RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy63
(585 letters)
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 45.8 bits (108), Expect = 4e-05
Identities = 68/454 (14%), Positives = 127/454 (27%), Gaps = 59/454 (12%)
Query: 126 ENVREHQCSVCGKAFADITNMKVHMRIHTGEKKYVC--ETCGASFALWGSLNVHSYSHTN 183
R C C +F+ + ++ H+R HTGEK C C SF+ L+ H +H N
Sbjct: 29 NAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHN 88
Query: 184 -TQFVCSYCGNTYKNPKALTSHIRNSHTIHQKSICDVCGKEFRMKRQLKEHMAVHTTDRP 242
+ S + + +S +S + ++ ++ P
Sbjct: 89 NPSDLNSKSLPLSNSKASSSSLSSSSSNSNDNNLLSSHSL-------------PPSSRDP 135
Query: 243 FVCNMCPSTFKLKKHLRQHYKVHLKMENHLNRHTNIHTGPGYQCNICGRVMNDRTNLKVH 302
+ ++ + L + + + H + ++ ++ + L
Sbjct: 136 QLPDLLSISNLRNNPLPGNNSSSVNTPQSNSLHPPLP-----ANSLSKDPSSNLSLLISS 190
Query: 303 MRNHTGEKKYICEVCGKGFVQWSSHYYHMFTHSESRNFQCTVCDKKFATPAGLREHKRVH 362
+ + + SS +S S T + L +
Sbjct: 191 NVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSL--------PLTTNSQLSPKSLLS 242
Query: 363 VTNRKNMIDHQRSVHELLKPYECDTCGHGLSSKKSLDDHYRIHTG-EKKYVCQQCGASFT 421
+ S + S + G +QC SF+
Sbjct: 243 QSPSSLSSSD--SSSSASESPRSSLPTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFS 300
Query: 422 QWASLFYHK------FSHSETRNQVCSYCGKTYKNPNHLRSHLNTHTKKRLYVC--ETCG 473
+ + L H + + S CGK + + L+ H+ HT
Sbjct: 301 RSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSS 360
Query: 474 KEFMKLELLKSHLTTH-----LAARPFICE--FCSAGFKTKKHLSQHHRTHKRKDTLENH 526
+F L + + + C FK +LS H TH
Sbjct: 361 SKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCK 420
Query: 527 MKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIHT 560
C ++F YNL H +IHT
Sbjct: 421 ------------NPPCSKSFNRHYNLIPHKKIHT 442
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 35.4 bits (82), Expect = 0.002
Identities = 17/26 (65%), Positives = 18/26 (69%)
Query: 298 NLKVHMRNHTGEKKYICEVCGKGFVQ 323
NL+ HMR HTGEK Y C VCGK F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 33.9 bits (78), Expect = 0.008
Identities = 15/25 (60%), Positives = 18/25 (72%)
Query: 145 NMKVHMRIHTGEKKYVCETCGASFA 169
N++ HMR HTGEK Y C CG SF+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 31.6 bits (72), Expect = 0.044
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 397 SLDDHYRIHTGEKKYVCQQCGASFTQ 422
+L H R HTGEK Y C CG SF+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 29.3 bits (66), Expect = 0.32
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 453 HLRSHLNTHTKKRLYVCETCGKEF 476
+LR H+ THT ++ Y C CGK F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSF 24
Score = 28.1 bits (63), Expect = 0.93
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 230 LKEHMAVHTTDRPFVCNMCPSTFK 253
L+ HM HT ++P+ C +C +F
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 27.0 bits (60), Expect = 1.9
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 329 YHMFTHSESRNFQCTVCDKKFAT 351
HM TH+ + ++C VC K F++
Sbjct: 4 RHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 33.7 bits (77), Expect = 0.068
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 180 SHTNTQFVCSYCGNTYKNPKALTSHIRNSHTIHQKSICDVCGKEFRMKRQLKEHM 234
S + +VC C + + +L HIR +T H K +C VCGKEFR +H+
Sbjct: 68 SKAVSPYVCPLCLMPFSSSVSLKQHIR--YTEHSK-VCPVCGKEFRNTDSTLDHV 119
Score = 31.0 bits (70), Expect = 0.69
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 159 YVCETCGASFALWGSLNVHSYSHTNTQFVCSYCGNTYKNPKALTSHIRNSHTI 211
YVC C F+ SL H +++ VC CG ++N + H+ H I
Sbjct: 74 YVCPLCLMPFSSSVSLKQHIRYTEHSK-VCPVCGKEFRNTDSTLDHVCKKHNI 125
Score = 29.5 bits (66), Expect = 1.9
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 411 YVCQQCGASFTQWASLFYHKFSHSETRNQVCSYCGKTYKNPNHLRSHL 458
YVC C F+ SL H ++VC CGK ++N + H+
Sbjct: 74 YVCPLCLMPFSSSVSLKQH--IRYTEHSKVCPVCGKEFRNTDSTLDHV 119
Score = 28.7 bits (64), Expect = 4.6
Identities = 18/48 (37%), Positives = 18/48 (37%), Gaps = 2/48 (4%)
Query: 382 PYECDTCGHGLSSKKSLDDHYRIHTGEKKYVCQQCGASFTQWASLFYH 429
PY C C SS SL H R K VC CG F S H
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSK--VCPVCGKEFRNTDSTLDH 118
>gnl|CDD|177300 PHA00732, PHA00732, hypothetical protein.
