RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2466
(224 letters)
>gnl|CDD|212549 cd11711, GINS_A_Sld5, Alpha-helical domain of GINS complex protein
Sld5. Sld5 is a component of GINS tetrameric protein
complex, and within the complex Sld5 interacts with Psf1
via its N-terminal A-domain, and with Psf2 through a
combination of the A and B domains. Sld5 in Drosophila
is required for normal cell cycle progression and the
maintenance of genomic integrity. GINS is a complex of
four subunits (Sld5, Psf1, Psf2 and Psf3) that is
involved in both initiation and elongation stages of
eukaryotic chromosome replication. Besides being
essential for the maintenance of genomic integrity, GINS
plays a central role in coordinating DNA replication
with cell cycle checkpoints and is involved in cell
growth. The eukaryotic GINS subunits are homologous and
homologs are also found in the archaea; the complex is
not found in bacteria. The four subunits of the complex
consist of two domains each, termed the alpha-helical
(A) and beta-strand (B) domains. The A and B domains of
Sld5/Psf1 are permuted with respect to Psf1/Psf3.
Length = 119
Score = 129 bits (326), Expect = 2e-38
Identities = 56/120 (46%), Positives = 85/120 (70%), Gaps = 7/120 (5%)
Query: 30 VLETIKTAWKNEKLSPEILPNKVEYIDCMLEQIKQMEENIEKLR---KDDIRIEIHRMEI 86
LE +K AW NEK +PE+LP + E ++ +LEQI+Q EEN+E+L+ KDD+R+ +H ME+
Sbjct: 1 DLELLKRAWVNEKFAPELLPYQEELVERVLEQIEQQEENLEELKASEKDDLRLSLHEMEL 60
Query: 87 ERIRFVITSYLRVRIEKIEKFTLDIVQQDFERSSDNMYLSHDELKYAKSYLKSIDNHFDK 146
ERIRF++ SYLR R++KIEK+ L I+ ++ S LS +EL++AK Y + ++NH
Sbjct: 61 ERIRFLLRSYLRTRLQKIEKYALHILSEEELPS----RLSPEELEFAKRYAELLENHLKS 116
>gnl|CDD|227418 COG5086, COG5086, Uncharacterized conserved protein [Function
unknown].
Length = 218
Score = 79.6 bits (196), Expect = 3e-18
Identities = 54/208 (25%), Positives = 97/208 (46%), Gaps = 17/208 (8%)
Query: 26 SVQKVLETIKTAWKNEKLSPEILPNKVEYIDCMLEQIKQMEENIE----KLRKDDIRIEI 81
L + AW+NE+ +P +LP + ID L++I + E+++ K + +
Sbjct: 19 MSFPDLNDLILAWQNERSTPRLLPYALHLIDRFLDRISEQTEHVKIALGKSIAKNNESIL 78
Query: 82 HRMEIERIRFVITSYLRVRIEKIEKFTLDIVQQDFERSSDNMYLSHDELKY-AKSYLKSI 140
E+ER++FV+ SY+R R++KI+K + + + + LS EL Y K L I
Sbjct: 79 METELERVKFVVRSYIRTRLKKIDKNLYYDLSDE----NSLILLSGGELAYYEKHSLIYI 134
Query: 141 DNHFDKYLNMLPPNLRTLEENKKLI----KPDLNTYVFLRAGKDVANVYIRDMSENKEDE 196
D D L + P + + +PD N +VF +D+ + E + E
Sbjct: 135 DLLKDSDLYVTPQKFHKVHDFVGFYCMTDEPDWNKFVFGAVNEDLQEND--TVGEKELLE 192
Query: 197 FVLDEGSQHILPYESIAEFVKNNDVQLL 224
L +G + Y+ I +F++ N+V L+
Sbjct: 193 --LFKGDFFVARYDVIMDFLRRNEVILI 218
>gnl|CDD|212547 cd11581, GINS_A, Alpha-helical domain of GINS complex proteins;
Sld5, Psf1, Psf2 and Psf3. The GINS complex is involved
in both initiation and elongation stages of eukaryotic
chromosome replication, with GINS being the component
that most likely serves as the replicative helicase that
unwinds duplex DNA ahead of the moving replication fork.
