RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18077
(451 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 39.7 bits (93), Expect = 5e-05
Identities = 16/24 (66%), Positives = 21/24 (87%)
Query: 219 LQGHIRTHTGEKPFKCKVCDKAFA 242
L+ H+RTHTGEKP+KC VC K+F+
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 35.8 bits (83), Expect = 0.001
Identities = 13/25 (52%), Positives = 19/25 (76%)
Query: 246 NLRAHIQTHSKVKPFVCEKCGKAFA 270
NLR H++TH+ KP+ C CGK+F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 35.8 bits (83), Expect = 0.001
Identities = 13/25 (52%), Positives = 19/25 (76%)
Query: 310 NLRAHIQTHSKVKPFVCEKCGKAFA 334
NLR H++TH+ KP+ C CGK+F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 26.2 bits (58), Expect = 3.5
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 291 SSEKPFKCKVCDKAFA 306
+ EKP+KC VC K+F+
Sbjct: 10 TGEKPYKCPVCGKSFS 25
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 42.8 bits (101), Expect = 3e-04
Identities = 29/107 (27%), Positives = 40/107 (37%), Gaps = 26/107 (24%)
Query: 234 CKVCDKAFADKSNLRAHIQTHSKVKPF-VCEKCGKAFA-LKSYLYKHEDSSCLKSYDSSS 291
C+ C + D ++ R PF C CG F +++ Y E++S
Sbjct: 104 CEDCLEEIFDPNSRRYLY-------PFINCTNCGPRFTIIEALPYDRENTSM-------- 148
Query: 292 SEKPFK-CKVCDKAFADKSNLRAHIQTHSKVKPFVCEKCGKAFALKS 337
F C CDK + D N R H Q P C KCG L +
Sbjct: 149 --ADFPLCPFCDKEYKDPLNRRFHAQ------PIACPKCGPHLFLVN 187
Score = 36.2 bits (84), Expect = 0.032
Identities = 21/71 (29%), Positives = 30/71 (42%), Gaps = 12/71 (16%)
Query: 206 CPHCSKSFSRPWLLQG--HIRTHTGEKPFK-CKVCDKAFADKSNLRAHIQTHSKVKPFVC 262
C +C F+ +++ + R +T F C CDK + D N R H Q P C
Sbjct: 126 CTNCGPRFT---IIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFHAQ------PIAC 176
Query: 263 EKCGKAFALKS 273
KCG L +
Sbjct: 177 PKCGPHLFLVN 187
>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF. A
previously described regulatory effect of HypF
mutatation is attributable to loss of activity of a
regulatory hydrogenase. A zinc finger-like region
CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
the regulatory hypothesis. However, more recent work
(PUBMED:11375153) shows the direct effect is on the
activity of expressed hydrogenases with nickel/iron
centers, rather than on expression [Protein fate,
Protein modification and repair].
Length = 711
Score = 41.3 bits (97), Expect = 0.001
Identities = 27/107 (25%), Positives = 39/107 (36%), Gaps = 26/107 (24%)
Query: 234 CKVCDKAFADKSNLRAHIQTHSKVKPFV-CEKCGKAFAL-KSYLYKHEDSSCLKSYDSSS 291
C C + DK++ R PF+ C CG F + ++ Y E++S
Sbjct: 71 CSDCLEEMLDKNDRRYLY-------PFISCTHCGPRFTIIEALPYDRENTSM-------- 115
Query: 292 SEKPFK-CKVCDKAFADKSNLRAHIQTHSKVKPFVCEKCGKAFALKS 337
F C C K + D + R H Q P C +CG S
Sbjct: 116 --ADFPLCPDCAKEYKDPLDRRFHAQ------PIACPRCGPQLNFVS 154
Score = 32.4 bits (74), Expect = 0.50
Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 12/71 (16%)
Query: 206 CPHCSKSFSRPWLLQG--HIRTHTGEKPFK-CKVCDKAFADKSNLRAHIQTHSKVKPFVC 262
C HC F+ +++ + R +T F C C K + D + R H Q P C
Sbjct: 93 CTHCGPRFT---IIEALPYDRENTSMADFPLCPDCAKEYKDPLDRRFHAQ------PIAC 143
Query: 263 EKCGKAFALKS 273
+CG S
Sbjct: 144 PRCGPQLNFVS 154
>gnl|CDD|223500 COG0423, GRS1, Glycyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 558
Score = 38.1 bits (89), Expect = 0.008
Identities = 22/121 (18%), Positives = 43/121 (35%), Gaps = 26/121 (21%)
Query: 336 KSYLYKHE-----DSSCLKSYD---SSSNGHLNKFTTISFQCRDCGKHYSTSSNLARHRQ 387
KS++ + E D+ + + +S GH++KF+ +C+ CG+ R+R
Sbjct: 52 KSFVTEREDVVEIDTPIILPEEVWKAS--GHVDKFSDPLVECKKCGE---------RYRA 100
Query: 388 IHRSPDDTKARTCPQCGKLYVSMPAYSMHLRTHNQICQCPHCSKSFSRPWLLQGHIRTHT 447
H + S + +R ++ CP C + +T
Sbjct: 101 DHLIEEYLGKDGHGNM-----SPEELTEIIREYDIR--CPECGGELNEVREFNLMFKTTI 153
Query: 448 G 448
G
Sbjct: 154 G 154
