RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2363
(156 letters)
>gnl|CDD|188067 TIGR00590, pcna, proliferating cell nuclear antigen (pcna). All
proteins in this family for which functions are known
form sliding DNA clamps that are used in DNA replication
processes. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 259
Score = 185 bits (471), Expect = 1e-59
Identities = 83/155 (53%), Positives = 102/155 (65%), Gaps = 34/155 (21%)
Query: 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVE 60
MPS EFARICRDL+QF +S+ ISCTKEGVKFSA GDIGS N+KL QT + DK
Sbjct: 139 MPSSEFARICRDLSQFSDSVVISCTKEGVKFSAKGDIGSGNVKLKQTSDTDK-------- 190
Query: 61 MQEPVSLNFACRYLLNFAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQ 120
EEEAVT+EM++PV+L FA +YL F KA PLS++
Sbjct: 191 --------------------------EEEAVTIEMKQPVTLTFAIKYLNLFTKATPLSDR 224
Query: 121 VCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD 155
V LSMS DVPLVVE+KI D+G +R++LAPKIE ++
Sbjct: 225 VTLSMSNDVPLVVEYKIKDMGFLRFFLAPKIEDEE 259
>gnl|CDD|202372 pfam02747, PCNA_C, Proliferating cell nuclear antigen, C-terminal
domain. N-terminal and C-terminal domains of PCNA are
topologically identical. Three PCNA molecules are
tightly associated to form a closed ring encircling
duplex DNA.
Length = 128
Score = 180 bits (458), Expect = 2e-59
Identities = 80/150 (53%), Positives = 96/150 (64%), Gaps = 34/150 (22%)
Query: 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVE 60
MPS EFARICRDL+Q G+S+ ISCTKEGVKFSA+GDIG+ NIKL QT +VDK
Sbjct: 13 MPSAEFARICRDLSQIGDSVVISCTKEGVKFSASGDIGTGNIKLKQTTDVDK-------- 64
Query: 61 MQEPVSLNFACRYLLNFAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQ 120
EEA+ +EM EPV+L FA RYL +F KA PLS
Sbjct: 65 --------------------------PEEAIIIEMNEPVTLTFALRYLNSFTKATPLSPT 98
Query: 121 VCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 150
V +SMS ++PLVVE+KI D+G +RYYLAPK
Sbjct: 99 VTISMSSELPLVVEYKIADMGLLRYYLAPK 128
>gnl|CDD|177688 PLN00057, PLN00057, proliferating cell nuclear antigen;
Provisional.
Length = 263
Score = 169 bits (431), Expect = 1e-53
Identities = 76/156 (48%), Positives = 96/156 (61%), Gaps = 34/156 (21%)
Query: 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVE 60
MPS EF RIC+DL+ G+++ IS TKEGVKFS +GDIG+ANI L Q VDK
Sbjct: 139 MPSAEFQRICKDLSSIGDTVVISVTKEGVKFSTSGDIGTANIVLRQNTTVDK-------- 190
Query: 61 MQEPVSLNFACRYLLNFAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQ 120
EE +EMQEPVSL FA RYL +F KA PLS+
Sbjct: 191 --------------------------PEEKTVIEMQEPVSLTFALRYLNSFTKATPLSDT 224
Query: 121 VCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDDN 156
V LS+S ++P+VVE+KI ++G+IRYYLAPKIE D++
Sbjct: 225 VTLSLSKELPVVVEYKIAEMGYIRYYLAPKIEEDED 260
>gnl|CDD|238322 cd00577, PCNA, Proliferating Cell Nuclear Antigen (PCNA) domain
found in eukaryotes and archaea. These polymerase
processivity factors play a role in DNA replication and
repair. PCNA encircles duplex DNA in its central
cavity, providing a DNA-bound platform for the
attachment of the polymerase. The trimeric PCNA ring is
structurally similar to the dimeric ring formed by the
DNA polymerase processivity factors in bacteria (beta
subunit DNA polymerase III holoenzyme) and in
bacteriophages (catalytic subunits in T4 and RB69). This
structural correspondence further substantiates the
mechanistic connection between eukaryotic and
prokaryotic DNA replication that has been suggested on
biochemical grounds. PCNA is also involved with
proteins involved in cell cycle processes such as DNA
repair and apoptosis. Many of these proteins contain a
highly conserved motif known as the PIP-box (PCNA
interacting protein box) which contains the sequence
Qxx[LIM]xxF[FY]. .
