAPLLCSILKS 454
Score = 32.4 bits (73), Expect = 0.47
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 244 PFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQC 275
P +C C SF++ L +H+ H G K QC
Sbjct: 33 PDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQC 64
Score = 29.7 bits (66), Expect = 2.7
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 299 RNVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCGKRFAKK 341
R C C + + HL RH+ HTG++P +CS G +
Sbjct: 32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFS 74
Score = 28.1 bits (62), Expect = 8.2
Identities = 53/333 (15%), Positives = 94/333 (28%), Gaps = 42/333 (12%)
Query: 5 CDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFNSRNG--LYVHLKKVHN------ 56
C CT F R + H + H G+ P+QC++ + L HL+ HN
Sbjct: 36 CPNCTDSFSRLEHLTRH-IRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNPSDLN 94
Query: 57 -----------VEYSERIELV-SNIPLDEDITDAALLVDKALTIKPKESEQSSQSEDEGM 104
S SN + G
Sbjct: 95 SKSLPLSNSKASSSSLSSSSSNSNDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGN 154
Query: 105 DEGGRDSSGSEWTEETDVFKADKANLDLQGLEMSPEDRAESEVLGWKCFICDAQLTTETS 164
+ ++ S +L + + ++ L++ S
Sbjct: 155 NSSSVNTPQSNSLH----PPLPANSLSKDPSSNLSLLISSNVSTSIPSSSENSPLSSSYS 210
Query: 165 YSVFYTML----SQSGVLLSERACMPLIHECPTCGKKWRTVSELNAHIQTHSDLRPFVCE 220
+ S S + L+ + + ++ S L++ + S
Sbjct: 211 IPSSSSDQNLENSSSSLPLTTNSQLSPKSLLS------QSPSSLSSSDSSSSASESPRSS 264
Query: 221 ICGQGYKMKKALLVHVGMHSGI-HPFTCHFCNKSFTQKIGLVKHLN--IHNG--TKKYQC 275
+ + G P CN SF++ L +HL H+G K + C
Sbjct: 265 LPTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSC 324
Query: 276 --HLCGKGFIHHTSYKFHQLVHSGERNVKCDIC 306
LCGK F + + K H L+H+ K +
Sbjct: 325 PYSLCGKLFSRNDALKRHILLHTSISPAKEKLL 357
>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 = 29.6 bits (67), Expect = 0.14
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 302 KCDICGLALTTKSHLNRHMLVH 323
KC CG + + KS+L RH+ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 28.9 bits (65), Expect = 0.31
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 246 TCHFCNKSFTQKIGLVKHLNIH 267
C C KSF++K L +HL H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 26.9 bits (60), Expect = 1.3
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 274 QCHLCGKGFIHHTSYKFHQLVH 295
+C CGK F ++ K H H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 29.7 bits (67), Expect = 0.17
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 245 FTCHFCNKSFTQKIGLVKHLNIH 267
+ C C K F K L +H+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 28.6 bits (64), Expect = 0.33
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 302 KCDICGLALTTKSHLNRHMLVH 323
+C CG +KS L HM H
Sbjct: 2 RCPECGKVFKSKSALREHMRTH 23
Score = 27.0 bits (60), Expect = 1.4
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 273 YQCHLCGKGFIHHTSYKFHQLVH 295
Y+C CGK F ++ + H H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 25.9 bits (57), Expect = 4.0
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 189 HECPTCGKKWRTVSELNAHIQTH 211
+ CP CGK +++ S L H++TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 25.5 bits (56), Expect = 4.7
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 33 QCTFCEKKFNSRNGLYVHLKK 53
+C C K F S++ L H++
Sbjct: 2 RCPECGKVFKSKSALREHMRT 22
Score = 25.1 bits (55), Expect = 6.0
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 217 FVCEICGQGYKMKKALLVHVGMH 239