>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 = 32.3 bits (74), Expect = 0.023
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 233 KCKVCDKAFADKSNLRAHIQTH 254
KC C K+F+ KSNL+ H++TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 32.3 bits (74), Expect = 0.023
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 297 KCKVCDKAFADKSNLRAHIQTH 318
KC C K+F+ KSNL+ H++TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 31.2 bits (71), Expect = 0.054
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 205 QCPHCSKSFSRPWLLQGHIRTH 226
+CP C KSFSR L+ H+RTH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 31.2 bits (71), Expect = 0.054
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 425 QCPHCSKSFSRPWLLQGHIRTH 446
+CP C KSFSR L+ H+RTH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 30.8 bits (70), Expect = 0.067
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 148 QCRDCGKHYSTSSNLARHRQIH 169
+C DCGK +S SNL RH + H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 30.8 bits (70), Expect = 0.067
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 368 QCRDCGKHYSTSSNLARHRQIH 389
+C DCGK +S SNL RH + H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.0 bits (55), Expect = 8.9
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 261 VCEKCGKAFALKSYLYKH 278
C CGK+F+ KS L +H
Sbjct: 1 KCPDCGKSFSRKSNLKRH 18
Score = 25.0 bits (55), Expect = 8.9
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 325 VCEKCGKAFALKSYLYKH 342
C CGK+F+ KS L +H
Sbjct: 1 KCPDCGKSFSRKSNLKRH 18
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 33.1 bits (75), Expect = 0.026
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 180 CPQCGKLYVSMPAYSMHLRTHNQICQCPHCSK 211
CP CG++Y+ + HLR HN + +C +
Sbjct: 8 CPICGEIYIKRKSMITHLRKHNTNLKLSNCKR 39
Score = 33.1 bits (75), Expect = 0.026
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 400 CPQCGKLYVSMPAYSMHLRTHNQICQCPHCSK 431
CP CG++Y+ + HLR HN + +C +
Sbjct: 8 CPICGEIYIKRKSMITHLRKHNTNLKLSNCKR 39
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 35.5 bits (81), Expect = 0.047
Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 20/94 (21%)
Query: 228 GEKPFKCKV--CDKAFADKSNLRAHIQTHSKVKPFVCEKCGKAFALKSYLYKHEDSSCLK 285
KP+KC V C+K + +++ L+ H H + HE+ S K
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYH-MLHGHQNQKL----------------HENPSPEK 388
Query: 286 SYDSSSSEKPFKCKVCDKAFADKSNLRAHIQTHS 319
S+ +KP++C+VCDK + + + L+ H HS
Sbjct: 389 MNIFSAKDKPYRCEVCDKRYKNLNGLKYHR-KHS 421
Score = 28.1 bits (62), Expect = 9.9
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 21/62 (33%)
Query: 293 EKPFKCKV--CDKAFADKSNLRAH-IQTH------------------SKVKPFVCEKCGK 331
KP+KC V C+K + +++ L+ H + H +K KP+ CE C K
Sbjct: 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDK 406
Query: 332 AF 333
+
Sbjct: 407 RY 408
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 30.9 bits (70), Expect = 0.073
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 232 FKCKVCDKAFADKSNLRAHIQTH 254
++C C K F KS LR H++TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 30.9 bits (70), Expect = 0.073
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 296 FKCKVCDKAFADKSNLRAHIQTH 318
++C C K F KS LR H++TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 28.2 bits (63), Expect = 0.52
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 147 FQCRDCGKHYSTSSNLARHRQIH 169
++C +CGK + + S L H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 28.2 bits (63), Expect = 0.52
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 367 FQCRDCGKHYSTSSNLARHRQIH 389
++C +CGK + + S L H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 28.2 bits (63), Expect = 0.65
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 205 QCPHCSKSFSRPWLLQGHIRTH 226
+CP C K F L+ H+RTH
Sbjct: 2 RCPECGKVFKSKSALREHMRTH 23