Length = 79
Score = 32.1 bits (73), Expect = 0.12
Identities = 27/84 (32%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 186 FVCSYCGNTYKNPKALTSHIRNSHTIHQKSICDVCGKEFRMKRQLKEHMAVHTTDRPFVC 245
F C CG T AL H R +HT+ + C VC K + R+L +H +
Sbjct: 2 FKCPICGFTTVTLFALKQHARRNHTLTK---CPVCNKSY---RRLNQHFYSQYDIEHLIY 55
Query: 246 NMCPSTFKLKKHLRQHYKVHLKME 269
ST+KL H+R K L++E
Sbjct: 56 CYLFSTYKLPYHVRLAIKRKLEVE 79
Score = 26.7 bits (59), Expect = 9.1
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 284 YQCNICGRVMNDRTNLKVHMR-NHTGEKKYICEVCGKGFVQWSSHYY 329
++C ICG LK H R NHT K C VC K + + + H+Y
Sbjct: 2 FKCPICGFTTVTLFALKQHARRNHTLTK---CPVCNKSYRRLNQHFY 45
>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 = 31.8 bits (73), Expect = 0.19
Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 22/69 (31%)
Query: 188 CSYCGNTYKNPKALTSHIRNSH----------------------TIHQKSICDVCGKEFR 225
C +C +T + H+ SH IH+ + C CGK+F+
Sbjct: 2 CLFCNHTSDTVEENLEHMFKSHGFFIPEREYLVDLEGLLNYLREKIHEGNECLYCGKQFK 61
Query: 226 MKRQLKEHM 234
L++HM
Sbjct: 62 SLEALRQHM 70
>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 = 34.0 bits (78), Expect = 0.25
Identities = 19/61 (31%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 413 CQQCGASFTQWASLFYHKFSHSETRNQVCSYCGKTYKNPNHLRSHLNTHTKKRLYVCETC 472
C CG FT +L Y + + S +C C K YK+P R H C C
Sbjct: 93 CTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDPLDRRFHAQPIA------CPRC 146
Query: 473 G 473
G
Sbjct: 147 G 147
Score = 29.3 bits (66), Expect = 6.9
Identities = 18/72 (25%), Positives = 23/72 (31%), Gaps = 14/72 (19%)
Query: 161 CETCGASFALWGSLNVHSYSHTNTQF----VCSYCGNTYKNPKALTSHIRNSHTIHQKSI 216
C CG F + +L Y NT +C C YK+P H Q
Sbjct: 93 CTHCGPRFTIIEAL---PYDRENTSMADFPLCPDCAKEYKDPLDRRFHA-------QPIA 142
Query: 217 CDVCGKEFRMKR 228
C CG +
Sbjct: 143 CPRCGPQLNFVS 154
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 33.5 bits (76), Expect = 0.36
Identities = 29/119 (24%), Positives = 43/119 (36%), Gaps = 23/119 (19%)
Query: 248 CPSTFKLKKHLR-QHYKV----------------HLKMENHLNRHTNI-HTGPGYQ---- 285
C S +LKKH + QH V L + L H N G++
Sbjct: 163 CGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPL 222
Query: 286 CNICGRVMNDRTNLKVHMRNHTGEKKYICEVCGKGFVQWSSHYYHMFTHSESRNFQCTV 344
C C D L+ H R E +IC++ G Q+ Y + H + ++ CT
Sbjct: 223 CIFCKIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTF 280
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 33.2 bits (75), Expect = 0.44
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 12/75 (16%)
Query: 444 CGKTYKNPNHLRSH-LNTHTKKRLYVCETCGKEFMKLELLKSHLTTHLAARPFICEFCSA 502
C K YKN N L+ H L+ H ++L+ E E M + K +P+ CE C
Sbjct: 357 CNKKYKNQNGLKYHMLHGHQNQKLH--ENPSPEKMNIFSAKD--------KPYRCEVCDK 406
Query: 503 GFKTKKHLSQHHRTH 517
+K L ++HR H
Sbjct: 407 RYKNLNGL-KYHRKH 420
Score = 30.5 bits (68), Expect = 2.9
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 10/83 (12%)
Query: 129 REHQCSV--CGKAFADITNMKVHMRIHTGEKKYVCETCGASFALWGSLNVHSYSHTNTQF 186
+ ++C V C K + + +K HM +H + + + E ++ +S + +
Sbjct: 348 KPYKCPVEGCNKKYKNQNGLKYHM-LHGHQNQKLHENPS-------PEKMNIFSAKDKPY 399
Query: 187 VCSYCGNTYKNPKALTSHIRNSH 209
C C YKN L H ++SH
Sbjct: 400 RCEVCDKRYKNLNGLKYHRKHSH 422
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 32.8 bits (76), Expect = 0.46
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 410 KYVCQQCGASFTQWA 424
YVCQ+CGA +W
Sbjct: 7 AYVCQECGAESPKWL 21
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 32.4 bits (74), Expect = 0.72
Identities = 11/24 (45%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 467 YVCETCGKEFMKLELLKSHL-TTH 489
YVC C EF ++ L H TTH
Sbjct: 74 YVCNVCMAEFSSMDQLAEHQRTTH 97
Score = 31.3 bits (71), Expect = 1.6