+ C CG+ +K K AL H+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 33.1 bits (76), Expect = 0.26
Identities = 9/38 (23%), Positives = 14/38 (36%), Gaps = 10/38 (26%)
Query: 243 HPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGK 280
+ C C+ T +H T + +CH CG
Sbjct: 443 YIAECPNCDSPLT----------LHKATGQLRCHYCGY 470
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 31.4 bits (71), Expect = 0.33
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 233 LVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGF 282
L + + P+ C C F+ + L +H+ +K C +CGK F
Sbjct: 62 LYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKV--CPVCGKEF 109
Score = 29.8 bits (67), Expect = 1.1
Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 3/55 (5%)
Query: 3 YTCDYCTRLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFNSRNGLYVHLKKVHNV 57
Y C C F +K H+ K C C K+F + + H+ K HN+
Sbjct: 74 YVCPLCLMPFSSSVSLKQHIRYTEHSK---VCPVCGKEFRNTDSTLDHVCKKHNI 125
Score = 28.3 bits (63), Expect = 4.0
Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 2/49 (4%)
Query: 216 PFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHL 264
P+VC +C + +L H+ H C C K F + H+
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHIRYTE--HSKVCPVCGKEFRNTDSTLDHV 119
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 32.2 bits (73), Expect = 0.45
Identities = 26/111 (23%), Positives = 45/111 (40%), Gaps = 5/111 (4%)
Query: 64 ELVSNIPLDEDITDAALLVDKALTI--KPKESEQSSQSEDEGMDEGGRDSSGSEWTEETD 121
E++ ++ L E++ D D+ +P E+EQ Q E EG + G SE T+ +
Sbjct: 192 EMLRSMELAEEMGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDR-E 250
Query: 122 VFKADKANLDLQGLEMSPEDRAESEVLG--WKCFICDAQLTTETSYSVFYT 170
++ + ++ E +SE G + E Y VF T
Sbjct: 251 SESGEEEMVQSDQDDLPDESDDDSETPGEGARPARPFTSTGGEPDYKVFTT 301
>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 = 28.0 bits (62), Expect = 0.72
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 33 QCTFCEKKFNSRNGLYVHLKKVH 55
+C C K F+S++ L HL+K H
Sbjct: 2 KCPLCGKSFSSKDALKRHLRKHH 24
Score = 26.4 bits (58), Expect = 2.3
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 245 FTCHFCNKSFTQKIGLVKHLNIH 267
F C C KSF+ K L +HL H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 25.7 bits (56), Expect = 5.0
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 302 KCDICGLALTTKSHLNRHMLVH 323
KC +CG + ++K L RH+ H
Sbjct: 2 KCPLCGKSFSSKDALKRHLRKH 23
Score = 24.9 bits (54), Expect = 7.1
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 329 HECSVCGKRFAKKWNAQVHKKKVH 352
+C +CGK F+ K + H +K H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|234754 PRK00418, PRK00418, DNA gyrase inhibitor; Reviewed.
Length = 62
Score = 28.5 bits (64), Expect = 0.87
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 12/40 (30%)
Query: 185 MPLIHECPTCGKK--WRTVSELNAHIQTHSDLRPFVCEIC 222
+ CPTCGK W E++ RPF + C
Sbjct: 3 ETITVNCPTCGKPVEW---GEISPF-------RPFCSKRC 32
>gnl|CDD|188657 cd09825, thyroid_peroxidase, Thyroid peroxidase (TPO). TPO is a
member of the animal heme peroxidase family, which is
expressed in the thyroid and involved in the processing
of iodine and iodine compounds. Specifically, TPO
oxidizes iodide via hydrogen peroxide to form active
iodine, which is then, for example, incorporated into
the tyrosine residues of thyroglobulin to yield mono-
and di-iodotyrosines.