Score = 28.2 bits (63), Expect = 0.65
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 425 QCPHCSKSFSRPWLLQGHIRTH 446
+CP C K F L+ H+RTH
Sbjct: 2 RCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 33.3 bits (76), Expect = 0.082
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 279 EDSSCLKSYDSSSSEKPFKCKVCDKAFADKSNLRAHIQ--THSKVKPFVCEKCGKAFALK 336
++SS L +S + P+ C +C F+ +L+ HI+ HSK VC CGK F
Sbjct: 57 DESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSK----VCPVCGKEFRNT 112
Query: 337 SYLYKH 342
H
Sbjct: 113 DSTLDH 118
Score = 29.8 bits (67), Expect = 1.3
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 206 CPHCSKSFSRPWLLQGHIRTHTGEKPFKCKVCDKAFADKSNLRAHI 251
CP C FS L+ HIR K C VC K F + + H+
Sbjct: 76 CPLCLMPFSSSVSLKQHIRYTEHSK--VCPVCGKEFRNTDSTLDHV 119
Score = 29.1 bits (65), Expect = 2.5
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 231 PFKCKVCDKAFADKSNLRAHIQ--THSKVKPFVCEKCGKAFALKSYLYKH 278
P+ C +C F+ +L+ HI+ HSK VC CGK F H
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSK----VCPVCGKEFRNTDSTLDH 118
>gnl|CDD|225542 COG2995, PqiA, Uncharacterized paraquat-inducible protein A
[Function unknown].
Length = 418
Score = 33.9 bits (78), Expect = 0.19
Identities = 17/69 (24%), Positives = 21/69 (30%), Gaps = 17/69 (24%)
Query: 165 HRQIHRSPDDTKARTCPQCGKLYVSMPAYSMHLRTHNQICQCPHCSKSFSRPWLLQGHIR 224
H I CP+C L VS+P Q CP C GH
Sbjct: 6 HMGITEELPPGHLILCPECDML-VSLPRLD-----SGQSAYCPRC-----------GHTL 48
Query: 225 THTGEKPFK 233
T G+ +
Sbjct: 49 TRGGDWSLQ 57
Score = 33.5 bits (77), Expect = 0.25
Identities = 16/60 (26%), Positives = 18/60 (30%), Gaps = 14/60 (23%)
Query: 385 HRQIHRSPDDTKARTCPQCGKLYVSMPAYSMHLRTHNQICQCPHC--------SKSFSRP 436
H I CP+C L VS+P Q CP C S RP
Sbjct: 6 HMGITEELPPGHLILCPECDML-VSLPRLD-----SGQSAYCPRCGHTLTRGGDWSLQRP 59
>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 = 29.5 bits (66), Expect = 0.20
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 204 CQCPHCSKSFSRPWLLQGHIRTH 226
+CP C KSFS L+ H+R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 29.5 bits (66), Expect = 0.20
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 424 CQCPHCSKSFSRPWLLQGHIRTH 446
+CP C KSFS L+ H+R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 28.8 bits (64), Expect = 0.38
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 232 FKCKVCDKAFADKSNLRAHIQTH 254
FKC +C K+F+ K L+ H++ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 28.8 bits (64), Expect = 0.38
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 296 FKCKVCDKAFADKSNLRAHIQTH 318
FKC +C K+F+ K L+ H++ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 25.7 bits (56), Expect = 5.4
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 147 FQCRDCGKHYSTSSNLARHRQIH 169
F+C CGK +S+ L RH + H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 25.7 bits (56), Expect = 5.4
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 367 FQCRDCGKHYSTSSNLARHRQIH 389
F+C CGK +S+ L RH + H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 33.8 bits (78), Expect = 0.20
Identities = 10/62 (16%), Positives = 17/62 (27%), Gaps = 25/62 (40%)
Query: 205 QCPHCSKSFSRPWLLQGHIRTHTGEKPFKCKVCDKAFADKSNLRAHIQTHSKVKPFVCEK 264
+CP+C + H +C C + + P C +
Sbjct: 446 ECPNCDSPLT----------LHKATGQLRCHYCG---------------YQEPIPQSCPE 480
Query: 265 CG 266
CG
Sbjct: 481 CG 482
Score = 28.4 bits (64), Expect = 8.3
Identities = 10/38 (26%), Positives = 14/38 (36%), Gaps = 3/38 (7%)
Query: 296 FKCKVCDKAFA---DKSNLRAHIQTHSKVKPFVCEKCG 330
+C CD LR H + + P C +CG
Sbjct: 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECG 482
>gnl|CDD|216695 pfam01780, Ribosomal_L37ae, Ribosomal L37ae protein family. This
ribosomal protein is found in archaebacteria and
eukaryotes. It contains four conserved cysteine residues
that may bind to zinc.