In eukaryotes, GINS is a tetrameric arrangement of four
subunits Sld5, Psf1, Psf2 and Psf3. The GINS complex has
been found in eukaryotes and archaea, but not in
bacteria. The four subunits of the complex are
homologous and consist of two domains each, termed the
alpha-helical (A) and beta-strand (B) domains. The A and
B domains of Sld5/Psf1 are permuted with respect to
Psf1/Psf3.
Length = 103
Score = 45.9 bits (109), Expect = 6e-07
Identities = 22/106 (20%), Positives = 53/106 (50%), Gaps = 9/106 (8%)
Query: 37 AWKNEKLSPEILPNKVEYIDCMLEQIKQMEENIEKLRKDDIRIEIHRMEIERIRFVITSY 96
A NE+ S +LP ++++ + E + ++ + ++ + + +E+ IR ++ +Y
Sbjct: 7 AIHNERKSENLLPPPPDFMEEVKELLHRLSKRQRSETQEILEHRLKILELSYIRDLLKTY 66
Query: 97 LRVRIEKIEKFTLDIVQQDFERSSDNMYLSHDELKYAKSYLKSIDN 142
L R++KI + +F S+ L+ +E+ Y ++Y K +
Sbjct: 67 LNSRLDKIRDLS-----PEFLPSN----LTEEEIGYFQTYWKEVAE 103
>gnl|CDD|236078 PRK07726, PRK07726, DNA topoisomerase III; Provisional.
Length = 658
Score = 34.8 bits (81), Expect = 0.031
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 8/57 (14%)
Query: 108 TLDIVQQDFERS-------SDNMYLSHDELKYAKSYLKSIDNHFDKYLNMLPPNLRT 157
TLDI Q +E +D+ YL D + L +I + D YL + PP L
Sbjct: 301 TLDIAQSLYETHKLITYPRTDSRYLPEDMVATLPEVLNAI-SKVDPYLLLAPPVLDP 356
>gnl|CDD|218810 pfam05916, Sld5, GINS complex protein. The eukaryotic GINS complex
is essential for the initiation and elongation phases of
DNA replication. It consists of four paralogous protein
subunits (Sld5, Psf1, Psf2 and Psf3), all of which are
included in this family. The GINS complex is conserved
from yeast to humans, and has been shown in human to
bind directly to DNA primase.
Length = 106
Score = 30.6 bits (69), Expect = 0.22
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 1/71 (1%)
Query: 60 EQIKQMEENIEKLRKDDIRIEIHRMEIERIRFVITSYLRVRIEKIEKFTLDIVQQDFERS 119
+ + + KL + +E+ R + ++ YLR+R+ KIEK + E
Sbjct: 37 PKNVDTKLQLSKLPPYFYELAELLLELLRNKRLLREYLRIRLRKIEKLAWHL-AGGNESE 95
Query: 120 SDNMYLSHDEL 130
LS +E
Sbjct: 96 DLLDNLSEEER 106
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil motif
at the N terminus region. Yeast cells with mutant Atg14
are defective not only in autophagy but also in sorting
of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically required
for the function of Apg6/Vps30p through the autophagic
pathway. There are 17 auto-phagosomal component proteins
which are categorized into six functional units, one of
which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The
AS-PI3K complex and the Atg2-Atg18 complex are essential
for nucleation, and the specific function of the AS-PI3K
apparently is to produce phosphatidylinositol
3-phosphate (PtdIns(3)P) at the pre-autophagosomal
structure (PAS). The localisation of this complex at the
PAS is controlled by Atg14. Autophagy mediates the
cellular response to nutrient deprivation, protein
aggregation, and pathogen invasion in humans, and
malfunction of autophagy has been implicated in multiple
human diseases including cancer. This effect seems to be
mediated through direct interaction of the human Atg14
with Beclin 1 in the human phosphatidylinositol 3-kinase
class III complex.
Length = 307
Score = 30.8 bits (70), Expect = 0.45
Identities = 27/114 (23%), Positives = 54/114 (47%), Gaps = 8/114 (7%)
Query: 27 VQKVLE---TIKTAWKNEKLSPEILPNKVEYIDCMLEQIKQMEENIEKLRKDDIRIEIHR 83
V++ LE + L E+ K E ++ + +I Q++E IE+ R+ RIE +
Sbjct: 43 VEEALEGATNEDGKLAADLLKLEVA-RKKERLNQIRARISQLKEEIEQKRE---RIEELK 98
Query: 84 MEIERIRFVITSYLRVRIEKIEKFTLDIVQQDFERSSDNMYLSHDELKYAKSYL 137
+ + R ++S ++EK L+ +Q + +R+ + H L +S+L
Sbjct: 99 RALAQRRSDLSSA-SYQLEKRRASQLEKLQDEIKRTRSKLNALHSLLAEKRSFL 151
>gnl|CDD|217039 pfam02446, Glyco_hydro_77, 4-alpha-glucanotransferase. These
enzymes EC:2.4.1.25 transfer a segment of a
(1,4)-alpha-D-glucan to a new 4-position in an acceptor,
which may be glucose or (1,4)-alpha-D-glucan.