Length = 565
Score = 31.3 bits (71), Expect = 0.94
Identities = 14/59 (23%), Positives = 20/59 (33%), Gaps = 5/59 (8%)
Query: 156 DAQLTTETSYSVFYTMLSQSGVLLSERACMPLIHECPTCGK-----KWRTVSELNAHIQ 209
D ++T E F L + RAC+P CG + +S N Q
Sbjct: 92 DCKMTCENQNPCFPIQLPSEDPRILGRACLPFFRSSAVCGTGDTSTLFGNLSLANPREQ 150
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 30.8 bits (69), Expect = 1.2
Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 11/81 (13%)
Query: 213 DLRPFVCEI--CGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIHNGT 270
D +P+ C + C + YK + L H M G N+ + K
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYH--MLHG-------HQNQKLHENPSPEKMNIFSAKD 396
Query: 271 KKYQCHLCGKGFIHHTSYKFH 291
K Y+C +C K + + K+H
Sbjct: 397 KPYRCEVCDKRYKNLNGLKYH 417
Score = 29.3 bits (65), Expect = 3.8
Identities = 22/86 (25%), Positives = 35/86 (40%), Gaps = 11/86 (12%)
Query: 269 GTKKYQCHL--CGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSHLNRHMLVHTGD 326
K Y+C + C K + + K+H L G +N K L + + D
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHML--HGHQNQK-------LHENPSPEKMNIFSAKD 396
Query: 327 RPHECSVCGKRFAKKWNAQVHKKKVH 352
+P+ C VC KR+ + H+K H
Sbjct: 397 KPYRCEVCDKRYKNLNGLKYHRKHSH 422
Score = 28.9 bits (64), Expect = 4.6
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 31 PNQCTFCEKKFNSRNGLYVHLKKVH 55
P +C C+K++ + NGL H K H
Sbjct: 398 PYRCEVCDKRYKNLNGLKYHRKHSH 422
>gnl|CDD|219939 pfam08619, Nha1_C, Alkali metal cation/H+ antiporter Nha1 C
terminus. The C terminus of the plasma membrane Nha1
antiporter plays an important role in the immediate cell
response to hypo-osmotic shock which prevents an
execessive loss of ions and water. This domain is found
with pfam00999.
Length = 430
Score = 30.2 bits (68), Expect = 2.2
Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 10/78 (12%)
Query: 71 LDEDITDAALLVDKALTIKPKESEQSSQ------SEDEGMDEGGRDSSGSEWTEETDVFK 124
L++D+ + L + + K +E SS D ++ RD S S+ EET +
Sbjct: 351 LEDDLAHSLLGSEASERRKNREPSSSSPPSRPRSRRDSEDEDTERDDSDSDDEEETPAER 410
Query: 125 ADKANLDLQGLEMSPEDR 142
L L P R
Sbjct: 411 RR----RLAALGELPSAR 424
>gnl|CDD|227515 COG5188, PRP9, Splicing factor 3a, subunit 3 [RNA processing and
modification].
Length = 470
Score = 30.0 bits (67), Expect = 2.4
Identities = 23/103 (22%), Positives = 40/103 (38%), Gaps = 9/103 (8%)
Query: 34 CTFCEKKFNSRNGLYVHLK-KVHNVEYSERIELVSNIP--------LDEDITDAALLVDK 84
C C ++F+ HL+ K H E + E V + L + +++ LV +
Sbjct: 241 CVKCGREFSRSKVFEYHLEGKRHCKEGQGKEEFVYSEYVLHRYLKYLGDPVSETRSLVLR 300
Query: 85 ALTIKPKESEQSSQSEDEGMDEGGRDSSGSEWTEETDVFKADK 127
+L I KE + + SS E E+ D + D+
Sbjct: 301 SLAITAKERKAEISLLSRRKKQPATKSSEKEGAEQVDGEQRDE 343
>gnl|CDD|221870 pfam12950, TaqI_C, TaqI-like C-terminal specificity domain. This
domain is found at the C-terminus of the TaqI protein
and is involved in DNA-binding and substrate
recognition.
Length = 118
Score = 27.5 bits (62), Expect = 5.0
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 10 RLFRRPGEVKNHVLVKHLGKNPNQCTFCEKKFNSRNGLYVHLKKVHNVEY 59
F +P +LV+ +G + E+++ N LY+ + K N+
Sbjct: 35 EFFEKP-----KILVRQIG-GRLVAAYDEEQYYWLNSLYLLIPKDENISL 78
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 27.2 bits (61), Expect = 5.2
Identities = 6/24 (25%), Positives = 9/24 (37%)
Query: 33 QCTFCEKKFNSRNGLYVHLKKVHN 56
C FC ++ H+ K H
Sbjct: 1 DCLFCNHTSDTVEENLEHMFKSHG 24
>gnl|CDD|222358 pfam13743, Thioredoxin_5, Thioredoxin.
Length = 177
Score = 27.9 bits (63), Expect = 5.7
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 11/63 (17%)
Query: 125 ADKANLDLQGLEMSPEDRAESEVLGWKCFICDAQLT-----TETSYSVFY-TMLSQSGVL 178
A+KA LD+ EM EDR K F CD ++ TET VF+ + G+
Sbjct: 111 AEKAGLDV---EMFKEDRHSDLAK--KAFQCDQKIAREMGVTETPTLVFFNENVEDEGLK 165
Query: 179 LSE 181
+
Sbjct: 166 IEG 168
>gnl|CDD|217778 pfam03884, DUF329, Domain of unknown function (DUF329). The
function of this short domain is unknown it contains
four conserved cysteines and may therefore be involved
in zinc binding.