Length = 90
Score = 30.3 bits (69), Expect = 0.39
Identities = 13/35 (37%), Positives = 15/35 (42%), Gaps = 8/35 (22%)
Query: 179 TCPQCGKLYVSMPAYSMHLRTHNQICQCPHCSKSF 213
TCP CGK V R I +C C K+F
Sbjct: 37 TCPFCGKDAVK--------RKAVGIWKCRKCGKTF 63
Score = 30.3 bits (69), Expect = 0.39
Identities = 13/35 (37%), Positives = 15/35 (42%), Gaps = 8/35 (22%)
Query: 399 TCPQCGKLYVSMPAYSMHLRTHNQICQCPHCSKSF 433
TCP CGK V R I +C C K+F
Sbjct: 37 TCPFCGKDAVK--------RKAVGIWKCRKCGKTF 63
>gnl|CDD|225807 COG3268, COG3268, Uncharacterized conserved protein [Function
unknown].
Length = 382
Score = 32.4 bits (74), Expect = 0.42
Identities = 18/94 (19%), Positives = 26/94 (27%), Gaps = 15/94 (15%)
Query: 369 CRDCGKHY-STSSNLARHRQIHRSPD----DTKARTCPQCGKLYVSMP-------AYSMH 416
C G Y + + D AR P CG + S+P
Sbjct: 93 CAAAGTDYADITGEIMFFENSIDLYHAQAADAGARIIPGCG--FDSIPSDLGVYALLKQA 150
Query: 417 LRTHNQICQCPHCS-KSFSRPWLLQGHIRTHTGG 449
L + H + SF+ + G T G
Sbjct: 151 LPDGTEELIATHLALGSFTGSGISGGTAATSVEG 184
Score = 32.0 bits (73), Expect = 0.57
Identities = 17/90 (18%), Positives = 25/90 (27%), Gaps = 15/90 (16%)
Query: 149 CRDCGKHY-STSSNLARHRQIHRSPD----DTKARTCPQCGKLYVSMP-------AYSMH 196
C G Y + + D AR P CG + S+P
Sbjct: 93 CAAAGTDYADITGEIMFFENSIDLYHAQAADAGARIIPGCG--FDSIPSDLGVYALLKQA 150
Query: 197 LRTHNQICQCPHCS-KSFSRPWLLQGHIRT 225
L + H + SF+ + G T
Sbjct: 151 LPDGTEELIATHLALGSFTGSGISGGTAAT 180
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 32.4 bits (73), Expect = 0.46
Identities = 31/94 (32%), Positives = 44/94 (46%), Gaps = 2/94 (2%)
Query: 206 CPHCSKSFSRPWLLQGHIRTHTGEKPFKCKV--CDKAFADKSNLRAHIQTHSKVKPFVCE 263
CP+C+ SFSR L HIR+HTGEKP +C CDK+F+ L H++TH +
Sbjct: 36 CPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNPSDLNS 95
Query: 264 KCGKAFALKSYLYKHEDSSCLKSYDSSSSEKPFK 297
K K+ SS + ++ S
Sbjct: 96 KSLPLSNSKASSSSLSSSSSNSNDNNLLSSHSLP 129
Score = 30.0 bits (67), Expect = 2.5
Identities = 39/222 (17%), Positives = 66/222 (29%), Gaps = 27/222 (12%)
Query: 138 TANNNNNESFQCRDCGKHYSTSSNLARHRQIHRSPDDTKARTCPQCGKLYVSMPAYSMHL 197
++ ++++ S + + +++ K + P K + S L
Sbjct: 246 SSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRSSPL 305
Query: 198 RTHNQIC----------QCPH--CSKSFSRPWLLQGHIRTHTGEKPFKCKVCDKAFADKS 245
H + CP+ C K FSR L+ HI HT P K K+ + +
Sbjct: 306 TRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSP 365
Query: 246 NLRA-------HIQTHSKVKPFVCE--KCGKAFALKSYLYKHEDSSCLKSYDSSSSEKPF 296
L + K C + F S L H + +
Sbjct: 366 LLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYN------C 419
Query: 297 KCKVCDKAFADKSNLRAHIQTHSKVKPFVCEKCGKAFALKSY 338