Length = 493
Score = 30.8 bits (70), Expect = 0.64
Identities = 23/148 (15%), Positives = 52/148 (35%), Gaps = 25/148 (16%)
Query: 77 IRIEIHRMEI--ERIRFVITSYLRVRIEKIEKFTLDIVQQDFERSSDNMYLSHDELKYAK 134
+ E M I E + + + ++ + I++ F+ S+N +L H+ + +
Sbjct: 320 LLEESGEMLIIGEDLGTIPEEVRELL-DEFGIPGMKILRFAFDWDSENPFLPHNYPENSV 378
Query: 135 SYLKSIDN----------------HFDKYLNMLPPNLRTLEENKKLIKPDLNTYVFLRAG 178
Y + DN +F +YL + E + L++ ++
Sbjct: 379 VYTGTHDNDTLRGWWEELLPEEKKYFAEYLGLPYTETEEEEVHWALLRLAHSSVSRF--- 435
Query: 179 KDVANVYIRDMSENKEDEFVLDEGSQHI 206
A ++D+ + L E +I
Sbjct: 436 ---AINPMQDLLALGPELVSLQEERINI 460
>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional.
Length = 1021
Score = 30.1 bits (67), Expect = 1.0
Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 19/77 (24%)
Query: 67 ENIEKLRKDDIRIEIHRMEIERIRFVITSYLRVRIEKIEKFTLDIVQQD-FERSSDNMYL 125
E IE+ R + R+E R+E +R+ R R++++E+ +D +++D E++ N Y
Sbjct: 477 ERIERERLERERLERERLERDRLE-------RDRLDRLERERVDRLERDRLEKARRNSY- 528
Query: 126 SHDELKYAKSYLKSIDN 142
+LK ++N
Sbjct: 529 ----------FLKGMEN 535
>gnl|CDD|217563 pfam03446, NAD_binding_2, NAD binding domain of 6-phosphogluconate
dehydrogenase. The NAD binding domain of
6-phosphogluconate dehydrogenase adopts a Rossmann fold.
Length = 163
Score = 29.0 bits (66), Expect = 1.1
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 174 FLRAGKDVANVYIRDMSENKEDEFVLDEGSQHILPYESIAEFVKNNDV 221
L+AG V VY + + K +E V ++ + S AEFV + DV
Sbjct: 19 LLKAGYTVT-VY--NRTPEKVEELV----AEGAVGAASPAEFVASADV 59
>gnl|CDD|132370 TIGR03327, AMP_phos, AMP phosphorylase. This enzyme family is
found, so far, strictly in the Archaea, and only in
those with a type III Rubisco enzyme. Most of the
members previously were annotated as thymidine
phosphorylase, or DeoA. The AMP metabolized by this
enzyme may be produced by ADP-dependent sugar kinases.
Length = 500
Score = 29.7 bits (67), Expect = 1.2
Identities = 27/103 (26%), Positives = 48/103 (46%), Gaps = 20/103 (19%)
Query: 28 QKVLETIKTAWKNE-KLSPEILPNKVEYIDCMLEQIKQMEENIEKLRKDDIRIEIHRMEI 86
+VLE + + +++P P VEYI K+M+ EKL KD+IR + +
Sbjct: 63 HEVLEELGISEGEVVEVTPAEKPESVEYIK------KKMDG--EKLTKDEIRAIVADIVD 114
Query: 87 ERIR------FVITSYLR-VRIEKIEKFTLDIV----QQDFER 118
+++ FV SY+ + +++IE T + F+R
Sbjct: 115 DKLSDIEISAFVTASYINGMDMDEIEWLTRAMAETGDMLSFDR 157
>gnl|CDD|215615 PLN03180, PLN03180, reversibly glycosylated polypeptide;
Provisional.