Length = 57
Score = 26.1 bits (58), Expect = 6.0
Identities = 15/38 (39%), Positives = 17/38 (44%), Gaps = 12/38 (31%)
Query: 187 LIHECPTCGKK--WRTVSELNAHIQTHSDLRPFVCEIC 222
+ +CPTCGK W SE N RPF E C
Sbjct: 1 MTVKCPTCGKPVVW---SEENPF-------RPFCSERC 28
>gnl|CDD|226202 COG3677, COG3677, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 129
Score = 27.4 bits (61), Expect = 6.6
Identities = 11/67 (16%), Positives = 17/67 (25%), Gaps = 11/67 (16%)
Query: 218 VCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHL 277
C C +K + G + C C +FT + G Y+ L
Sbjct: 32 NCPRCKSSNVVKIGGIR-----RGHQRYKCKSCGSTFTVETGSPL------SKALYKIKL 80
Query: 278 CGKGFIH 284
Sbjct: 81 QAVTLYM 87
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 28.6 bits (65), Expect = 7.6
Identities = 9/37 (24%), Positives = 14/37 (37%), Gaps = 10/37 (27%)
Query: 243 HPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCG 279
C C+ S T +H ++ +CH CG
Sbjct: 389 WVAECPHCDASLT----------LHRFQRRLRCHHCG 415
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 28.6 bits (64), Expect = 8.1
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 73 EDITDAALLVDKALTIKPKESEQSSQSEDEGMDEG-GRDSSGSEWTEETDVFKADKAN 129
D A + D +E E + E+E DEG ++ S E EE DV + +
Sbjct: 373 LDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDS 430
>gnl|CDD|215520 PLN02964, PLN02964, phosphatidylserine decarboxylase.
Length = 644
Score = 28.3 bits (63), Expect = 8.5
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 186 PLIHECPTCGKKWRTVSELNAHI 208
P+I+ CP CG+ +LNA I
Sbjct: 249 PIINNCPVCGEALGVSDKLNAMI 271
>gnl|CDD|192074 pfam08573, SAE2, DNA repair protein endonuclease SAE2/CtIP
C-terminus. SAE2 is a protein involved in repairing
meiotic and mitotic double-strand breaks in DNA. It has
been shown to negatively regulate DNA damage checkpoint
signalling. SAE2 is homologous to the CtIP proteins in
mammals and an homologous protein in plants. Crucial
sequence motifs that are highly conserved are the CxxC
and the RHR motifs in this C-terminal part of the
protein. It is now known to be an endonuclease. In
budding yeast, genetic evidence suggests that the SAE2
protein is essential for the processing of hairpin DNA
intermediates and meiotic double-strand breaks by
Mre11/Rad50 complexes. SAE2 binds DNA and exhibits
endonuclease activity on single-stranded DNA
independently of Mre11/Rad50 complexes, but hairpin DNA
structures are cleaved cooperatively in the presence of
Mre11/Rad50 or Mre11/Rad50/Xrs2. Hairpin structures are
not processed at the tip by SAE2 but rather at
single-stranded DNA regions adjacent to the hairpin. The
catalytic activities of SAE2 are important for its
biological functions.
Length = 93
Score = 26.7 bits (59), Expect = 8.7
Identities = 8/30 (26%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 180 SERACMP--LIHECPTCGKKWRTVSELNAH 207
ER C+ C CGK + ++ L
Sbjct: 10 DERKCLKGCTRPSCKKCGKFYEALARLEEK 39
>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 = 24.8 bits (55), Expect = 9.5
Identities = 12/23 (52%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 34 CTFCEKKFNSRNGLYVHLK-KVH 55
C C+K F S N L HLK K H
Sbjct: 4 CVACDKYFKSENALENHLKSKKH 26
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 0.135 0.424
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,965,920
Number of extensions: 1719899
Number of successful extensions: 1723
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1708
Number of HSP's successfully gapped: 78
Length of query: 392
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 293
Effective length of database: 6,546,556
Effective search space: 1918140908
Effective search space used: 1918140908
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 (27.0 bits)