K C K+F NL H + H+ P +C
Sbjct: 420 KNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKSFRRDLDL 461
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 32.7 bits (74), Expect = 0.57
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 6/35 (17%)
Query: 53 ASDSSDLDDDDDDPRL------QINEDEAEMSDPV 81
A++ SDL +DD + Q EDE EMSD V
Sbjct: 3929 ANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDDV 3963
>gnl|CDD|220362 pfam09723, CxxC_CxxC_SSSS, Zinc ribbon domain. This entry
represents a region of about 41 amino acids found in a
number of small proteins in a wide range of bacteria.
The region usually begins with the initiator Met and
contains two CxxC motifs separated by 17 amino acids.
One protein in this entry has been noted as a putative
regulatory protein, designated FmdB. Most proteins in
this entry have a C-terminal region containing highly
degenerate sequence.
Length = 42
Score = 28.3 bits (64), Expect = 0.78
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 10/39 (25%)
Query: 147 FQCRDCGKHYSTSSNLARHRQIHRSPDDTKARTCPQCGK 185
++C DCG + ++ + D TCP+CG
Sbjct: 6 YRCEDCGHTF----------EVLQKISDDPLATCPECGS 34
Score = 28.3 bits (64), Expect = 0.78
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 10/39 (25%)
Query: 367 FQCRDCGKHYSTSSNLARHRQIHRSPDDTKARTCPQCGK 405
++C DCG + ++ + D TCP+CG
Sbjct: 6 YRCEDCGHTF----------EVLQKISDDPLATCPECGS 34
>gnl|CDD|235183 PRK03976, rpl37ae, 50S ribosomal protein L37Ae; Reviewed.
Length = 90
Score = 29.6 bits (67), Expect = 0.80
Identities = 10/35 (28%), Positives = 12/35 (34%), Gaps = 8/35 (22%)
Query: 179 TCPQCGKLYVSMPAYSMHLRTHNQICQCPHCSKSF 213
CP CG+ V R I +C C F
Sbjct: 38 VCPVCGRPKVK--------RVGTGIWECRKCGAKF 64
Score = 29.6 bits (67), Expect = 0.80
Identities = 10/35 (28%), Positives = 12/35 (34%), Gaps = 8/35 (22%)
Query: 399 TCPQCGKLYVSMPAYSMHLRTHNQICQCPHCSKSF 433
CP CG+ V R I +C C F
Sbjct: 38 VCPVCGRPKVK--------RVGTGIWECRKCGAKF 64
>gnl|CDD|172627 PRK14138, PRK14138, NAD-dependent deacetylase; Provisional.
Length = 244
Score = 31.3 bits (71), Expect = 0.87
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 251 IQTHSKVKPFVCEKCGKAFALKSYLYKHEDSSCLKSYDSSSSEKP 295
I+ H V+ + C +CGK + ++ + K E S + D S +P
Sbjct: 111 IELHGNVEEYYCVRCGKRYTVEDVIEKLEKSDVPRCDDCSGLIRP 155
Score = 29.4 bits (66), Expect = 3.7
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 315 IQTHSKVKPFVCEKCGKAFALKSYLYKHEDSSCLKSYDSSS 355
I+ H V+ + C +CGK + ++ + K E S + D S
Sbjct: 111 IELHGNVEEYYCVRCGKRYTVEDVIEKLEKSDVPRCDDCSG 151
>gnl|CDD|177300 PHA00732, PHA00732, hypothetical protein.