Length = 346
Score = 29.3 bits (66), Expect = 1.6
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 12/55 (21%)
Query: 31 LETIKTAWKNEKLSPEILP---------NKVEYIDCMLEQIKQMEENIEKLRKDD 76
+K +K EI+P V DC +E KQ++ EKL K D
Sbjct: 271 FVNLKKEYKGIFWQEEIIPFFQSVRLPKEAVTVEDCYIELAKQVK---EKLGKVD 322
>gnl|CDD|218236 pfam04735, Baculo_helicase, Baculovirus DNA helicase.
Length = 1173
Score = 29.5 bits (67), Expect = 1.6
Identities = 17/110 (15%), Positives = 41/110 (37%), Gaps = 11/110 (10%)
Query: 48 LPNKVEYIDCMLEQIKQMEENIEKLRKDDIRIEIHRMEI-ERIRFVITSYLRVRIEKIEK 106
L + Y +L+ + +E N E + +R +I E + + RI+ ++
Sbjct: 691 LYSNKLYSTTLLDSVDSLETNSELVENYAEFFYKNRKKIIEYLHRKLD-----RIDFVDT 745
Query: 107 F-----TLDIVQQDFERSSDNMYLSHDELKYAKSYLKSIDNHFDKYLNML 151
+ + + + ++ D+ +K+ H+ K L +L
Sbjct: 746 LIDELSDPERFLEMLQNAVNDDSDPDDKKYEQNRIVKNFYLHYAKTLKIL 795
>gnl|CDD|184731 PRK14536, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 490
Score = 29.1 bits (65), Expect = 2.2
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 45 PEILPNKVEYIDCMLEQIKQMEEN 68
P I+ N E+I M+ IK++E
Sbjct: 119 PSIVCNATEHIQDMIALIKRLEAR 142
>gnl|CDD|223779 COG0707, MurG, UDP-N-acetylglucosamine:LPS N-acetylglucosamine
transferase [Cell envelope biogenesis, outer membrane].
Length = 357
Score = 28.4 bits (64), Expect = 2.8
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 29 KVLETIKTAW--KNEKLSPEILPNKVEYIDCMLEQIKQMEENIEKLRKDDIRIEIHRMEI 86
K LE A + +L+PE L + + E++K M EN +KL K D I + +
Sbjct: 293 KFLEKAGAALVIRQSELTPEKLAELILRLLSNPEKLKAMAENAKKLGKPDAAERIADLLL 352
Query: 87 ERIRF 91
+
Sbjct: 353 ALAKK 357
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 28.9 bits (65), Expect = 2.9
Identities = 17/97 (17%), Positives = 38/97 (39%), Gaps = 1/97 (1%)
Query: 10 DIIETEPAANEDENCLSVQKVLETIKTAWKNEKLSPEILPNKVEYIDCMLEQIKQMEENI 69
E E A ED+ E + LS I E ++ + ++++ E+ +
Sbjct: 1059 ITAEEEEGAEEDDEADDEDDEEELGAAVSYDYLLSMPIWSLTKEKVEKLNAELEKKEKEL 1118
Query: 70 EKLRKDDIRIEIHRMEIERIRFVITSYLRVRIEKIEK 106
EKL+ ++ ++++ + V ++I K
Sbjct: 1119 EKLKNTTP-KDMWLEDLDKFEEALEEQEEVEEKEIAK 1154
>gnl|CDD|129951 TIGR00873, gnd, 6-phosphogluconate dehydrogenase (decarboxylating).
This model does not specify whether the cofactor is
NADP only (EC 1.1.1.44), NAD only, or both. The model
does not assign an EC number for that reason [Energy
metabolism, Pentose phosphate pathway].
Length = 467
Score = 28.5 bits (64), Expect = 3.2
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 183 NVYIRDMSENKEDEFVLDEGS-QHILPYESIAEFVK 217
V + + + K DEF+ + + I+ SI EFV+
Sbjct: 24 TVSVYNRTPEKTDEFLAEHAKGKKIVGAYSIEEFVQ 59
>gnl|CDD|240354 PTZ00310, PTZ00310, AMP deaminase; Provisional.