Length = 248
Score = 124 bits (314), Expect = 3e-36
Identities = 54/152 (35%), Positives = 73/152 (48%), Gaps = 38/152 (25%)
Query: 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVE 60
+PS E I RDL +S+ IS +K+G KFSA G++G A++ L +
Sbjct: 135 LPSDELKDIVRDLESISDSVTISASKDGFKFSAEGELGGASVTLLPKDSDLLVTI----- 189
Query: 61 MQEPVSLNFACRYLLNFAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQ 120
E EPVS ++ +YL +F KAAPLS++
Sbjct: 190 ---------------------------------ECSEPVSSTYSLKYLKDFTKAAPLSDK 216
Query: 121 VCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 152
V LS D PL +EFKI D GH+ +YLAPKIE
Sbjct: 217 VTLSFGSDGPLSLEFKIADGGHLTFYLAPKIE 248
>gnl|CDD|240275 PTZ00113, PTZ00113, proliferating cell nuclear antigen;
Provisional.
Length = 275
Score = 80.6 bits (199), Expect = 5e-19
Identities = 39/164 (23%), Positives = 78/164 (47%), Gaps = 44/164 (26%)
Query: 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVE 60
+ S E ICR + +F +++ I +KF+ GD+G + L
Sbjct: 141 LSSKELTNICRQMNEFSDTVKIEIDSNSIKFTTQGDLGDGEVVL---------------- 184
Query: 61 MQEPVSLNFACRYLLNFAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQ 120
K P +++++ VT+++++P+ ++A +YL FAK+ LS+
Sbjct: 185 ------------------KPRPPTSEDDCGVTIKVRKPIKQSYATKYLNMFAKSGCLSDV 226
Query: 121 VCLSMSLDVPLVVEFKIDD----------IGHIRYYLAPKIESD 154
V L +S + P+ V+++I D +G ++++LAPK++ D
Sbjct: 227 VTLGLSDNRPIEVKYEIKDTSPDARHTHKLGEVKFFLAPKMDDD 270
>gnl|CDD|234903 PRK01115, PRK01115, DNA polymerase sliding clamp; Validated.
Length = 247
Score = 58.3 bits (142), Expect = 5e-11
Identities = 28/152 (18%), Positives = 54/152 (35%), Gaps = 40/152 (26%)
Query: 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVE 60
+ + +D + I + ++ A G+ G ++
Sbjct: 136 ILGDDLKDAIKDAELVSDHIELEADEDKFYIEAEGE-GEDEVE----------------- 177
Query: 61 MQEPVSLNFACRYLLNFAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQ 120
LS + + ++EP +++ YL + KA S++
Sbjct: 178 ----------------------LSLDSGPLIELSVEEPAKSSYSLDYLKDMVKATSASDE 215
Query: 121 VCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 152
V + D+PL +EF+I G + Y LAP+IE
Sbjct: 216 VTIEFGSDMPLKLEFEIAGGGKVTYLLAPRIE 247
>gnl|CDD|185661 PTZ00483, PTZ00483, proliferating cell nuclear antigen;
Provisional.
Length = 264
Score = 57.2 bits (138), Expect = 2e-10
Identities = 41/152 (26%), Positives = 66/152 (43%), Gaps = 33/152 (21%)
Query: 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVE 60
M S +F + L G++++IS K+ ++ G+ IK ++ + D + V V
Sbjct: 145 MNSKKFQEFAKYLHSIGDTVSISMKKDEMRLETEGE----GIKASKQFHNDVGD--VRVT 198
Query: 61 MQEPVSLNFACRYLLNFAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQ 120
E +S FA RYL+ F+KA L+ +E ++ + P+S+ F NF
Sbjct: 199 STESLSQEFATRYLVLFSKATSLA--DEVSINLSAGIPLSVKF------NFKD------- 243
Query: 121 VCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 152
PL D I +YLAP IE
Sbjct: 244 ---------PLTDL---QDSSFINFYLAPNIE 263
>gnl|CDD|177619 PHA03383, PHA03383, PCNA-like protein; Provisional.
Length = 262
Score = 50.3 bits (120), Expect = 5e-08
Identities = 30/153 (19%), Positives = 63/153 (41%), Gaps = 37/153 (24%)
Query: 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVE 60
+PS F R+CRD++ + + I TK+G + S D
Sbjct: 146 LPSNYFQRLCRDMSNITDDLEI--TKKGKEVSFRSDYTCVT------------------- 184
Query: 61 MQEPVSLNFACRYLLNFAKAAPLSNQEEEAVTVEMQEP-VSLNFACRYLLNFAKAAPLSN 119
+FA + + + P + F+ +YL +F KA+ +S+
Sbjct: 185 ---------------DFASQETIIGDSDNGQITCNESPDYTGKFSLKYLTSFTKASGMSS 229
Query: 120 QVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 152
V + + PL++++ + +G++++ +APK+
Sbjct: 230 SVEIYLKESNPLILKYNVGSLGNLKFVIAPKVS 262
>gnl|CDD|223665 COG0592, DnaN, DNA polymerase sliding clamp subunit (PCNA homolog)
[DNA replication, recombination, and repair].