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 122 KAVHENVREHQCSVCGKAFADITNMKVHMR 151
KA N + C+VC F+ + + H R
Sbjct: 65 KATPINPSSYVCNVCMAEFSSMDQLAEHQR 94
>gnl|CDD|220553 pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN8. This PCI_Csn8
domain is conserved from plants to humans. It is a
signature protein motif found in components of CSN (COP9
signalosome). It functions as a structural scaffold for
subunit-subunit interactions within the complex and is a
key regulator of photomorphogenic development.
Length = 144
Score = 30.3 bits (69), Expect = 1.3
Identities = 10/63 (15%), Positives = 22/63 (34%), Gaps = 11/63 (17%)
Query: 521 DTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGE-KKYLSMRMSENISAQFA 579
+ + + + IRD + +A+ I + + L + E + +FA
Sbjct: 70 EDYTPFIAGLEDTIRDEIAALVGKAY---------SSISIDDLAELLGLSSDEEL-EKFA 119
Query: 580 VKH 582
K
Sbjct: 120 KKR 122
>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 = 27.3 bits (61), Expect = 1.6
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 440 VCSYCGKTYKNPNHLRSHLNTH 461
C CGK++ ++L+ HL TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 26.9 bits (60), Expect = 2.4
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 32 VCDTCGRTYKTKHSLNQHMKIH 53
C CG+++ K +L +H++ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 26.5 bits (59), Expect = 2.6
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 285 QCNICGRVMNDRTNLKVHMRNH 306
+C CG+ + ++NLK H+R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.8 bits (57), Expect = 5.8
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 538 QCKVCDRAFFDVYNLKLHMRIH 559
+C C ++F NLK H+R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.8 bits (57), Expect = 6.4
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 132 QCSVCGKAFADITNMKVHMRIH 153
+C CGK+F+ +N+K H+R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.0 bits (55), Expect = 9.7
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 216 ICDVCGKEFRMKRQLKEHMAVH 237
C CGK F K LK H+ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 27.0 bits (60), Expect = 1.7
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 340 FQCTVCDKKFATPAGLREHKRVH 362
++C C K F + + LREH R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.7 bits (59), Expect = 2.8
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 131 HQCSVCGKAFADITNMKVHMRIH 153
++C CGK F + ++ HMR H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.7 bits (59), Expect = 3.2
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 284 YQCNICGRVMNDRTNLKVHMRNH 306
Y+C CG+V ++ L+ HMR H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.3 bits (58), Expect = 4.1
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 537 FQCKVCDRAFFDVYNLKLHMRIH 559
++C C + F L+ HMR H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.3 bits (58), Expect = 4.4
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 32 VCDTCGRTYKTKHSLNQHMKIH 53
C CG+ +K+K +L +HM+ H
Sbjct: 2 RCPECGKVFKSKSALREHMRTH 23
Score = 25.9 bits (57), Expect = 5.3
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 217 CDVCGKEFRMKRQLKEHMAVH 237
C CGK F+ K L+EHM H
Sbjct: 3 CPECGKVFKSKSALREHMRTH 23
Score = 25.5 bits (56), Expect = 6.1
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 440 VCSYCGKTYKNPNHLRSHLNTH 461
C CGK +K+ + LR H+ TH
Sbjct: 2 RCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 28.1 bits (62), Expect = 1.8
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 283 GYQCNICGRVMNDRTNLKVHMRNHTGEKK 311
GY+C ICG + R ++ H+R H K
Sbjct: 5 GYECPICGEIYIKRKSMITHLRKHNTNLK 33
>gnl|CDD|223965 COG1034, NuoG, NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75
kD subunit (chain G) [Energy production and conversion].