Length = 79
Score = 29.4 bits (66), Expect = 0.88
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 180 CPQCGKLYVSMPAYSMHLRTHNQICQCPHCSKSFSR 215
CP CG V++ A H R ++ + +CP C+KS+ R
Sbjct: 4 CPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYRR 39
Score = 29.4 bits (66), Expect = 0.88
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 400 CPQCGKLYVSMPAYSMHLRTHNQICQCPHCSKSFSR 435
CP CG V++ A H R ++ + +CP C+KS+ R
Sbjct: 4 CPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYRR 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 = 27.2 bits (61), Expect = 1.3
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 231 PFKCKVCDKAFADKSNLRAHIQT 253
F C CDK F ++ L H+++
Sbjct: 1 QFYCVACDKYFKSENALENHLKS 23
Score = 27.2 bits (61), Expect = 1.3
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 295 PFKCKVCDKAFADKSNLRAHIQT 317
F C CDK F ++ L H+++
Sbjct: 1 QFYCVACDKYFKSENALENHLKS 23
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 27.2 bits (61), Expect = 1.4
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 232 FKCKVCDKAFADKSNLRAHIQTHSK 256
C VC K F+ L H ++H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSHCS 26
Score = 27.2 bits (61), Expect = 1.4
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 296 FKCKVCDKAFADKSNLRAHIQTHSK 320
C VC K F+ L H ++H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSHCS 26
>gnl|CDD|222432 pfam13882, Bravo_FIGEY, C-terminal domain of Fibronectin type III.
This is the very C-terminal region of neural adhesion
molecule L1 proteins that are also known as Bravo or
NrCAM. It lies upstream of the IG and Fn3 domains and
has the highly conserved motif FIGEY. The function is
not known.
Length = 118
Score = 29.6 bits (67), Expect = 1.4
Identities = 13/54 (24%), Positives = 16/54 (29%), Gaps = 8/54 (14%)
Query: 29 PDNSHIPDVSHLPANSHLPGVSDYASDSSDLDDDDDD--------PRLQINEDE 74
+ + S N LP S + D DD D Q NED
Sbjct: 53 MKDEGFGEYSRPEDNKPLPRGSQQSLDGEIGDDSSTDSLDEYGDGDTGQFNEDG 106
>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 = 27.1 bits (61), Expect = 1.5
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 232 FKCKVCDKAFADKSNLRAHIQ 252
F C++C+ F +S L++H++
Sbjct: 1 FYCELCNVTFTSESQLKSHLR 21
Score = 27.1 bits (61), Expect = 1.5
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 296 FKCKVCDKAFADKSNLRAHIQ 316
F C++C+ F +S L++H++
Sbjct: 1 FYCELCNVTFTSESQLKSHLR 21
>gnl|CDD|226907 COG4530, COG4530, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 129
Score = 29.5 bits (66), Expect = 1.6
Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 46 LPGVSDYASDSSDLDDDDDDPRLQINEDE 74
LP + D + DLDDDDDD L+ ED+
Sbjct: 86 LPDLGD--DEDVDLDDDDDDTFLEDEEDD 112
>gnl|CDD|150045 pfam09237, GAGA, GAGA factor. Members of this family bind to a
5'-GAGAG-3' DNA consensus binding site, and contain a
Cys2-His2 zinc finger core as well as an N-terminal
extension containing two highly basic regions. The zinc
finger core binds in the DNA major groove and recognises
the first three GAG bases of the consensus in a manner
similar to that seen in other classical zinc finger-DNA
complexes. The second basic region forms a helix that
interacts in the major groove recognising the last G of
the consensus, while the first basic region wraps around
the DNA in the minor groove and recognises the A in the
fourth position of the consensus sequence.