Length = 1453
Score = 28.6 bits (64), Expect = 3.7
Identities = 26/87 (29%), Positives = 37/87 (42%), Gaps = 12/87 (13%)
Query: 114 QDFERSSDNMYLSHDELKYA--KSYLKSIDNHFDKYLNMLPPNLRTLEENKKLIKPD--L 169
Q F + L+ D+L + + DN KY M P+LR+L L+K D +
Sbjct: 890 QLFSKYGITPNLTVDQLNVQADHTLFERFDNFNSKYNPMENPDLRSL-----LLKTDNFM 944
Query: 170 NTYVFLRAGKDVANVYIRD---MSENK 193
F KDV Y RD +EN+
Sbjct: 945 KGRYFAELIKDVFEQYSRDRFTYAENR 971
>gnl|CDD|226206 COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and
metabolism].
Length = 433
Score = 28.3 bits (63), Expect = 3.8
Identities = 23/115 (20%), Positives = 38/115 (33%), Gaps = 14/115 (12%)
Query: 99 VRIEKIEKFTLDIVQQDFERSSDNMYLSHDELKYAKSYLKSIDNHFDKYLNMLPPNLRTL 158
VRIE +K + E+ S L LK ++ I + + L ++
Sbjct: 153 VRIETHDKVLFTQQANEGEQESPLTVLKRLTLKEILDFVNEIP------FDAIKFILDSI 206
Query: 159 EENKKLIKPDLNTYVFLRAGKDVANVYIRDMSENKEDEFVLDEGSQHILPYESIA 213
N L + L+ L G + + E + + S IL S A
Sbjct: 207 RLNCALSQEGLSGKWGLHIGATLE--------DQIERGLLAKDLSNSILIRTSAA 253
>gnl|CDD|223439 COG0362, Gnd, 6-phosphogluconate dehydrogenase [Carbohydrate
transport and metabolism].
Length = 473
Score = 28.0 bits (63), Expect = 4.4
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 184 VYIRDMSENKEDEFVLDEGS-QHILPYESIAEFVKN 218
VY R + K DEF+ + ++I+P SI EFV +
Sbjct: 31 VYNR--TTEKTDEFLAERAKGKNIVPAYSIEEFVAS 64
>gnl|CDD|178955 PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit;
Reviewed.
Length = 200
Score = 27.4 bits (62), Expect = 5.0
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 18/62 (29%)
Query: 79 IEIHRMEIERIRFVITSYLRVR----IEKIEKFTLDIVQQDFERSSDNMYLSHDELKYAK 134
IEIH EI +++ + L +EKIEK D +R DN ++S +E AK
Sbjct: 140 IEIHAREILKLKKRLNEILAEHTGQPLEKIEK--------DTDR--DN-FMSAEE---AK 185
Query: 135 SY 136
Y
Sbjct: 186 EY 187
>gnl|CDD|222253 pfam13597, NRDD, Anaerobic ribonucleoside-triphosphate reductase.
Length = 542
Score = 27.5 bits (62), Expect = 5.6
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 6/45 (13%)
Query: 100 RIEKIEKFTLDIVQQDFERSSDNMYLSHDELKYAKSYLKSIDNHF 144
E+++++ L ++ E ++ L + K YL +DNHF
Sbjct: 300 FFEELDRYDL-AKRKLIEE-----LIAAGLLPFYKQYLWRLDNHF 338
>gnl|CDD|236453 PRK09287, PRK09287, 6-phosphogluconate dehydrogenase; Validated.
Length = 459
Score = 27.8 bits (63), Expect = 5.8
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 184 VYIRDMSENKEDEFVLDEGS-QHILPYESIAEFVK 217
VY R + K DEF+ +EG + I+P ++ EFV
Sbjct: 18 VYNR--TPEKTDEFLAEEGKGKKIVPAYTLEEFVA 50
>gnl|CDD|152481 pfam12046, DUF3529, Protein of unknown function (DUF3529). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 176 to 190 amino acids
in length.
Length = 173
Score = 26.8 bits (60), Expect = 6.3
Identities = 8/32 (25%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 60 EQIK-QMEENIEKLRKDDIRIEIHRMEIERIR 90
EQ++ ++ E + D+R+ HR E+ +
Sbjct: 134 EQVELKLVE-ADDDGGSDLRVRAHRDELIELA 164
>gnl|CDD|219308 pfam07146, DUF1389, Protein of unknown function (DUF1389). This
family consists of several hypothetical bacterial
proteins which seem to be specific to Chlamydia
pneumoniae. Members of this family are typically around
400 residues in length. The function of this family is
unknown.