Length = 693
Score = 30.8 bits (70), Expect = 2.5
Identities = 23/113 (20%), Positives = 33/113 (29%), Gaps = 37/113 (32%)
Query: 464 KRLYVCETCGKEFMK---------------LELLKSHLTTHLAARPFICEFCSAG----- 503
K + C T + M +E L L H P C C G
Sbjct: 57 KLVASCATPVTDGMVISTNSEEVKKAREGVMEFL---LINH----PLDCPVCDKGGECEL 109
Query: 504 ----FKTKKHLSQHH---RTHKRKDTLENHMKAVHEKIRDFQCKVCDRAFFDV 549
K S++ RTH+ KD ++ R C C R ++
Sbjct: 110 QDLAVKYGVSHSRYRETKRTHRDKD---LGPLVKYDMNRCILCTRCVRFCKEI 159
>gnl|CDD|237404 PRK13506, PRK13506, formate--tetrahydrofolate ligase; Provisional.
Length = 578
Score = 30.7 bits (70), Expect = 2.6
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 67 NINKKVSYKCPDCSVIVVSYSGFKSH 92
NI + S K PDC+V+V + K++
Sbjct: 326 NIKARQSGKAPDCAVLVATLRALKAN 351
>gnl|CDD|224908 COG1997, RPL43A, Ribosomal protein L37AE/L43A [Translation,
ribosomal structure and biogenesis].
Length = 89
Score = 28.1 bits (63), Expect = 3.0
Identities = 14/41 (34%), Positives = 17/41 (41%), Gaps = 10/41 (24%)
Query: 129 REHQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASFA 169
+H C CG+ RI TG + C CGA FA
Sbjct: 34 AKHVCPFCGR--------TTVKRIATG--IWKCRKCGAKFA 64
>gnl|CDD|192445 pfam10018, Med4, Vitamin-D-receptor interacting Mediator subunit 4.
Members of this family function as part of the Mediator
(Med) complex, which links DNA-bound transcriptional
regulators and the general transcription machinery,
particularly the RNA polymerase II enzyme. They play a
role in basal transcription by mediating activation or
repression according to the specific complement of
transcriptional regulators bound to the promoter.
Length = 176
Score = 29.7 bits (67), Expect = 3.1
Identities = 9/35 (25%), Positives = 16/35 (45%)
Query: 504 FKTKKHLSQHHRTHKRKDTLENHMKAVHEKIRDFQ 538
K L +H +R L ++++ EKI+D
Sbjct: 15 KSALKELEEHQENQQRILELRAEVESLDEKIKDIL 49
>gnl|CDD|214384 CHL00174, accD, acetyl-CoA carboxylase beta subunit; Reviewed.
Length = 296
Score = 29.9 bits (68), Expect = 3.3
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 20/53 (37%)
Query: 384 ECDTCGHGLSSKKSLDDHYRIHTGEKKYVCQQCGASFTQWASLFYH-KFSHSE 435
+C+ C GL+ KK L K +C+QCG YH K S S+
Sbjct: 40 QCENCY-GLNYKKFLK--------SKMNICEQCG----------YHLKMSSSD 73
>gnl|CDD|232966 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 454
Score = 30.1 bits (68), Expect = 3.4
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 410 KYVCQQCGASFTQW 423
K+VCQ CGA +W
Sbjct: 7 KFVCQHCGADSPKW 20
>gnl|CDD|179886 PRK04860, PRK04860, hypothetical protein; Provisional.