Length = 54
Score = 27.6 bits (61), Expect = 1.7
Identities = 14/42 (33%), Positives = 18/42 (42%)
Query: 284 LKSYDSSSSEKPFKCKVCDKAFADKSNLRAHIQTHSKVKPFV 325
K S SE+P C +C NLR H++ KP V
Sbjct: 13 EKIKSKSQSEQPATCPICQAVIRQSRNLRRHLELRHFKKPGV 54
>gnl|CDD|224908 COG1997, RPL43A, Ribosomal protein L37AE/L43A [Translation,
ribosomal structure and biogenesis].
Length = 89
Score = 28.1 bits (63), Expect = 2.8
Identities = 10/35 (28%), Positives = 12/35 (34%), Gaps = 8/35 (22%)
Query: 179 TCPQCGKLYVSMPAYSMHLRTHNQICQCPHCSKSF 213
CP CG+ V R I +C C F
Sbjct: 37 VCPFCGRTTVK--------RIATGIWKCRKCGAKF 63
Score = 28.1 bits (63), Expect = 2.8
Identities = 10/35 (28%), Positives = 12/35 (34%), Gaps = 8/35 (22%)
Query: 399 TCPQCGKLYVSMPAYSMHLRTHNQICQCPHCSKSF 433
CP CG+ V R I +C C F
Sbjct: 37 VCPFCGRTTVK--------RIATGIWKCRKCGAKF 63
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 29.8 bits (67), Expect = 3.2
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 55 DSSDLDDDDDDPRLQINEDEAE-MSDPVSTSSQSSSEPVASFDPA 98
DSSD ++ ++ P + NED +E SD + S S + +
Sbjct: 213 DSSDEEEGEEAPSINYNEDTSESESDESDSEISESRSVSDSEESS 257
>gnl|CDD|225373 COG2816, NPY1, NTP pyrophosphohydrolases containing a Zn-finger,
probably nucleic-acid-binding [DNA replication,
recombination, and repair].
Length = 279
Score = 29.2 bits (66), Expect = 4.3
Identities = 10/64 (15%), Positives = 14/64 (21%), Gaps = 24/64 (37%)
Query: 166 RQIHRSPDDT----------------KARTCPQCGKLYVSMPAYSMHLRTHNQICQCPHC 209
R + D+ R C +CG + R CP C
Sbjct: 84 RSLLTELDEGLFGLAARAVQLLEWYRSHRFCGRCGT--------KTYPREGGWARVCPKC 135
Query: 210 SKSF 213
Sbjct: 136 GHEH 139
Score = 29.2 bits (66), Expect = 4.3
Identities = 10/64 (15%), Positives = 14/64 (21%), Gaps = 24/64 (37%)
Query: 386 RQIHRSPDDT----------------KARTCPQCGKLYVSMPAYSMHLRTHNQICQCPHC 429
R + D+ R C +CG + R CP C
Sbjct: 84 RSLLTELDEGLFGLAARAVQLLEWYRSHRFCGRCGT--------KTYPREGGWARVCPKC 135
Query: 430 SKSF 433
Sbjct: 136 GHEH 139
>gnl|CDD|235164 PRK03824, hypA, hydrogenase nickel incorporation protein;
Provisional.
Length = 135
Score = 28.1 bits (63), Expect = 5.1
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 147 FQCRDCGKHYSTSSNL----ARHRQ-IHRSPDDTKART-CPQCG 184
+CR+CG +S R+ IH P+ A CP+CG
Sbjct: 71 LKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCG 114
Score = 28.1 bits (63), Expect = 5.1
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 367 FQCRDCGKHYSTSSNL----ARHRQ-IHRSPDDTKART-CPQCG 404
+CR+CG +S R+ IH P+ A CP+CG
Sbjct: 71 LKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCG 114
>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation
domain. The centromere protein B (CENP-B) dimerisation
domain is composed of two alpha-helices, which are
folded into an antiparallel configuration. Dimerisation
of CENP-B is mediated by this domain, in which monomers
dimerise to form a symmetrical, antiparallel,
four-helix bundle structure with a large hydrophobic
patch in which 23 residues of one monomer form van der
Waals contacts with the other monomer. This CENP-B
dimer configuration may be suitable for capturing two
distant CENP-B boxes during centromeric heterochromatin
formation.