Length = 311
Score = 27.3 bits (61), Expect = 6.9
Identities = 11/48 (22%), Positives = 21/48 (43%)
Query: 70 EKLRKDDIRIEIHRMEIERIRFVITSYLRVRIEKIEKFTLDIVQQDFE 117
+ L ++R+ I + + + EK+E F +D +Q D E
Sbjct: 60 QNLTIQELRLLIDGLRNISSSKSLNNLSPKLREKLEDFGIDRLQSDCE 107
>gnl|CDD|221056 pfam11277, Med24_N, Mediator complex subunit 24 N-terminal. This
subunit of the Mediator complex appears to be conserved
only from insects to humans. It is essential for correct
retinal development in fish. Subunit composition of the
mediator contributes to the control of differentiation
in the vertebrate CNS as there are divergent functions
of the mediator subunits Crsp34/Med27, Trap100/Med24,
and Crsp150/Med14.
Length = 991
Score = 27.5 bits (61), Expect = 7.0
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 22 ENCLSVQKVLETIKTAWKNEKLSPE 46
E CLS+ + + AW+NE LS E
Sbjct: 576 EICLSIPAAILEVLNAWENEVLSSE 600
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 27.4 bits (62), Expect = 7.4
Identities = 13/47 (27%), Positives = 27/47 (57%), Gaps = 6/47 (12%)
Query: 28 QKVLETIKTAWKNEKLSPEILPNKVEYIDCMLEQIKQMEENIEKLRK 74
+ +L+ + K P LP +VE + LE++K++E+ +E+L+
Sbjct: 700 EALLKELAALLKA---KPSELPERVEAL---LEELKELEKELEQLKA 740
>gnl|CDD|179478 PRK02816, PRK02816, phycocyanobilin:ferredoxin oxidoreductase;
Validated.
Length = 243
Score = 26.8 bits (60), Expect = 8.4
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 27 VQKVLETIKTAW-KNEKLSPEILPNKVEYIDCMLE 60
+ ++ E I++ W + LSP LP + YI+ LE
Sbjct: 16 ILQLAERIRSHWQQLLDLSPYALPPDLGYIEGKLE 50
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 27.2 bits (61), Expect = 9.0
Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 3/80 (3%)
Query: 95 SYLRVRIEKIEKFTLDIVQQDFERSSDNMYLSHDELKYAKSYLKSIDNHFDKYLNMLP-P 153
SYLR R+ + + L ++ + + K YLK + F + ++
Sbjct: 446 SYLRRRLRNLSPYELQMLAFAIREGELLEGVLEELRSLVKEYLKDEE--FLEKISESGDL 503
Query: 154 NLRTLEENKKLIKPDLNTYV 173
LR E ++ PD+ TY+
Sbjct: 504 VLRKEEGKYYIVIPDVTTYI 523
>gnl|CDD|201316 pfam00574, CLP_protease, Clp protease. The Clp protease has an
active site catalytic triad. In E. coli Clp protease,
ser-111, his-136 and asp-185 form the catalytic triad.
Cyanophora parodoxa clpP-B has lost all of these active
site residues and is therefore inactive. Some members
contain one or two large insertions.
Length = 182
Score = 26.7 bits (60), Expect = 9.0
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 18/62 (29%)
Query: 79 IEIHRMEIERIRFVITSYLRVR----IEKIEKFTLDIVQQDFERSSDNMYLSHDELKYAK 134
IEI EI +IR + +EKIEK D +R + ++S +E AK
Sbjct: 125 IEIQAEEILKIRERLNEIYAEHTGQPLEKIEK--------DLDR---DTFMSAEE---AK 170
Query: 135 SY 136
Y
Sbjct: 171 EY 172
>gnl|CDD|222785 PHA00368, PHA00368, internal virion protein D.
Length = 1315
Score = 27.1 bits (60), Expect = 9.0
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 9/56 (16%)
Query: 71 KLRKDDIRIEIHR---MEIERIRFVITSYLRVRIEKIEKFTLDIVQQDFERSSDNM 123
K+ ++ R EI+R + IER L+ + K E+ +DI+++ F+ + M
Sbjct: 587 KMSREAARQEIYRRVALAIER------PELQANLTKAERKVMDILKEHFDLKREMM 636
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 0.135 0.373
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,672,584
Number of extensions: 1156663
Number of successful extensions: 1799
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1765
Number of HSP's successfully gapped: 171
Length of query: 224
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 131
Effective length of database: 6,812,680
Effective search space: 892461080
Effective search space used: 892461080
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 (25.7 bits)