Length = 160
Score = 29.1 bits (66), Expect = 3.7
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 382 PYECDTCGHGLSSKKSLDDHYRIHTGEKKYVCQQCGA 418
PY C H L+ ++ H R+ GE Y C++CG
Sbjct: 119 PYRCKCQEHQLTVRR----HNRVVRGEAVYRCRRCGE 151
>gnl|CDD|223993 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 29.9 bits (68), Expect = 4.4
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 409 KKYVCQQCGASFTQWA 424
+VCQ+CG +W
Sbjct: 6 TAFVCQECGYVSPKWL 21
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 30.0 bits (68), Expect = 4.5
Identities = 10/41 (24%), Positives = 12/41 (29%), Gaps = 10/41 (24%)
Query: 413 CQQCGASFTQWASLFYHKFSHSETRNQVCSYCGKTYKNPNH 453
C C + T HK + C YCG P
Sbjct: 447 CPNCDSPLT------LHKATGQ----LRCHYCGYQEPIPQS 477
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 29.7 bits (67), Expect = 5.0
Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 412 VCQQCGASFTQWASLFYHKFSHSETRN-QVCSYCGKTYKNPNHLRSHLNTHTKKRLYVCE 470
C CG FT +L Y + ++ + +C +C K YK+P + R H C
Sbjct: 125 NCTNCGPRFTIIEALPYDR-ENTSMADFPLCPFCDKEYKDPLNRRFHAQP------IACP 177
Query: 471 TCG 473
CG
Sbjct: 178 KCG 180
>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 29.3 bits (66), Expect = 7.2
Identities = 27/114 (23%), Positives = 33/114 (28%), Gaps = 37/114 (32%)
Query: 118 VCHIKAVHENVREHQCSVC-GKAFADITNMKVHMRIHTG------EKKYVCETCGASFAL 170
C K V E +C VC G F+D + K + + C C
Sbjct: 7 ECGGKG-KIVVGEEECPVCHGTGFSDDFDPKGVANLSRETVDLFASFEIPCPKCR----- 60
Query: 171 WGSLNVHSYSHTNTQFVCSYCGNTYKNPKALTSHIRNSHTIHQKSICDVCGKEF 224
G V Y C CG T K LT CD+CG
Sbjct: 61 -GKGTVTVYDT------CPECGGT---GKVLT--------------CDICGDII 90
>gnl|CDD|132511 TIGR03471, HpnJ, hopanoid biosynthesis associated radical SAM
protein HpnJ. The sequences represented by this model
are members of the radical SAM superfamily of enzymes
(pfam04055). These enzymes utilize an iron-sulfur redox
cluster and S-adenosylmethionine to carry out diverse
radical mediated reactions. The member of this clade
from Acidithiobacillus ferrooxidans ATCC 23270
(AFE_0975) is found in the same locus as squalene-hopene
cyclase (SHC, TIGR01507) and other genes associated with
the biosynthesis of hopanoid natural products.
Similarly, in Ralstonia eutropha JMP134 (Reut_B4901)
this gene is adjacent to HpnAB, IspH and HpnH
(TIGR03470), although SHC itself is elsewhere in the
genome. Notably, this gene (here named HpnJ) and three
others form a conserved set (HpnIJKL) which occur in a
subset of all genomes containing the SHC enzyme. This
relationship was discerned using the method of partial
phylogenetic profiling. This group includes Zymomonas
mobilis, the organism where the initial hopanoid
biosynthesis locus was described consisting of the genes
HpnA-E and SHC (HpnF). Continuing past SHC are found a
phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and
another radical SAM enzyme (ZMO0874), HpnH. Although
discontinuous in Z. mobilis, we continue the gene symbol
sequence with HpnIJKL. One of the well-described
hopanoid intermediates is bacteriohopanetetrol. In the
conversion from hopene several reactions must occur in
the side chain for which a radical mechanism might be
reasonable. These include the four (presumably
anaerobic) hydroxylations and a methyl shift.
Length = 472
Score = 28.9 bits (65), Expect = 8.3
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 16/63 (25%)
Query: 236 VHTTDRPFVCNM--CPSTFKLKKHLRQHYKVHLKMENH-----LNRHTNIHTGPG--YQC 286
VH DRP + +M P + YK L +E + + + +++TG G +C
Sbjct: 158 VHNPDRPMIEDMDALPFVAPV-------YKRDLDIERYFIGYLKHPYISLYTGRGCPSKC 210
Query: 287 NIC 289
C
Sbjct: 211 TFC 213
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
0.324 0.133 0.434
Gapped
Lambda K H
0.267 0.0804 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,650,371
Number of extensions: 2504175
Number of successful extensions: 4053
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4001
Number of HSP's successfully gapped: 181
Length of query: 585
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 483
Effective length of database: 6,413,494
Effective search space: 3097717602
Effective search space used: 3097717602
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 62 (27.5 bits)