Length = 101
Score = 27.4 bits (60), Expect = 5.5
Identities = 17/45 (37%), Positives = 22/45 (48%)
Query: 41 PANSHLPGVSDYASDSSDLDDDDDDPRLQINEDEAEMSDPVSTSS 85
P L G D SDS + +DDDD+ +ED+ E D V S
Sbjct: 1 PTLHFLEGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDEVPVPS 45
>gnl|CDD|213223 cd03256, ABC_PhnC_transporter, ATP-binding cassette domain of the
binding protein-dependent phosphonate transport system.
Phosphonates are a class of organophosphorus compounds
characterized by a chemically stable
carbon-to-phosphorus (C-P) bond. Phosphonates are
widespread among naturally occurring compounds in all
kingdoms of wildlife, but only prokaryotic
microorganisms are able to cleave this bond. Certain
bacteria such as E. coli can use alkylphosphonates as a
phosphorus source. 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 = 241
Score = 28.7 bits (65), Expect = 6.0
Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 9/46 (19%)
Query: 90 EPVASFDPAYDHLYNLTQLAEVSLAYFNQSNSFNRKSVICNTKDVD 135
EPVAS DPA + + + N +VI + VD
Sbjct: 170 EPVASLDPA---------SSRQVMDLLKRINREEGITVIVSLHQVD 206
>gnl|CDD|234699 PRK00241, nudC, NADH pyrophosphatase; Reviewed.
Length = 256
Score = 28.7 bits (65), Expect = 6.1
Identities = 12/41 (29%), Positives = 13/41 (31%), Gaps = 13/41 (31%)
Query: 169 HRSPDDTKARTCPQCGKLYVSMPAYSMHLRTHNQICQCPHC 209
+RS R C CG MH CPHC
Sbjct: 96 YRS-----HRFCGYCGH--------PMHPSKTEWAMLCPHC 123
Score = 28.7 bits (65), Expect = 6.1
Identities = 12/41 (29%), Positives = 13/41 (31%), Gaps = 13/41 (31%)
Query: 389 HRSPDDTKARTCPQCGKLYVSMPAYSMHLRTHNQICQCPHC 429
+RS R C CG MH CPHC
Sbjct: 96 YRS-----HRFCGYCGH--------PMHPSKTEWAMLCPHC 123
>gnl|CDD|232951 TIGR00389, glyS_dimeric, glycyl-tRNA synthetase, dimeric type.
This model describes a glycyl-tRNA synthetase distinct
from the two alpha and two beta chains of the tetrameric
E. coli glycyl-tRNA synthetase. This enzyme is a
homodimeric class II tRNA synthetase and is recognized
by pfam model tRNA-synt_2b, which recognizes His, Ser,
Pro, and this set of glycyl-tRNA synthetases [Protein
synthesis, tRNA aminoacylation].
Length = 551
Score = 28.7 bits (64), Expect = 7.2
Identities = 8/46 (17%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 336 KSYLYKHE----DSSCLKSYDS-SSNGHLNKFTTISFQCRDCGKHY 376
K ++ D+ + + ++GH++ FT C+ C + +
Sbjct: 49 KFFIKNERVLEIDTPIITPEEVLKASGHVDNFTDWMVDCKSCKERF 94
>gnl|CDD|218555 pfam05320, Pox_RNA_Pol_19, Poxvirus DNA-directed RNA polymerase
19 kDa subunit. This family contains several
DNA-directed RNA polymerase 19 kDa polypeptides. The
Poxvirus DNA-directed RNA polymerase (EC: 2.7.7.6)
catalyzes DNA-template-directed extension of the 3'-end
of an RNA strand by one nucleotide at a time.
Length = 167
Score = 27.8 bits (62), Expect = 7.6
Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 49 VSDYASDS---SDLDDDDDDPRLQINEDEAEMSDPVSTSSQSSSE-PVASFDP 97
+ DY SD + +++++D + E+ S VS+ QS+ + AS +
Sbjct: 7 IIDYESDDDDSEEYEEEEED----EEDAESLESSDVSSLKQSNYKIESASENI 55
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
0.317 0.128 0.400
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,861,213
Number of extensions: 1809587
Number of successful extensions: 2819
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2762
Number of HSP's successfully gapped: 151
Length of query: 451
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 351
Effective length of database: 6,502,202
Effective search space: 2282272902
Effective search space used: 2282272902
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 (21.7 bits)
S2: 61 (27.2 bits)