Length = 364
Score = 32.6 bits (75), Expect = 0.064
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 94 EMQEPVSLNFACRYLLNFAKAAPLS-NQVCLSMSLDVPLVVEFKIDDI-----GHIRYYL 147
E++E + ++ YL + K L+ +V LS+ D P E +ID I + L
Sbjct: 260 ELKEALKRVYSLSYLKDRGKKLSLADGEVKLSLGNDEPGKAEEEIDVGYTGEELKIGFNL 319
Query: 148 APKIESDDN 156
A ++
Sbjct: 320 AYLLDVLKA 328
>gnl|CDD|236901 PRK11360, PRK11360, sensory histidine kinase AtoS; Provisional.
Length = 607
Score = 30.3 bits (69), Expect = 0.42
Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 13/74 (17%)
Query: 62 QEPVSLNFACRYLLNFAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQV 121
+E LN LL F++ Q PVSLN +L + A + +V
Sbjct: 433 REVDRLNKVIDQLLEFSRPRESQWQ-----------PVSLNALVEEVLQLFQTAGVQARV 481
Query: 122 CLSMSLD--VPLVV 133
LD +P +
Sbjct: 482 DFETELDNELPPIW 495
>gnl|CDD|184944 PRK14982, PRK14982, acyl-ACP reductase; Provisional.
Length = 340
Score = 30.0 bits (68), Expect = 0.42
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 9 ICRDLAQFGESINISCTKEGVKF-SATGDIGSA 40
ICR + Q + I +K V ATGDIGSA
Sbjct: 138 ICRQVEQNAPRLGIDLSKATVAVVGATGDIGSA 170
>gnl|CDD|188573 TIGR04058, AcACP_reductase, long-chain fatty acyl-ACP reductase
(aldehyde-forming). This enzyme, found in
cyanobacteria, reduces a long-chain (mainly C16 or C18)
fatty acyl ACP ester to its corresponding fatty
aldehyde, releasing the acyl carrier protein (ACP).
NADPH or NADH is the reductant for this reaction. This
enzyme may be distantly related to the short-chain
dehydrogenase or reductase (SDR) family (pfam00106). The
purpose of this reaction is in the first step of alkane
biosynthesis (GenProp0942) [Central intermediary
metabolism, Other].
Length = 339
Score = 29.7 bits (67), Expect = 0.63
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 9 ICRDLAQFGESINISCTKEGVKF-SATGDIGSA 40
ICR + Q + I + V ATGDIGSA
Sbjct: 138 ICRQVEQAAPRLGIDLAQATVAVVGATGDIGSA 170
>gnl|CDD|235285 PRK04335, PRK04335, cell division protein ZipA; Provisional.
Length = 313
Score = 27.8 bits (62), Expect = 2.6
Identities = 12/52 (23%), Positives = 18/52 (34%)
Query: 51 DKEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQEEEAVTVEMQEPVSLN 102
+ E V +++EP AK Q EE +E+ EP
Sbjct: 119 QPQPEKVEPQVEEPRDEEVLEEPEPVAAKVPMAEVQPEEETEIEVDEPEEPK 170
>gnl|CDD|188511 TIGR03996, mycofact_OYE_1, mycofactocin system FadH/OYE family
oxidoreductase 1. The yeast protein called old yellow
enzyme and FadH from Escherichia coli (2,4-dienoyl CoA
reductase) are enzymes with 4Fe-4S, FMN, and FAD
prosthetic groups, and interact with NADPH as well as
substrate. Members of this related protein family occur
in the vicinity of the putative mycofactocin
biosynthesis operon in a number of Actinobacteria such
as Frankia sp. and Rhodococcus sp. The function of this
oxidoreductase is unknown.
Length = 633
Score = 27.2 bits (60), Expect = 4.2
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 13 LAQFGESINISCTKE--GVKFSATGDIGSANIKLAQTG 48
LA G ++I G + A+GD+ AN +L + G
Sbjct: 519 LAALGRPVSIVTPDSVVGSRLGASGDLAPANTRLQRAG 556
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 0.132 0.375
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,595,475
Number of extensions: 650587
Number of successful extensions: 472
Number of sequences better than 10.0: 1
Number of HSP's gapped: 466
Number of HSP's successfully gapped: 23
Length of query: 156
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 67
Effective length of database: 6,990,096
Effective search space: 468336432
Effective search space used: 468336432
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: 55 (24.9 bits)